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A problem with Illumina's implementation of a reversible terminator approach is that several reagent exchange steps need to be made over clusters of target polynucleotides that are immobilized in a flow cell. The reagents reside outside the flow cell are delivered into the flow cell using a syringe pump at each step of the sequencing cycle and several wash steps are needed in between the functional steps of the sequencing cycle. This means that a large volume of reagents is consumed in a sequencing run which, the sequencing instrument has to be large enough to accommodate.

As reagents are provided in excess, a large amount of costly reagent is wasted in the sequencing run. By contrast, Pacific Biosciences do not use a reversible terminator approach. The chain extension is viewed on individual target molecules near to real-time by attaching the label on a terminal phosphate, a natural leaving group of the incorporation reaction.

The advantage of this is that reagents needed for sequencing can be loaded at the start of the reaction without further reagent exchange. However, this is at the cost of not being able to stop the reaction to definitively determine which base has been incorporated and consequently the error rate is high. Also there is light-induced damage to the complex due to the reaction having to be continuously illuminated and the method is low-throughput because only one field of view can be sequenced at a time using a single detector; the cost of increasing the number of detectors is prohibitive.

Genia acquired by Roche sequencing purports to use PacBio-like chemistry with nanopore detectors but the throughput and error issues may well remain Kumar, Fuller et al. One ambitious approach that does not use SbS is nanopore sequencing introduced by Oxford Nanopore Technology.

However, so far the footprint of the nanopore detection is too large to achieve the required single base resolution; error rate is high and throughput is low. In molecular assays field those that are one-pot on homogeneous have advantages because no fluid exchange or wash steps are needed.

In imaging, the Nobel Prize for chemistry was awarded for super-resolution superresolution methods that allow imaging methods to go beyond the diffraction limit of light. These two approaches form the cornerstone of the inventions described in this invention.

The present invention provides sequencing methods that overcome the shortcomings of the methods disclosed in the prior art. The invention relates to SbS, which comprises a template-derived chain extension, where a sequencing cycle comprises determination of a single nucleotide in the growing chain.

Each sequencing cycle comprises multiple steps and multiple sequencing cycles are conducted to sequence the template with the advantage that a massive number of templates can be sequenced in parallel within the same reaction volume. In general, the sequencing assumes that the target polynucleotide contains nucleotides that are complementary to the ones incorporated a sequencing error is an example of a case where this assumption does not hold.

The method requires the target polynucleotide to act as a template for the template-derived chain extension, modified nucleotides, which are or can become detectably e. In this case the nucleotides are deoxyribonucleotides. In some embodiments the polymerization complex comprises a polymerizing agent such as a RNA Polymerase and a promoter sequence. In this case the nucleotides are ribonucleotides.

In some embodiments the method can be applied to bulk level sequencing as well as single molecule sequencing. In certain embodiments SbS is monitored at the individual molecule level. Hence, a much higher density of individually resolvable molecules can be sequenced in parallel compared to existing NGS methods.

The fact that molecules are arrayed at high density means a much smaller footprint is required in the flow cell and much less reagent volume is required over the smaller reaction area. Because of this, a smaller amount of reagents need to be loaded onto the array and the area where the molecules are arrayed can be much smaller and the space needed to store reagents before and after they have passed over the dense lawn of templates is much smaller than non-superresolution sequencing methods.

Because the distances over which fluids will have to move are shorter than current flow cells, there will be some savings in time too. With this it will be possible to make a single, consumable fluidic device for sequencing in which all reagents and buffers are pre-loaded before the sequencing commences. In some embodiments super-resolution methods require specific sets of compatible labeling methods to be used.

Rust, M. Bates, X. Zhuang Nature Methods 3: and similar methods and variants thereof. In some embodiments the PAINT comprises a tag or docking site attached to the nucleotide and anti-tag e. Imager free in solution that binds to the tag Sharonov, A.

Wide-field subdiffraction imaging by accumulated binding of diffusing probes. Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett. In some embodiments the sequencing of the target polynucleotide is conducted in a closed system with respect to solution exchange, in that after sample and reagent loading, the sequencing proceeds without exchange of reagents from outside the vessel, as has only to date been available for high-error real-time sequencing methods such as PacBio and ONT sequencing.

However, in some embodiments of the present invention, in contrast to real-time sequencing, the incorporation of each labeled nucleotide into the growing chain is controlled one nucleotide at a time, so that sufficient time is available between successive nucleotide additions to determine the identity of the incorporated base and retain high accuracy within a closed system. In some embodiments b - e is done without external reagent input into the vessel, thereby sequencing the target polynucleotide.

In some embodiments detection occurs when the nucleotide added is incorporated. In other embodiments detection occurs when the nucleotide added is bound to the polymerization complex without completion of incorporation. In some embodiments the same modification that includes the label functions as the reversible terminator so a separate modification is not required to attach the terminator to the nucleotide.

In some embodiments the excitation illumination acts in the vicinity of the target polynucleotide and diminishes in the broader reaction volume. In some embodiments the cleavage trigger acts in the vicinity of the target polynucleotide and diminishes in the broader reaction volume. In some embodiments the reaction mix is well agitated in order to remove spent reagents and to bring in fresh reagents to the sites of reaction. In some embodiment all the steps of the sequencing in the one pot reaction are conducted in a single reaction volume.

In some embodiments the nucleotides are not directly labeled. A method for template-directed sequencing of a polynucleotide template, the method comprising:. A method according to 1 where the signals are used to determine the location of the label associated with the polymerization complex or nucleotide and thereby the location of the sequence being determined. A method according to 1 where the localized signals are used to determine the location of the label associated with the polymerization complex or nucleotide and thereby the location of the sequence being determined within a high density of template sequences.

A method according to 1 where the label is associated with the polymerase. A method according to 1 where the signal is generated by the binding of a fluorescent label to the label attached to the nucleotide. A method according to one where the shift to the next position is done by forming a covalent bond between a nucleotide and the growing chain.

A method according to previous claims where the signal from the sequences is localized to sub-diffraction accuracy which can be as low as a few nanometers or even sub-nanometer accuracy. A method according to previous claims where the signal from the sequences is resolved within a high density of signals where such signals are separated by sub-diffraction distances, e. Specific embodiments of the following include the following numbered 1 to Intercalator dye intercalant donor, acceptor and terminator on base see FIG.

In some embodiments of the invention the method of sequencing a target polynucleotide can include:. Intercalator dye donor, acceptor and terminator on sugar see FIG. Intercalator dye donor, acceptor on base, terminator on sugar see FIG. In some embodiments, instead of using intercalating dyes in the above embodiments any DNA stain can be used or any entity that can act as a DNA stain can be used. For example the DNA stain may be a conjugated polymer.

The stain may be a labeled spermine polymer. Label on polymerase donor, acceptor and terminator on base see FIG. Label on polymerase donor, acceptor and terminator on sugar see FIG. Label on polymerase donor, acceptor on base and terminator on sugar see FIG.

In some embodiments the locations of the FRET donor and acceptor are reversed. For example the donor may be on the nucleotide and acceptor may be on the polymerase or in the duplex. In some embodiments the FRET described above in embodiments is replaced by photoactivation.

In this case the FRET donor Intercalator dye or label on the base becomes a photo activator and the FRET acceptor label on the nucleotide becomes a fluor in an inactivated or darkened state. When the darkened fluor is in close proximity to the activator its fluorescence is switched on.

Label on polymerase donor, quencher and terminator on nucleotide See FIG. The quenching mechanism can be a special case for RET, where the energy is not dissipated as light by the acceptor. The quencher and terminator can both be on the base or both be on the sugar. Alternatively, the quencher can be on the base and the terminator on the sugar.

The cleavable linkage can be chemically cleavable and is cleavage is performed chemically. The present invention relates to a method of sequencing a target polynucleotide. In various aspects and embodiments, the methods include the steps of:. In some BRET embodiments the linker is photocleavable linker and step e comprises illuminating the target polynucleotede.

The acceptor and terminator can both be on the base or both on the sugar. Alternatively, the acceptor can be on the base and the terminator on the sugar. In addition, the BRET acceptor can be a quencher rather than an emitter of fluorescence. Direct detection of label on nucleotide In some embodiments of the invention the method of sequencing a target polynucleotide can include:.

In some embodiments when the target polynucleotide is attached to a surface, the surface preferably has 3D gel architecture so that a higher concentration of polynucleotide can be loaded onto a location on a surface, without increasing its 2D footprint.

This can help obtain a signal detectable over background. A RET mechanism can be employed with the labels on the nucleotides being RET acceptors and an intercalator dye or a label or labels associated with the polymerizing agent being the RET donor. The RET acceptors can be quenchers. Optionally wherein e and f may require the same physical trigger.

In some embodiments the same packet comprising a set of sub-packets is passed over the target polynucleotides multiple times in the process of producing a sequencing read, once for each cycle see FIG. Such embodiments include the steps of:.

In some embodiments a different but in most cases, identical packet comprising a set of sub-packets is passed over the target polynucleotide for each cycle see FIG. The above embodiment can be carried out in a fluidic device comprising at least two compartments, one for the incorporation mix and one for the cleavage mix.

The above mechanism can be combined with other embodiments of the invention e. For 13, 14, and 15 optionally each of the four nucleotides is provided in a different sub-packet and are optionally not differently labeled from each other but the order of delivery of the sub-packets containing them is known. In some embodiments the four nucleotides are not labeled but a different component of the complex is labeled, for example the polymerizing agent and again the order of delivery of the sub-packets containing them is known.

Individual polynucleotides or clonal amplicons thereof are detected. Moving target polynucleotide sequence in and out of flowstream FIG. In some embodiments the pronounced or persistent PAINT signal at template locations is sufficient to distinguish the signal over background. The PAINT technique provides the background rejection without utilization of RET or other surface signal enhancement methods, it only requires the persistent signals at locations on the focal plane or surface to be detected.

In some embodiments of 19 the reversible terminators also labeled and provides an independent reading of the base ahead of the transient binding nucleotide or acts as a RET partner to the transiently binding nucleotide. In some embodiments the transiently binding nucleotide is in a darkened state for example Cy5 can be darkened by using NaBH4 prior to binding and is photoactivated by a label on the polymerization complex, including a label on the polymerase, a label on the incorporated terminator or a DNA stain in the template.

In some embodiments of aspects 19 and 20 the transient binding is not used for superresolution but is used just for imaging for example so that the labels are replenished. In some embodiments the excitation beam is a single beam that excites a FRET donor and in some embodiments the depletion beam is a single beam that depletes the FRET donor. Some super-resolution mechanisms described herein enable molecules to be superesolved, because labels in a closely packed field do not fluoresce at exactly the same times.

In some super-resolution PAINT methods the bases are coded by fluorescent wavelength, In some super-resolution PAINT methods the bases are coded by intensity of fluorescent signal rather than wavelength. The fast dissociation rate means that there is a sort dwell time of the anti-tag imagers at a particular location but sufficient photons need to be collected for high precision localization.

Consequently, much brighter imagers are used including multi-labeled structures and nanoparticles such as gold or silver nanoparticles. In some super-resolution methods, the labels on the label on the nucleotides are not chosen for special super-resolution qualities, e. In another embodiment, the nucleotides are imaged with high temporal resolution while they each binding to a molecule in the array of templates, and because the this binding is a stochastic process, each nucleotide within diffraction limited area will incorporate at slightly different times and can therefore be localized with high precision.

Similarly, when sequencing is conducted in a real-time manner using terminal phosphate labeled nucleotides, where the labeled phosphate is part of the leaving group upon incorporation, even where the molecules are densely packed, the majority of nucleotides incorporation events within a diffraction limited spot can be temporally resolved and hence super-resolved.

In some embodiments the chemical cleavage is by generation of acid, using photo-generation or electrical acid generation methods. In some embodiments the chemical cleavage is not homogenous but involves exchange of reagents atop the array of sequencing templates. In some embodiments the cleavage is due to biochemical reagents. In some embodiments of this invention methods to overcome the effect of non-specific adsorption are described.

These include passivation of surfaces and computational filtering of aberrant signals through the data stack. In some embodiments of this invention methods to overcome the effect of background signal from the bulk solution are described. In embodiments of the invention, the various methods described for reducing the amount of reagents used in sequencing or reducing or eliminating the background fluorescence problem in a homogeneous reaction or super-resolution, are combined with the cleavable terminator nucleotides and polymerases described in this invention.

In some embodiments the super-resolution sequencing methods of this invention are carried out in a homogeneous format. In some embodiments the cleavable linker is not a photocleavable linker but instead is cleavable by some other physical trigger. The physical trigger in some embodiments is an electrochemically generated e.

In some embodiments specific advantages of the mechanisms described in this invention are used in other sequencing scenarios, for example using neither homogeneous format nor super-resolution. One such case is a non-homogeneous sequencing reaction, where cleavage is conducted chemically with the exchange of reagents but where a DNA stain or intercalator dye is used as a fluorescent donor to four nucleotides bearing acceptors.

The advantage of this over conventional SbS is twofold. Firstly just a single wavelength of light is needed for excitation. Secondly, non-specific adsorption of labeled nucleotides on the surface can be differentiated form those that are incorporated, as only the latter will be subject to FRET. The method of the invention can be carried out on surface immobilized templates, or templates contained in micro- or nano-wells, channels, slits, droplets and beads.

In some embodiments, sequencing is conducted on templates that are closer than would be resolvable by diffraction limited optical imaging but are resolved by super-resolution imaging. Such a super-resolution method for template-directed sequencing-by-synthesis of a polynucleotide comprises:. The stochastic optical reconstruction method can be combined with all of the aspects described above.

In some embodiments the stochastic optical reconstruction is carried out by recording the transient binding of nucleotides or polymerase. In some embodiments stochastic optical reconstruction is carried out by recording the blinking or photoswitching of molecular or particulate single emitters or point light sources. While some super-resolution methods will still suffer from bleaching and photophysical effects.

The DNA PAINT system will not suffer appreciably from such effects but remains susceptible to incorporation of the wrong base before detection has occurred. The transient nucleotide binding approach is robust to both detecting the correct base and for avoiding photophysical effects and has the potential for the greatest accuracy of any sequencing approach. During the incorporation step it is desirable to have a high concentration of nucleotides and polymerizing agent in the vicinity of the target polynucleotide.

However, during the detection step it is undesirable to have unincorporated and unloaded polymerizing agent if labeled in the vicinity of the target polynucleotides. This is particularly the case for the unincorporated nucleotides.

This is because when the nucleotides are labeled, they cause unnecessary background fluorescence, which makes it hard to detect the incorporated nucleotides on the surface. In some embodiments the fluid is sandwiched between a top and a bottom surface.

The bottom surface contains the target polynucleotides. The bottom surface may contain features that promote the entry of the nucleotides to the bottom surface, for example the nucleotides bear a negative charge and the bottom surface may be provided with a positive bias to attract the nucleotides and the top surface may provide a negative bias. This is done during the incorporation step.

Then the bias may be switched between the top and bottom surface depending on whether it is desirable to have the nucleotides in the vicinity of the polynucleotide target during incorporation or away from the polynucleotide target during detection and cleavage. See FIG. The positive potential on the second surface not containing the templates being sequenced is applied after incorporation, before cleavage is directed at the first surface, to prevent the unincorporated nucleotides from being cleaved.

In this case the cleavage mechanism does not have a reach to the second surface, and does not cleave the nucleotides that have been attracted there. An electric field generated at the surface is a useful way for controlling the attraction and repulsion of nucleotides at the surface Asanov ; Sosnowski In the case of DNA PAINT, non-fluorescent nucleotides can be provided at the high concentrations nM range needed by polymerases to drive the incorporation reaction.

If the on-rate is increased by increasing concentration, then further measures such as FRET between the imager and a component of polymerization complex or quenching e. Similarly, when sequence detection is done by recording transiently binding nucleotides, a FRET mechanism can be used when a high concentration of transiently binding nucleotides is used. For example the FRET can be between a label on the reversible terminator and the incoming transiently binding nucleotides.

Alternatively it can be between intercalting dyes such as YOYO-1, Sytox Green, JOJO-1 or Sytox Orange intercalated in the template-primer duplex and a label on the transiently binding nucleotide each of which can be distinctly labelled. Every FRET event in this context does not need to be robustly detected, because other FRET events can be captured as transiently binding nucleotides repeatedly bind on and off.

Auer et al Nano Lett. Auer et al achieved localization precision of This independently shows what this invention claims, that sequencing using the transient binding aspects of this invention can be carried out at high speeds when a FRET mechanism is used. It is a remarkable aspect of the present invention that although a movie is taken rather than a single image and single molecules rather than clusers are detected, sequencing speeds faster than current Illumina sequencing by synthesis methods are possible.

The FRET mechanisms of this invention, especially the use of intercalator dyes can be extended to various end-point assays and analysis methods other than sequencing, such as Fluorescent In Situ Hybridization assays etc.

In some embodiments the binding of a probe such as an antibody or an oligonucleotide can be tagged with a DNA PAINT docking strand and a super-resolution image of the binding of the probe to sample molecules disposed in 2D or 3D can be obtained at high speeds by FRET-based imaging of the Imager. In some embodiments individual nucleotides are labeled with single fluors. In other embodiments individual nucleotides are labeled with multiple fluors. In some embodiments the multiple fluors are the same and enable an improved signal-to-noise.

In some embodiments the multiple fluors may comprise two or more different varieties, and enable coding to be implemented. In some embodiments all four nucleotides are not added simultaneously and therefore do not need to be labeled differently.

In some such embodiments, each of the four nucleotide types are added a nucleotide at a time. For example a fluorescent nucleotide bearing a terminator can be added one at a time, after addition of A for example, the locations on the surface where the label is incorporated are detected and then the label is removed from the nucleotide. In another example the nucleotide from the set that is added one nucleotide type at a time is unlabeled and detection is via a mechanism such as pyrosequencing using firefly luciferase for examples or pH as in Ion Torrent sequencing, or heat as in Genapsys sequencing.

If a and reversible terminator is used it is removed after step d; if one is not used a multiple of the nucleotide is added when there is a homopolymer in the target. This embodiment can be combined with 13, 14, and 15 described above. For example in 13 and 14, separate sub-packets are provided for each of the four nucleotides, or in 15, different compartments are provided for the storage of the different nucleotides. After initiation of the reaction the whole of the reaction is conducted in a closed vessel.

In some embodiments the reaction is homogeneous for certain steps but semi- or non-homogeneous for other steps. In some embodiments the homogeneous or one-pot sequencing reactions described in this invention are carried out multiple times. For example, the homogeneous reaction is carried out to sequence a length of 10 nucleotides. The homogeneous reaction is then stopped and a new set of reagents is added to carry out a second homogeneous sequencing reaction.

Then a third, and so on until the desired read-length has been obtained. Favourably, the method involves analysing molecules as members of an array and to sequence many molecules in parallel. Many target polynucleotides or many segments of a single target polynucleotide can be sequenced simultaneously. The invention is readily automated, both for small-scale and large-scale operation.

One aspect of the invention is a kit for sequencing comprising, a polymerizing agent, special nucleotides and optionally labels, anti-fade comprising antioxidants and, a flow cell or chip. We will start by discussing specific sequencing approaches in detail and then critical components of the sequencing system that are relevant across the board for the sequencing methods of the invention.

The processing of sequencing relies on the base pairing that occurs between nucleotides to form a double stranded polynucleotide molecule, according to the Watson-Crick base paring rules. At each position in a nucleotide molecule, one of the four nucleotides can be incorporated. The nucleotide incorporated into the extending primer or into an RNA copy is normally the correct base that pairs with the base in the target polynucleotide.

The identity of the base in the template can be determined as the Watson-Crick complement of the base that is incorporated. So if a T is incorporated, an A should be present in the template. In several embodiments of the present invention provides a method of sequencing a target polynucleotide comprising the steps:. Preferably the four nucleotides can be differentially labeled e.

In this case the primer and template polynucleotides are contacted with two or more of the labeled nucleotides at the same time. If required any free nucleotides are removed and incorporated bases are detected.

The use of four differentially labeled nucleotides can allow continuous real-time monitoring of the synthesis process or for the reaction to be conducted in a homogeneous or one-pot manner. The supply of all four nucleotides also reduces misincorporation. In one alternative embodiment sequencing may be of only two labeled bases and the other two bases are provided but are unlabeled. After sequence information is obtained of the first two bases the sequencing repeated with the other two bases labeled.

Some embodiments of the invention can be applied to direct sequencing of single molecules. It has been shown by PacBio and ONT, that single molecule analysis enables long sequencing reads to be obtained. The monitoring of individual molecules for sequencing by synthesis has the advantage over Illumina's cluster sequencing approach is that there is no phasing problem asynchronous extensions can be followed with ease. In some embodiments of the invention cycles are conducted to read one to three bases.

In some embodiments cycles are conducted to read bases. In other embodiments cycles are conducted to read bases. In some embodiments , cycles are conducted to read , bases. Polymerases can be adapted to incorporate non-native nucleotides and the non-native nucleotide can be structured in a way that makes them easier to incorporate e. The chemical composition of the linker is chosen so that it minimally perturbs the polymerase function.

The label is held at a distance greater than 1 nucleotide, 3 nucleotides, 6 nucleotides, 12 nucleotides and may be between atoms, atoms, atoms, atoms, atoms or atoms. The polymerase can also be engineered or evolved to deal with particular nucleotide modifications.

The fluorophore on the nucleotide may be bleached as required to detect subsequent incorporations more easily. Alternatively, the fluorophore and the label may be removed e. In another embodiment, synthesis can be done in a stepwise manner, by only allowing the synthesis to increase by only a single nucleotide at a time. This can be done by providing a block to nucleotide incorporation beyond a single nucleotide.

The nucleotide may be blocked by any type of terminator, for example a photocleavable 2-nitrobenzyl based blocking group. The cleavable bond can be cleaved by means of light if it is photocleavable Li et al PNAS; 2 In one embodiment the terminator is a group that can removed by an enzyme.

This can then be repaired to OH by Polynucleotide Kinases, making the end competent for extension. When STORM compatible nucleotides are used the super-resolution is achieved by taking a movie multiple frames, e. In some embodiment, the linkage attaching the label to the nucleotide comprises a binding pair. One member of the binding pair is linked to the nucleotide, preferably via a cleavable bond.

The other member of the binding pair is attached to the label such as a fluorescent dye or nanoparticle. A binding pair consists of two molecules, e. DNA or proteins, which specifically bind to one another. The members of a binding pair may be naturally derived or wholly or partially synthetically produced. One member of the pair of molecules has an area on its surface, which may have spatial organization of protrusion, cavity or physiochemical e.

Thus, the members of the pair have the property of binding specifically to each other. Examples of types of binding pairs are antigen-antibody, biotin-avidin, hormone-hormone receptor, receptor-ligand, enzyme-substrate. The use of a linkage comprising a member of a binding pair means that the nucleotide added onto the primer may be labeled after it has been incorporated into the primer.

The nucleotide is attached, preferably via a cleavable linker to one member of a binding pair. The detectable label is attached to the other member of the binding pair. The detectable label can then be attached indirectly to the nucleotide as the two members of the binding pair bind one another. Each of the four types of nucleotides can be attached to a different binding pair member.

The other members of the binding pair can be labeled differentially, e. This allows all of the nucleotides to be added at the same time. The nucleotide incorporated is then labeled with the respective fluorophore via the binding pair mechanism. For example adenine is attached to biotin, and cytosine is attached to digoxigenin. The fluorophore indicating the presence of adenine is attached to avidin, and that for cytosine is attached to anti-digoxigenin antibody.

In some embodiments the binding pairs are oligonucleotides that bear complementary sequences, this easily allows one to code for four different nucleotides with four different binding pairs. Thus in one aspect the present invention provides a method of sequencing a target polynucleotide comprising the steps of;.

In some embodiments the method comprises template-directed SbS of a polynucleotide comprising:. In some embodiments partner 2 is added under conditions that encourage transient binding. In some embodiments the transient on and off binding is recorded over multiple detection events movie. When partner 2 binds to the incorporated partner 1 a signal can be detected and then when after a period partner 2 dissociates signal from partner 1 disappears.

While the binding of partner 2 is absent for a given polynucleotide being sequenced, a partner 2 that is paired with partner 1 of an adjacent polynucleotide bins to that partner. The adjacent polynucleotide may be too closely spaced to the first polynucleotide for resolution to be achieved if partner 2 s are binding to the polynucleotides at the same time. However because there is a stochastic temporal aspect to the process, when the system is well tuned in terms of concentration of binding partner 2 s, association and dissociation constants, temperature etc.

Vertically through the stack of frames of the movie, it can be determined that there are many binding pair interactions per polynucleotides. In a typical experiment capturing 10, frames, 20 or substantially more binding pair interactions may occur, depending on how the system has been tuned. All the general nucleotide structures described in this invention can be applied to oligo-tagged nucleotides this includes the following class of nucleotides.

It should be borne in mind that compared with single molecule SbS, the next generation methods of sequencing which comprise library preparation and clonal amplification e. Illumina sequencing comprise two sets of polymerase copying reactions before the sequencing starts. These steps are susceptible to errors being introduced each time a polymerase makes a complementary strand.

By contrast in the present invention where sequencing is being done on single molecules, without amplification, error due to polymerase misincorporation is limited to one possible occurrence, when the nucleotide is actually being incorporated during sequencing. Hence if the error rate of the polymerase is low, the sequencing error rate will also be low, e.

Even such low error can be overcome by some embodiments of the invention that include testing the nucleotide to be incorporated multiple times before incorporation occurs, as described in the following embodiments: In some embodiment the approach is to incorporate a reversible terminator e. The incorporation of the nucleotide complementary to the next base cannot be completed because the growing chain is terminated, nevertheless the correct base will associate for a longer period than the incorrect base and this difference can be detected.

In this way the base in the target is interrogated multiple times by templating transient binding of complementary directly labeled nucleotides in which the nucleotide is not cleavable , improving accuracy in the base call; if a wrong base binds it will dissociate faster than the correct base. Moreover because multiple binding events will be recorded a consensus can be obtained, which is likely to be in strong favor of the correct base, if enough events are detected e.

The next step is to reverse termination, and then addition of the next reversible terminator followed again by transient binding of the fluorescent nucleotides. To reduce background fluorescence from the detectable fluorescent nucleotides are not incorporated, a lower concentration of nucleotides than normal may be used.

Alternatively the reversible terminator may bear FRET partner, for example a donor or the polymerase can contain a FRET partner or the template can contain a nucleic acid stain or intercalating dye which is used as a FRET partner.

A single wavelength donor can be used as a FRET partner for multiple acceptors used as distinct labels for each of the four fluorescent nucleotides. The multiple on-off binding is catalyzed by Klenow fragment; other polymerases can alternatively be tested. The correct versus incorrect base binding to the interrogation position can be differentiated by slow and fast dissociation rates. Alternatively, if the nucleotides are fed in one type at a time, they need not be labeled; instead the polymerase can be labeled and its on-off dissociation can analyzed: slow dissociation of the polymerase if the correct base is transiently bound, high if the incorrect base is transiently bound.

In one embodiment, which we shall call Sequencing by Anticipation, the base is initially called by the transient binding and subsequently the reversible terminator that is added also bears a base-specific label and confirms the base call or the reversible terminator is added first and called and the transient nucleotide is added second.

If the reversible terminator is negatively impacted by photophysics, the base can still be called on the basis of the subsequent transient binding nucleotides. Because the fluorescent transiently binding nucleotides are not consumed in the reaction, these can be shunted over the sample during the imaging step and then shunted back into a storage site on the flow cell and re-used in the next cycle.

In some embodiments the termination is reversed by a physical trigger and is able to be conducted in a homogeneous manner. In an alternative embodiment, unincorporable e. In the case where the labeled nucleotide binds transiently the label does not need to be connected via cleavable linker. It can be a simply be a nucleotide modified on the base or any other compatible position.

In this case the label can also be on the terminal phosphate position; in this case extra phosphates and the addition of manganese in the buffer promotes binding Terminal phosphate labeled nucleotides: synthesis, applications, and linker effect on incorporation by DNA polymerases.

Nucleosides Nucleotides Nucleic Acids. Terminal phosphate-labeled nucleotides with improved substrate properties for homogeneous nucleic acid assays. J Am Chem Soc. The transient binding reaction can be conducted as a continuous real time reaction by providing a DNA repair reagents that can convert the reversible terminator back to a —OH. The conditions e. This will enable the transient binding reagent to bind on and off multiple times before the termination is reversed.

When the nucleotide is incorporated the terminal phosphate label is a leaving group, leaving the chain extended by one nucleotide but terminated. The advantage of this real-time method over PacBio real-time sequencing is that there are several independent detection events for each nucleotide in the template. The apparent blinking in signal due to the on off binding, allows super-resolution of a dense lawn of molecules by PAINT.

The fact that each base is queried multiple times leads to increase confidence in the accuracy of the base call. As an alternative to real-time DNA repair, this terminal phosphate labeled terminator approach can also be conducted in stepwise manner either by cleavage or repair of the terminator by cycling reagents or by clocking cleavage by light or generated-acid. The labeled base may be a reversible terminator so that the sequencing proceeds one base at a time. The polymerase can be prevented from chewing back more than one nucleotide by providing a mixture of two types of nucleotides; the regular labeled sequencing nucleotides are supplemented with a phosphorothioate e.

The several incorporations and removals, can include incorrect incorporations, but these will typically be outnumbered by the correct incorporations. The phosporothioate nucleotide does not need to bear a fluorophore and a cleavage cycle to remove a fluorophore is not needed.

The modification on the base can act as the virtual terminator. Where termination is not complete and multiple nucleotides get incorporated, they can also be chewed back several times. This method can also be conducted in real time, when no cleavage mechanism is used.

The ratio of labeled nucleotides to unlabeled phosphorothioate nucleotides determines the duration of each incorporation step. These methods, share with the DNA PAINT mechanisms described herein, the ability to be superesolved, because labels in a closely packed field do not fluoresce at exactly the same times. Key to some embodiments of this invention, is removal of background fluorescence emanating directly from unreacted fluorescent nucleotides in solution, Raleigh scattering etc.

One means to do this is to separate the labeled target polynucleotides from unreacted fluors. The invention describes how to implement this in a number of ways. One is by removing the unreacted fluors e. Another means to remove background is by using an evanescent field e. Finally, Raleigh scattering can be filtered from fluorescence by its time dependence.

Raleigh scattering is short-lived and can be gated from the longer lifetime of fluorescence. In addition, the surfaces of the vessel, especially where the target polynucleotide is present should be non-sticky to the fluorescent labels and this can be achieved via passivation, e. Methods of this invention can be carried out in a mode where reaction components for the different steps of the reaction are provided at separate stages.

Then cyclical electromagnetic modulation, for example for cleaving a linkage provides a clocking mechanism for shifting the sequence register. In current Illumina SbS an excess of reagents are provided at each cycle. As not all of the reagents are used up at each cycle, a large amount of reagent is wasted, at a considerable cost. Further as enough solution for lots of these reagents need to be stored if cycles are to be conducted, sufficient space is needed on the instrument for storage.

This necessitates a large instrument, which is not conducive to building an instrument suitable for clinical applications. In some embodiment all the steps of the sequencing in the one pot reaction are conducted in a single container, but the container contains more than one reaction volume separated by an immiscible gaseous or liquid pocket, with each volume shuttled over the site of reaction at different steps of the reaction cycle.

In some embodiments the container comprises a fluidic network and different reaction volumes are stored at different locations in the fluidic network. In some embodiments after the start of the sequencing process no new reagents are shuttled into the container or pot. In some embodiments the one pot reaction contains a packet of reagents and this packet of reagents contains sub-packets of reagents and the packets and thereby the sub-packets are passed over the template polynucleotides multiple times i.

In some embodiments, the one pot reaction contains multiple packets of reagents stored in the pot FIG. Then each packed is delivered one after another. The packet for each cycle comprises a serial arrangement of sub-packets comprising reaction reagents or immiscible separation reagents or air gap: aqueous solutions separated by immiscible solutions or a gas e. The immiscible sub-packets may comprise an air pocket or may contain an immiscible fluid such as oil.

In some embodiments the compartments are aqueous in oil droplets or each aqueous packet is separated by an air gap or other medium, such that reagents for each packet cannot mix. One sub-packet is for incorporation, one sub-packet for imaging buffer, one sub-packet for cleavage buffer; these sub-packets are interspersed with sub-packets containing wash buffers etc. The loop may start with priming solution or stretching solution. In another embodiment the one pot reaction contains therein storage locations from which reagents are introduced and then removed again from the reaction site the array of templates and this is iterated to carry out the sequencing cycles.

In this embodiment the reagents are not necessarily stored in packets, but certain components of the solution are moved to different locations in the vessel, for example where the reaction is occurring on surface bound templates on one of the surfaces of a flow cell, then some components of the reaction solution are moved to a surface not comprising the templates being sequenced. The components may be nucleotides, and these may be moved to prevent their terminator and or label being cleaved before the nucleotide has been incorporated.

The packets may be aqueous feeds into a fluidic channel punctuated by the immiscible pocket. The fluidic channel may be formed in tubing, capillary or it may be part of a monolithic fluidic structure such as a microfluidic device. Each packet in the channel is separated by an air pocket. One sequencing cycle comprises several different sequencing and wash reagents each separated from another via an air pocket.

An air pocket also separates one cycle from the next. The different reagents and air pockets can be put into a continuous loop. In some cases the loop of reagents is repeated, with the same reagent sets contacting the elongation complex at every cycle. In other cases a large loop is provided where multiple iterations of the reagent sets are provided one set after the other, wherein each set comprises the reagents for one sequencing cycle, and each set contacts the elongation complex only once.

For a base read from the elongation complex, reagent sets are needed. In some embodiments different sub-packets are provided for each of the four bases which means the nucleotides do not need to be labeled and a different component of the reaction is optionally labeled or to be labeled differently if the order of the delivery of each of the four nucleotides is known.

In some embodiments more than four nucleotides are delivered in separate sub-packet, where the nucleotides beyond the four provide a different a different functional purpose see Transiently binding nucleotides section. It should be noted that that a frequent changing of polymerizing reagent is justifiable if sequencing is done on a large number of molecules in parallel in small volumes.

If the reactions are done in microfluidic channels the amount of reagents will be small and if a system of valves is incorporated onto a sequencing chip, the reagents, which will usually be provided in excess amounts, can be stored in designated chambers on the chip and re-used. The system is not completely closed system, and resembles a Terrarium in that the system can be sealed or open to the atmosphere and allows heat and light to enter but does not require tending for an extended period, e.

In embodiments where one or more sequencing reactions are being conducted on a single long polynucleotide, such as Kbp or longer length of genomic DNA, which would measure around 30 um in crystallographic length, different zones in the vessel over which the polynucleotide can be disposed can be used to carry out different steps of the reaction. In some embodiments a DNA polymer can be spooled back and forth between a reaction area and a detection area to carry out the steps of a sequencing by synthesis cycle.

The reaction area contains the reagents required for the reaction and detection area is devoid of the reaction reagents; in particular it is devoid of the fluorescently labeled nucleotides. When the incorporation and cleavage steps are conducted the target polynucleotide is bathed in a solution rich in incorporation and cleavage reagents. In some embodiments the target polynucleotide is tethered to a planar surface from one of its ends.

Without a flow or an electrophoretic potential, the polynucleotide forms a blob like random coil close to the site of attachment. When a flow or an electrophoretic effect is induced, the polynucleotide stretches out and the majority of the polynucleotide stretches away from the point of attachment.

In some embodiments the labeled long strand is stretched beyond the area where nucleotides are flowed. In an alternative embodiment during the biochemical steps the polynucleotide can be in a 3D area e. During the detection step, the polynucleotide is confined to a 1D or 2D area in the detection area.

When the DNA is to be detected it is spooled into the detection area and when a reaction step is to be conducted it is spooled back into the reaction area. In some embodiments of the present invention wash steps may be introduced between certain steps as required, and the invention is homogeneous for some steps and then becomes semi-homogeneous when fresh reagents are introduced again, after which steps may become homogeneous again.

Particularly unreacted fluorescent nucleotides can be removed before the detection steps and after a cleavage reagent or cleavage buffer is introduced. In some embodiments some steps are semi-homogeneous in that introduced from a different location on the chip.

In some cases the homogeneous or one-pot sequencing reactions described in this invention are carried out multiple times. For example after starting the reaction with fresh reagents, five to ten cycles are conducted, after which reagents are refreshed for another five to ten cycles. Nevertheless the infrequent reagent exchange is different from the reagents that are exchanged in conventional sequencing by synthesis.

In conventional sequencing by synthesis, reagents are exchanged between each step of sequencing, whereas in the present invention, a whole set of reagents comprising the homogeneous sequencing mix is exchanged in one go, so that all the steps of the sequencing cycle can be done with the same reaction mix. In some embodiments even when cleavage is done photo-chemically, local generation of acid shunting of reagents from one location in the vessel to another is done, because the photocleavage process or acid cleavage process requires a specific chemical environment around the nucleotide in order to be efficient.

This is because signal becomes concentrated on the surface where the objective lens focuses. Out of focus signal is weak compared to the intensity of signal at the surface and the signal to noise ratio of the in-focus signal from the microarray or clonally amplified spot is sufficient for the label to be detected and the base to be called.

Thus in some embodiments the signal from reacted binding pairs is distinguished over background from unreacted binding pairs due to its persistent or pronounced occurrence at a location on a surface. In some embodiments the separation of signal from noise occurs via applying an intensity threshold. In some embodiments the templates are placed within a structure where signal is enhanced. Such a structure can be a zero-mode waveguide or a V-groove or a nanogroove, where illumination is confined or which comprises a plasmonic material or structure which enhances fluorescence.

The fluorescence of the labeled reactants floating in solution, distal from the signal enhancing structures is not enhanced and remain relatively dark compared to the reactants associating with the template and hence the single molecule signals proximal to the structures can be distinguished. In some embodiments the reaction involves energy transfer ET pairs comprising a fluorescent donor and a quencher. In one such embodiment, the donor fluorophore is on the polymerase and the differently labeled nucleotides are differently labeled with different quencher groups or different numbers of the same quencher group.

In one embodiment the donor and acceptor or the donor and quencher are present on the polymerase. The donor are located at different residues of the polymerase, such the finger opening closing action of the polymerase leads to a different levels of FRET signals or different levels of quenching. The four different nucleotides can be detected by adding them one at a time, and the FRET or quenching due to finger closing indicates how many nucleotides are added.

In another embodiment all four nucleotide are added at the same time and the identity of the nucleotide is detected via the extent of FRET or quenching. In some embodiments the nucleotides are unlabeled.

In some embodiments the nucleotides are reversible terminators. When the reversible terminator quencher nucleotide is incorporated the decrease in fluorescence of the label on the polymerase is detected. In some embodiments after such changes in fluorescence have been measured across an array, the termination is reversed allowing the next nucleotide to be incorporated.

In some cases photophysics leads to photobleaching or dark states of the fluorescent labels, which means an incorporation event is not detected or there is ambiguity over which base has been incorporated. In some cases different molecules of an array of templates may bear donors on the polymerase which may have individual fluorescent character.

For example their brightness of fluorescence may differ or their rate of blinking may differ. In some embodiments, rather than the decrease in fluorescence level from one absolute level range to another absolute level range, the change in fluorescence level range is detected. The main advantage of coding the nucleotides with quenchers is that there is no background due to fluorescent nucleotides in solution.

Also, only a single illumination wavelength is required for excitation. Further, there is no concern for the bleaching of labels on nucleotides. In some cases the coding of the nucleotides is done by providing a mixture comprising quencher labels and fluorescence labels. D Week 63 plasma from neutralization positive ZM gpimmunized RLk17 was tested for neutralization activity against a global panel of envelope PV [ 48 ]. Plasma serial dilutions began at and ID 50 values are shown.

All experiments had duplicate wells and were repeated at least twice independently. We next tested whether IgG purified from the serum of ROa17, RLk17, and another RM from the same vaccine group that did not develop serum autologous nAb activity, RPz16, could mediate the observed neutralization. The tier 1 Env 93MW We also tested RLk17 week 63 plasma for neutralization of a tier 2 global Env panel [ 48 ].

Except for modest inhibitory activity against Env CNE8, which is among the more sensitive tier 2 Envs, there was no evidence of neutralization breadth Fig 4D. In contrast, the TF3 chimeras were as resistant to neutralization as the parental 5-month D10 and D11 Envs.

Fig 5C and 5D show that the V5 mutants were completely resistant to neutralization by RLk17 and ROa17 serum, unequivocally demonstrating that nAb is dependent on residues in V5. All experiments had duplicate wells and were repeated at least twice independently, and error bars indicate the standard deviation. Key Env regions are shaded and labeled.

The positions of restriction sites used to generate chimeras shown in panel B are indicated with arrows. B The scheme for construction of the chimeras is shown. The V5 constructs contained only the changes present in V5, which were two amino acid differences in D10 and one amino acid deletion in D We also determined the ability of longitudinal plasma samples from HIV-1 infected subject ZM to neutralize the chimeras and mutants Fig 5E. Overall, viral escape from plasma neutralization was complex and could not be mapped to a single region of D10 or D It is interesting to speculate that the autologous escape pathway involving two V5 amino acid substitutions D10 was less advantageous than the amino acid deletion D11 because the former also created a vulnerability by exposing the CD4bs.

We reasoned that we could use the mAbs from natural infection to refine our understanding of the vaccine-elicited serum nAb. The third human mAb, 1E12, was also derived from VH4. The CDRL regions for the three mAbs were 11 amino acids in length and shared some amino acid homology. We therefore used mAbs 1A8 and 1E12 to further probe the vaccine-elicited neutralization specificities. Vaccine elicited autologous nAb often target glycan hole regions that are exposed on both the immunogen and the native Env trimer [ 12 , 13 , 40 ].

For two sites located within the V4 loop, N HXB2 residue and N HXB2 residue , a definitive glycoform assignment was not possible since the two sites could not be enzymatically separated. However, it was evident that both sites were significantly glycosylated. These findings are consistent with previous studies that have demonstrated heterogeneity with a high proportion of complex type glycans on recombinant gp molecules [ 49 — 51 ]. The hyper-variable domains are indicated above the graph.

B For each glycan position, the equivalent HXB2 reference position is indicated as well as the most abundant glycoform observed at that site that was subsequently used for computational modeling. Therefore, both sites were represented by Man5. The heterogeneity and flexibility of glycans over Env makes high resolution structural characterization of the glycan shield extremely challenging. We therefore employed computational methods to model the ZM Env glycoprotein and its glycan shield topology in atomistic detail as described [ 52 , 53 ].

The most abundant glycoform was selected for each N-glycan site, as determined by mass spectrometry Fig 7B. Of the 22 N-linked glycans that were characterized, 12 displayed Man5 as the predominant glycoform with others as minor glycoforms. This approach resulted in a model ensemble close to the native-like glycan shield. In a static representation of the glycoprotein, each glycan takes a single conformation Fig 8A. However, glycans are much more dynamic than the underlying protein and the overall cumulative effect resembles a cloud that provides a physical barrier over the antigen surface Fig 8B.

Expressing the GEF as a colormap over the surface of the monomeric gp protein demonstrates that the apex and the V4 loop regions have high shielding, whereas, as expected, the region that would form the interface between monomers within the trimer is highly exposed. A protomer gp within a trimer construct may not fully represent a native gp monomer conformation. Due to the conformational plasticity of Env, a monomer gp could fold differently from a trimer construct, not necessarily having the same placement of flexible regions such as V1, V2, and V3.

Therefore, we generated an independent glycosylated gp monomer model based on previously observed x-ray diffraction structures of HIV-1 Env monomers Fig 8E. Further, gp monomers have been found to have a different glycosylation pattern with higher processing of glycans as compared to stabilized trimers [ 51 , 54 ]. A A single protomer of ZM gp glycoprotein in a trimeric fold structure. Static representation of native glycans green sticks over Env protein grey ribbon , with each glycan occupying only one of many possible positions.

B Cumulative shielding effect due to the flexibility of glycans represented by a density of points over the monomer surface. Regions having high GEF or shielding are colored in blue, exposed regions are red. E ZM gp glycoprotein with monomeric conformation different from the trimer, colored by normalized GEF. This monomer was modeled using previously observed X-ray diffraction structures of HIV-1 Env monomers.

The V5 loop remains exposed in all three different models. Of these, the glycan at N HXB2 N is spatially closest to V5 but is oriented such that it is inserted below the loop. To gain further insight into mechanisms of resistance, D10 and D11 Env sequences were subjected to modeling. Remarkably, the local V5 changes in D10 and D11 were sufficient to drive the outward projection of the glycan at N, indicating that the other glycans N, N, N HXB2 N and N with no corresponding glycan at N and sequence differences outside of V5 do not contribute to the evolving V5 glycan coverage.

The V5 hypervariable loop is shown in red. The glycan structural distribution is represented by green density of points. The underlying protein surface is represented in gray and the V5 loop in red. To further examine how a substitution in the protein backbone could have such a significant effect on the glycan N coverage of the V5 loop, we considered the V5 loop conformation as well. There are minor changes to the secondary structural content of the loop upon these modifications.

C Chi1 distribution of glycosylated asparagines obtained from pdb structures, calculated using GlyTorsion [ ]. This difference in chi1 dihedral influences the overall orientation of the glycan. For example, changes in glycan coverage around residues —, —, —, —, and — HXB2 —, —, —, —, — are due to the N no HXB2 residue and N HXB2 N glycan deletions. In contrast, the shielding of residues —, —, —, —, and — HXB2 —, —, —, —, — are driven by the change in N HXB2 N glycan orientation.

Most of the latter residues —, —, —, — HXB2 —, —, —, — comprise the CD4bs, suggesting that the N HXB2 N glycan orientation affects shielding of this conserved region. As the glycan reorients from below to above the V5 loop, the coverage of the adjacent CD4bs region is reduced. This is consistent with several observations. These observations suggest that projection of the N HXB2 N glycan with respect to the V5 loop is sufficient to significantly change exposure of the CD4bs.

This was likely one of several viral escape pathways that occurred in response to autologous nAb and potentially contributed to the development of nAb breadth. Amino acid positions are shown below each bar graph panel. The V5 loop region is indicated, and residues that comprise the CD4bs are marked by black horizontal bars. The bars correspond to HXB2 residues —, —, —, —, —, —,. All mAbs bound well to the gp protein, except for 2 mAbs that bound weakly like VRC01 Fig 13A ; however, none of the 54 antigen-specific mAbs had autologous neutralizing activity Fig 13B.

All assays contained duplicate wells and were repeated independently at least twice, with the means and standard deviation shown. In parallel, we tested 2 non-neutralizing mAbs isolated from RLk Nine mAbs from this clonotype were used for further characterization Fig 14A.

Thus, this enriched clonotype completely recapitulated the V5-dependent nature of serum nAb elicited by vaccination of RLk17 and ROa The nmAbs had nucleotide identities to germline ranging from Thus, this RM-derived nmAb clonotype elicited by immunization shares key properties with an analogous V5 dependent human nmAb that arose during early HIV-1 infection against the same Env. The last row shows the same characteristics for the ZM human neutralizing mAb 1A8. Dashes represent identical residues and substitutions are shown.

The CDR regions are highlighted in the germline sequences. We selected 3 representative nmAbs for these studies. Consistent with these findings, the clonotype nmAbs did not reduce binding of the bnAb PGT, which targets V3 and the high mannose patch on the outer domain Fig 15D. Together these results provide more evidence that the clonotype nmAbs recognize a V5 dependent epitope proximal to the CD4bs.

Each assay was independently repeated twice and the means with standard deviation are shown. We also delivered the Envs in multiple forms, as it remains unclear what the best immunogens are for eliciting autologous tier 2 nAb and for ultimately developing breadth. However, according to our modeling, V5 would have likely been exposed on ZM Env forms if it had taken on a stable trimer conformation.

It could also be that the stabilizing change introduced near V5 HXB2 AP altered the exposure or conformation of this region. Indeed, there was little evidence of nAb pressure on R66M Envs during early infection, contrasting markedly with ZM, where there were changes in V2, V4, and V5 [ 4 ]. A unique aspect of our study was the availability of acute infection and longitudinal samples from participants in Zambia and Rwanda [ 57 ].

This enabled the use of Envs isolated from the infected subject, ZM, as a guide for defining vaccine elicited nAb targets. Two Envs that had escaped plasma nAb in early infection were also resistant to vaccine-elicited serum nAb. Using a combination of computational and experimental approaches, our study revealed that these viruses used a potentially novel mechanism in which the glycan shield was manipulated without removing, adding, or shifting a glycan.

Essentially, an existing glycan was reoriented by changing the conformation of the V5 loop through amino acid changes outside of the sequon. However, through mutations the virus can alter the projection of the existing glycan s. This escape mechanism employed by two early Envs during infection appears to have increased shielding of V5, while differentially influencing the accessibility of VRC01 contact sites within the CD4bs.

This finding suggests that shielding of the CD4bs could be subject to strategic manipulation in this Env background. In that case, elongation of the V5 loop drove reorientation of CH bnAb to facilitate neutralization of the escape variants. In a previous study of autologous nAb responses and escape in a different clade C HIV-1 infected subject ZF , we described another case of V5 dependent nAb targeting at 5 months after the estimated date of infection [ 58 ].

Taken together, these findings point to the CD4bs as a common nAb target in early clade C HIV-1 infection that is rapidly and effectively shielded by V5 dependent pathways. The possibility of exploiting these naturally occurring modifications through combined experimental and computational methods to enhance recognition of the CD4bs is a viable and enriching approach to immunogen design. Unfortunately, we do not have definitive information on what type or types of specificities were involved in the nAb breadth that developed in ZM.

However, plasma from ZM was identified as broadly neutralizing in an independent study [ 16 ]. Therefore, isolation of mAbs from ZM at nAb breadth associated time points is worth pursuing. A striking feature of our study is that we were able to eliminate all serum nAb activity by one or two changes in V5 that were derived from in vivo escape.

The predictability of eliciting nAb that target a single region could be an advantage for driving them down a path towards breadth, with the caveat that there were also many other non-neutralizing antibody specificities elicited. In our study, a V5 dependent escape pathway in two different Env variants had distinct effects of VRC01 neutralization and exposure of the CD4bs. Thus, if the initial nAb target is well defined on an Env immunogen, then computational approaches could facilitate sequential modifications to shift nAb while avoiding other changes selected in vivo that could be counterproductive.

Such re-direction of nAb could be achieved by altering the structural flexibility of the V5 loop or restricting the N HXB2 N glycan in an orientation away from CD4bs. To provide a more detailed understanding of vaccine-elicited nAb in comparison to the HIV-1 infected subject, mAbs were isolated from the immunized RM that developed the highest ID 50 titer. The nmAbs were also remarkably similar to the human nmAb 1A8, which was even less mutated from its assigned germline than the RM mAbs.

In ZM, there were also other nAb specificities that developed during early infection besides that represented by 1A8. For example, the nmAb 1E12 competed modestly with 1A8 but was only partially sensitive to the V5 changes, reflecting ongoing evolution of the immune response against viral variants. Our approach also highlights the complexity of generating soluble HIV trimers in the context of diverse variants. They also likely generated non-neutralizing antibodies directed against the trimer base, although we did not measure this directly.

ZM also has some unique features that could have contributed to its lack of soluble trimer stability. For one, the V3 loop is 32 amino acids instead of the more usual 33 for clade C Env. Furthermore, stabilization methods other than the UFO might improve trimerization. Nevertheless, the results illustrate variation in stabilizing genetically diverse HIV-1 Envs as well as highlighting gaps between in vitro stabilization vs the native Env trimer.

It is noteworthy that a gp Env immunogen elicited tier 2, autologous nAb in nonhuman primates. Examples of gp containing regimens that did not elicit autologous nAb in human subjects include the Vaxgen and trials that delivered recombinant gp proteins, and the RV and HVTN trials that administered gp following canarypox viral vector [ 63 ].

However, the Envs in those trials were not selected for their propensity to elicit tier 2 nAb. In addition, there are several approaches that can potentially be used to increase the frequency of immunized RM that develop autologous nAb and boost the nAb titers, including additional immunizations, different delivery methods, and a more powerful adjuvant than what was done in this study.

Others have also shown that an escalating dose approach is more effective than a bolus in eliciting higher nAb titers and potentially enhancing breadth [ 64 ]. Indeed, other studies including our own have described V5 loop targeting on other HIV-1 strains by autologous nAb following vaccination, HIV-1 infection, and SHIV infection of RM, including in settings involving the CD4bs and development of breadth [ 6 , 8 , 12 , 13 , 58 , 61 , 65 — 70 ].

Animal research was also in compliance with the Animal Welfare Act and other Federal statutes and regulations relating to experiments involving animals. All animal research adhered to the principles stated in the Guide for the Care and Use of Laboratory Animals prepared by the National Research Council. Methods of euthanasia were consistent with the American Veterinary Medical Association with Guidelines.

This study also utilized samples obtained previously from individuals enrolled in heterosexual discordant couple cohorts in Rwanda and Zambia [ 4 , 71 , 72 ]. After obtaining written informed consent, blood samples were collected from HIV-1 infected participants longitudinally.

All couples in the cohorts were provided monthly counseling and testing prior to the HIV-negative partner becoming positive. The procedures for written informed consent and research activities were approved by institutional review boards at all collaborating clinical research centers, with further compliance to human experimentation guidelines set forth by the United States Department of Health and Human Services.

To protect confidentiality, all subject identification numbers were anonymized by assigning a coded ID that removes any identifying information. All animals were between 3 and 5 years of age at the start of the study. Immunizations were as follows: week 0 lt. All immunizations were performed intramuscularly with each immunization dose split equally between left and right anatomic sites. For the protein immunizations, the groups of 10 were further subdivided with 5 animals receiving gp protein and the other 5 animals receiving the stabilized gp trimer.

Safety mutations were incorporated into gag to inactivate RNA packaging and into pol corresponding to protease and reverse transcriptase to inactivate their functions. Nucleotide sequences were confirmed. After 48 hours, lysates were prepared and used to infect DF-1 cells. After 7 rounds of plaque purification, seed stocks were developed from a final recombinant that expresses Gag and Env but not GFP.

Vaccine stocks were developed using seed stocks, purified on sucrose cushions, characterized by flow cytometry and western blot, sequence verified, titered, and used for immunization. Western blot analysis confirmed Gag and Env in the lysate and in supernatants of the infected cells suggesting virus-like particle formation S4D Fig. The transfected culture supernatant was collected at days 5—7, clarified via low-speed centrifugation, and passed through a 0.

The clarified, filtered supernatant was passed through Galanthus nivalis lectin coupled agarose beads Vector Laboratories, AL reconstituted in an Econo-Column chromatography column Bio-Rad, for purification of the protein. Peak fractions corresponding to monomeric gp were further visualized on Blue Native gel electrophoresis. In addition, each construct contained a series of amino acid substitutions that had been described previously to stabilize other HIV-1 Env gp proteins.

The supernatant was centrifuged at 3, rpm for 45 min, followed by filtration through a 0. All Env antigens were produced in F cells. Preimmunization serum samples week -4 and those collected at weeks 2, 10, 18, 26, 55, and 63 from 20 immunized RM were analyzed one did not have samples at weeks 55 and Six 5-fold serial dilutions of serum starting at were analyzed for IgG binding to the antigen panel and the mean fluorescence intensity at each dilution was then used to generate an area under the curve AUC value for each sample.

Bound IgG was detected using biotinylated anti-macaque IgG. The immunogen proteins were directly coupled to polystyrene beads and binding of antibodies was measured using mouse anti-human IgG-biotin followed by streptavidin-PE. Each antibody-protein combination was tested in duplicate.

Normal human serum was used as a negative control. An analysis was conducted using a two-level linear mixed effects model LMM with the function lmer under the package lme4 1. Time points and subject ID antiID were considered to have random effects, for which a random intercept as well as a random slope were added to the model.

Four dummy variables were created and corresponded to four vaccines, respectively. Another dummy variable was created to indicate the type of protein gp or trimer. The antigen gpTT31P. The effects of the four vaccines were evaluated by LMM with time points visits , specific vaccine and their interactions as the covariates.

Additionally, the effects of the two proteins were compared with visits, proteins, and their interactions as the covariates. To produce the protein, the coding sequence was synthesized and inserted into pcDNA3. Methods for the isolation of IgG variable domains from ZM antigen-specific B cells and production of mAbs has been described [ 15 ]. For the second round PCR reaction, 2. Sensors were regenerated before each kinetics assay. Data was analyzed using ForteBio Data Analysis 9.

Sensors were then immersed in 0. After a second baseline reading for 30 s in kinetics buffer, sensors were immersed in 0. Reference mAb as primary and secondary mAb was included as a positive control for competition reduced reference binding. Binning values were calculated using ForteBio Data Analysis 9.

Richard Wyatt at the Scripps Research Institute. Jens Wrammert at Emory University. Neutralization was measured using serially diluted, heat-inactivated immunized RM serum, RM or human plasma, or mAbs in the TZM-bl assay as previously described, using cells plated one day prior to the assay [ 4 , 15 , 58 , 83 — 94 ]. At 48 h post-infection, the cells were lysed and luciferase activity was measured using a BioTek Cytation3 multimode microplate reader.

The average background luminescence from a series of uninfected wells was subtracted from each experimental well. All assays contained duplicate wells and were repeated at least once independently. Neutralization ID 50 or IC 50 titer values were calculated in Graphpad Prism using the dose—response inhibition analysis function with variable slope, log-transformed x values, and normalized y values.

The plates were washed 3x with PBS-T 0. Heat inactivated RM serum samples were diluted in blocking buffer to starting concentrations between and Quantitation of gpspecific serum IgG was performed by including a standard curve for IgG on each plate. Concentrations of serum IgG that bound to gp were determined using all dilutions that fell within the quantitative range of the standard curve and were represented by the average for each sample.

Each assay was run with duplicate wells and one independent repeat. Heat inactivated RM serum samples, flow through and elution fractions from the column were diluted in blocking buffer to starting concentrations of Concentrations of IgG present were determined using all dilutions that fell within the range of the standard curve and were represented by the average for each sample. Each assay was run with duplicate wells. These plasmids include the full-length patient derived Env coding region as derived from single genome PCR amplification as well as upstream and downstream flanking sequences.

All final constructs were verified by nucleotide sequencing. David Montefiori. All other reagents were purchased from Sigma Aldrich unless indicated otherwise. Data analysis was performed using Byonic 2. The protein was reduced in 12 mM dithiothreitol solution, and subsequently alkylated in 30 mM iodoacetamide. The three digests were individually filtered through 0. A pre-packed nano-LC column Cat. Dynamic exclusion was enabled for an exclusion duration of 30 s after 2x detection within 20 s.

Carbamidomethylation of cysteine was set as a fixed modification, whereby oxidation of methionine and common human N-glycans found in plasma variable were set as variable modifications. The HCDpdCID MS 2 spectra of glycopeptides were evaluated for the glycan neutral loss pattern, oxonium ions and glycopeptide fragmentations to assign the sequence and the presence of glycans in the glycopeptides.

Spectra for the most common glycoform at each site used for computer modelling are included in S1 Appendix that also includes the glycoproteomics workflow, which was created with the help of BioRender. Glycoprotein conformational ensemble was generated by a previously established high throughput atomistic modeling pipeline HTAM [ 52 , 53 ]. Ten distinct underlying protein scaffolds were homology modeled from different experimentally determined SOSIP structures deposited in the Protein Data Bank, by assimilating the variations in local structural regions including loops, that arise due to flexibility.

The resulting collection of glycoprotein conformations were relaxed by conjugate gradient energy minimization followed by simulated annealing, with template-based protein backbone restraints and glycan topological restraints to enforce proper stereochemistry.

This integrated technique can sufficiently sample a physiologically relevant conformational space, as has been extensively validated with cryo-electron microscopy experiments [ 53 ]. The most probable glycan-type was selected for each N-glycan site, as determined by the site-specific mass spectrometry results.

Protein templates used for trimers and trimeric sfold of gp are as listed in Table S2 of reference [ 52 ]. The non-trimeric gp structure was built by a combination of different intact segments of monomeric structures. Shielding effect over the protein surface was calculated per-residue, based on the glycan encounter factor GEF score [ 52 ]. This was calculated as the geometric mean of the probability that a probe approaching a surface residue would encounter glycan heavy atoms, in perpendicular and tangential directions.

Probe size of 6 angstrom diameter was chosen to mimic a typical hairpin loop. Computational modeling calculations were implemented with VMD 1. All structural graphics were generated using VMD 1. Particles were picked automatically using Relion 3. Particles corresponding to trimers, not aggregates or fragments, were selected into a subset for another round of 2D reference-free alignment. In the end, 20 classes were generated. The gp proteins were tested at concentrations ranging from 0.

The individual sensorgrams are shown in S2 Fig. For the BAMA experiments, the untagged immunogen proteins were directly coupled to polystyrene beads and antibody binding was measured using mouse anti-human IgG-biotin primary followed by a streptavidin-PE secondary detection reagent, which was quantified by fluorescence intensity. In panels A-C , the antibody, binding specificity, and detection method is shown for each antibody-protein combination. Some antibody-protein combinations e.

F, VRC01, 17b were analyzed using both methods and the results of both are shown. The trimers were tested at concentrations ranging from 0. Response units are indicated on the y axis and are plotted against time on the x axis. Related to Fig 1. The fluorescence intensity data generated via antibody binding to the immunogen proteins in the BAMA assay is shown.

Surface and intracellular Gag was detected using mAb 2F Serum IgG binding to 8 gp proteins, 8 gp proteins, and 16 scaffolded V1V2 antigens from the BAMA antigen panel, as well as the R66M gp and trimer and ZM gp and trimer, was analyzed with respect to time weeks. The data was colored according to the type of protein in A and the subtype of the Env proteins in B. The mean MFI mean fluorescence intensity was calculated for RMs in the four vaccination groups and is plotted on the y-axis on a log10 scale for each binding antigen.

The time points of the immunizations are indicated on each graph. Error bars represent the standard deviation of mean serum IgG binding to the antigen panel for the RMs in each vaccination group. Each graph shows neutralization by serum normalized by IgG content , purified IgG, and the flow through fraction at a dilution FT.

Lower values indicate greater susceptibility to neutralization. Percent viral infectivity is shown on the y-axis relative to no test mAb. Three neutralizing mAbs from ZM are indicated by color. The percent residual binding of the reference mAb in the presence of the competitor is shown, with red indicating strong competition and blue representing weak or no competition.

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