Building better polymerases: Engineering the replication of expanded genetic alphabets

Enhancing the reverse transcriptase function in Taq polymerase via AI-driven multiparametric rational design

Introduction

Modification of natural enzymes to introduce new properties and enhance existing ones is a central challenge in bioengineering. This study is focused on the development of Taq polymerase mutants that show enhanced reverse transcriptase (RTase) activity while retaining other desirable properties such as fidelity, 5'- 3' exonuclease activity, effective deoxyuracyl incorporation, and tolerance to locked nucleic acid (LNA)-containing substrates. Our objective was to use AI-driven rational design combined with multiparametric wet-lab analysis to identify and validate Taq polymerase mutants with an optimal combination of these properties.

Methods

The experimental procedure was conducted in several stages: 1) On the basis of a foundational paper, we selected 18 candidate mutations known to affect RTase activity across six sites. These candidates, along with the wild type, were assessed in the wet lab for multiple properties to establish an initial training dataset. 2) Using embeddings of Taq polymerase variants generated by a protein language model, we trained a Ridge regression model to predict multiple enzyme properties. This model guided the selection of 14 new candidates for experimental validation, expanding the dataset for further refinement. 3) To better manage risk by assessing confidence intervals on predictions, we transitioned to Gaussian process regression and trained this model on an expanded dataset comprising 33 data points. 4) With this enhanced model, we conducted an in silico screen of over 18 million potential mutations, narrowing the field to 16 top candidates for comprehensive wet-lab evaluation.

Results and Discussion

This iterative, data-driven strategy ultimately led to the identification of 18 enzyme variants that exhibited markedly improved RTase activity while maintaining a favorable balance of other key properties. These enhancements were generally accompanied by lower Kd, moderately reduced fidelity, and greater tolerance to noncanonical substrates, thereby illustrating a strong interdependence among these traits. Several enzymes validated via this procedure were effective in single-enzyme real-time reverse-transcription PCR setups, implying their utility for the development of new tools for real-time reverse-transcription PCR technologies, such as pathogen RNA detection and gene expression analysis. This study illustrates how AI can be effectively integrated with experimental bioengineering to enhance enzyme functionality systematically. Our approach offers a robust framework for designing enzyme mutants tailored to specific biotechnological applications. The results of our biological activity predictions for mutated Taq polymerases can be accessed at https://huggingface.co/datasets/nerusskikh/taqpol_insilico_dms.

Correct Nucleotide Selection Is Confined at the Binding Site of Polymerase Enzymes

DNA polymerases (Pols) add incoming nucleotides (deoxyribonucleoside triphosphate (dNTPs)) to growing DNA strands, a crucial step for DNA synthesis. The insertion of correct (vs incorrect) nucleotides relates to Pols' fidelity, which defines Pols' ability to faithfully replicate DNA strands in a template-dependent manner. We and others have demonstrated that reactant alignment and correct base pairing at the Pols catalytic site are crucial structural features to fidelity. Here, we first used equilibrium molecular simulations to demonstrate that the local dynamics at the protein-DNA interface in the proximity of the catalytic site is different when correct vs incorrect dNTPs are bound to polymerase β (Pol β). Formation and dynamic stability of specific interatomic interactions around the incoming nucleotide influence the overall binding site architecture. This explains why certain Pols' mutants can affect the local catalytic environment and influence the selection of correct vs incorrect nucleotides. In particular, this is here demonstrated by analyzing the interaction network formed by the residue R283, whose mutant R283A has an experimentally measured lower capacity of differentiating correct (G:dCTP) vs incorrect (G:dATP) base pairing in Pol β. We also used alchemical free-energy calculations to quantify the G:dCTP →G:dATP transformation in Pol β wild-type and mutant R283A. These results correlate well with the experimental trend, thus corroborating our mechanistic insights. Sequence and structural comparisons with other Pols from the same family suggest that these findings may also be valid in similar enzymes.

Amplifying PCR productivity and environmental sustainability through shortened cycling protocols

Since its inception in the 1980s, advancements in PCR technology using improved thermal cyclers, engineered DNA polymerases and commercial master mixes, have led to increased PCR productivity. Despite these advancements, PCR cycling protocols have largely remained unchanged over the same period. This study aimed to systemically evaluate the effect of reduced PCR cycling parameters on amplicon production. The 1466bp fragment from the 16S rRNA gene present in low-, medium- and high-CG bacteria was amplified using three commercially available PCR master mixes. The shortest cycling parameters required to successfully amplify the 16S fragment from all bacteria and master mixes comprised 30-cycles of 5 s denaturation, 25 s annealing, and 25 s extension. While all produced an amplicon with sufficient yield to enable downstream sequence analysis, the PCRBIO Ultra Mix in conjunction with the shortened parameters was found to achieve the highest amplicon yield across low-, medium- and high CG bacteria. Comparing the run times to that of a typical 16S PCR protocol, the shortened cycling parameters reduced the program duration by 46 % and consumed 50 % less electricity, translating into increased productivity and helping to improve laboratory environmental sustainability.

Theoretical insights into the photophysics of an unnatural base Z: A MS-CASPT2 investigation

We have employed the highly accurate multistate complete active space second-order perturbation theory (MS-CASPT2) method to investigate the photoinduced excited state relaxation properties of one unnatural base, namely Z. Upon excitation to the S2 state of Z, the internal conversion to the S1 state would be dominant. From the S1 state, two intersystem crossing paths leading to the T2 and T1 states and one internal conversion path to the S0 state are possible. However, considering the large barrier to access the S1 /S0 conical intersection and the strong spin-orbit coupling between S1 and T2 states (>40 cm-1 ), the intersystem crossing to the triplet manifolds is predicted to be more preferred. Arriving at the T2 state, the internal conversion to the T1 state and the intersystem crossing back to the S1 state are both possible considering the S1 /T2 /T1 three-state intersection near the T2 minimum. Upon arrival at the T1 state, the deactivation to S0 can be efficient after overcoming a small barrier to access T1 /S0 crossing point, where the spin-orbit coupling (SOC) is as large as 39.7 cm-1 . Our present work not only provides in-depth insights into the photoinduced process of unnatural base Z, but can also help the future design of novel unnatural bases with better photostability.

A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase

Artificially Expanded Genetic Information Systems (AEGIS) add independently replicable unnatural nucleotide pairs to the natural G:C and A:T/U pairs found in native DNA, joining the unnatural pairs through alternative modes of hydrogen bonding. Whether and how AEGIS pairs are recognized and processed by multi-subunit cellular RNA polymerases (RNAPs) remains unknown. Here, we show that E. coli RNAP selectively recognizes unnatural nucleobases in a six-letter expanded genetic system. High-resolution cryo-EM structures of three RNAP elongation complexes containing template-substrate UBPs reveal the shared principles behind the recognition of AEGIS and natural base pairs. In these structures, RNAPs are captured in an active state, poised to perform the chemistry step. At this point, the unnatural base pair adopts a Watson-Crick geometry, and the trigger loop is folded into an active conformation, indicating that the mechanistic principles underlying recognition and incorporation of natural base pairs also apply to AEGIS unnatural base pairs. These data validate the design philosophy of AEGIS unnatural basepairs. Further, we provide structural evidence supporting a long-standing hypothesis that pair mismatch during transcription occurs via tautomerization. Together, our work highlights the importance of Watson-Crick complementarity underlying the design principles of AEGIS base pair recognition.

Two are not enough: synthetic strategies and applications of unnatural base pairs

Nucleic acid chemistry is a rapidly evolving field, and the need for novel nucleotide modifications and artificial nucleotide building blocks for diagnostic and therapeutic use, material science or for studying cellular processes continues unabated. This review focusses on the development and application of unnatural base pairs as part of an expanded genetic alphabet. Not only recent developments in "nature-like" artificial base pairs are presented, but also current synthetic methods to get access to C-glycosidic nucleotides. Wide-ranging viability in synthesis is a prerequisite for the successful use of unnatural base pairs in a broader spectrum and will be discussed.

The origin of genetic and metabolic systems: Evolutionary structuralinsights

DNA is derived from reverse transcription and its origin is related to reverse transcriptase, DNA polymerase and integrase. The gene structure originated from the evolution of the first RNA polymerase. Thus, an explanation of the origin of the genetic system must also explain the evolution of these enzymes. This paper proposes a polymer structure model, termed the stable complex evolution model, which explains the evolution of enzymes and functional molecules. Enzymes evolved their functions by forming locally tightly packed complexes with specific substrates. A metabolic reaction can therefore be considered to be the result of adaptive evolution in this way when a certain essential molecule is lacking in a cell. The evolution of the primitive genetic and metabolic systems was thus coordinated and synchronized. According to the stable complex model, almost all functional molecules establish binding affinity and specific recognition through complementary interactions, and functional molecules therefore have the nature of being auto-reactive. This is thermodynamically favorable and leads to functional duplication and self-organization. Therefore, it can be speculated that biological systems have a certain tendency to maintain functional stability or are influenced by an inherent selective power. The evolution of dormant bacteria may support this hypothesis, and inherent selectivity can be unified with natural selection at the molecular level.

Loop-Mediated Isothermal Amplification: From Theory to Practice

Increasing the accuracy of pathogen identification and reducing the duration of analysis remain relevant for modern molecular diagnostics up to this day. In laboratory and clinical practice, detection of pathogens mostly relies on methods of nucleic acid amplification, among which the polymerase chain reaction (PCR) is considered the "gold standard." Nevertheless, in some cases, isothermal amplification methods act as an alternative to PCR diagnostics. Upon more than thirty years of the development of isothermal DNA synthesis, the appearance of loop-mediated isothermal amplification (LAMP) has enabled new directions of in-field diagnostics of bacterial and viral infections. This review examines the key characteristics of the LAMP method and corresponding features in practice. We discuss the structure of LAMP amplicons with single-stranded loops, which have the sites for primer annealing under isothermal conditions. The latest achievements in the modification of the LAMP method are analyzed, which allow considering it as a unique platform for creating the next-generation diagnostic assays.

From polymerase engineering to semi-synthetic life: artificial expansion of the central dogma

Nucleic acids have been extensively modified in different moieties to expand the scope of genetic materials in the past few decades. While the development of unnatural base pairs (UBPs) has expanded the genetic information capacity of nucleic acids, the production of synthetic alternatives of DNA and RNA has increased the types of genetic information carriers and introduced novel properties and functionalities into nucleic acids. Moreover, the efforts of tailoring DNA polymerases (DNAPs) and RNA polymerases (RNAPs) to be efficient unnatural nucleic acid polymerases have enabled broad application of these unnatural nucleic acids, ranging from production of stable aptamers to evolution of novel catalysts. The introduction of unnatural nucleic acids into living organisms has also started expanding the central dogma in vivo. In this article, we first summarize the development of unnatural nucleic acids with modifications or alterations in different moieties. The strategies for engineering DNAPs and RNAPs are then extensively reviewed, followed by summarization of predominant polymerase mutants with good activities for synthesizing, reverse transcribing, or even amplifying unnatural nucleic acids. Some recent application examples of unnatural nucleic acids with their polymerases are then introduced. At the end, the approaches of introducing UBPs and synthetic genetic polymers into living organisms for the creation of semi-synthetic organisms are reviewed and discussed.

Enzymatic Synthesis of the Unnatural Nucleotide 2'-Deoxyisoguanosine 5'-Monophosphate

Naturally occurring DNA contains four canonical bases, forming two Watson-Crick base pairs (adenine-thymine, guanine-cytosine). Efforts over the past decades have led to the development of several unnatural base pairs, enabling the synthesis of unnatural DNA with an expanded genetic alphabet. The engineering of organisms capable of de novo biosynthesis of unnatural DNA would have significant technological and philosophical implications, but remains a challenge. Here we report the enzymatic conversion of 2'-deoxyxanthosine 5'-monophosphate (dXMP) into deoxyisoguanosine monophosphate (dBMP), a precursor of the unnatural isoguanine-isocytosine base pair. The reaction is catalyzed by the bacteriophage enzyme PurZ and bacterial PurB, and is a key addition to the toolbox for de novo biosynthesis of unnatural DNA.

Evaluation of 3'-phosphate as a transient protecting group for controlled enzymatic synthesis of DNA and XNA oligonucleotides

Chemically modified oligonucleotides have advanced as important therapeutic tools as reflected by the recent advent of mRNA vaccines and the FDA-approval of various siRNA and antisense oligonucleotides. These sequences are typically accessed by solid-phase synthesis which despite numerous advantages is restricted to short sequences and displays a limited tolerance to functional groups. Controlled enzymatic synthesis is an emerging alternative synthetic methodology that circumvents the limitations of traditional solid-phase synthesis. So far, most approaches strived to improve controlled enzymatic synthesis of canonical DNA and no potential routes to access xenonucleic acids (XNAs) have been reported. In this context, we have investigated the possibility of using phosphate as a transient protecting group for controlled enzymatic synthesis of DNA and locked nucleic acid (LNA) oligonucleotides. Phosphate is ubiquitously employed in natural systems and we demonstrate that this group displays most characteristics required for controlled enzymatic synthesis. We have devised robust synthetic pathways leading to these challenging compounds and we have discovered a hitherto unknown phosphatase activity of various DNA polymerases. These findings open up directions for the design of protected DNA and XNA nucleoside triphosphates for controlled enzymatic synthesis of chemically modified nucleic acids.

Chemical modifications for a next generation of nucleic acid aptamers

In the past three decades, in vitro systematic evolution of ligands by exponential enrichment (SELEX) has yielded many aptamers for translational applications in both research and clinical settings. Despite their promise as an alternative to antibodies, the low success rate of SELEX (~ 30%) has been a major bottleneck that hampers the further development of aptamers. One hurdle is the lack of chemical diversity in nucleic acids. To address this, the aptamer chemical repertoire has been extended by introducing exotic chemical groups, which provide novel binding functionalities. This review will focus on how modified aptamers can be selected and evolved, with illustration of some successful examples. In particular, unique chemistries are exemplified. Various strategies of incorporating modified building blocks into the standard SELEX protocol are highlighted, with a comparison of the differences between pre-SELEX and post-SELEX modifications. Nucleic acid aptamers with extended functionality evolved from non-natural chemistries will open up new vistas for function and application of nucleic acids.

Access to Photostability-Enhanced Unnatural Base Pairs via Local Structural Modifications

Completing the storage and retrieval of increased genetic information in vivo and producing therapeutic proteins have been achieved by the unnatural base pair dNaM-dTPT3. Up to now, some biological and chemical approaches are implemented to improve the semi-synthetic organism (SSO). However, the photosensitivity of this pair, suggested as a potential threat to the healthy growth of cells, is still a problem to solve. Hence, we designed and synthesized a panel of TPT3 analogues with the basic structural skeletons of TPT3 but modified thiophene rings at variant sites to improve the photostability of unnatural base pairs. A comprehensive screening strategy, including photosensitivity tests, kinetic experiments, and replication in vitro by PCR and in vivo by amplification, was implemented. A new pair, dNaM-dTAT1, which had almost equally high efficiency and fidelity with the dNaM-dTPT3 pair itself both in vivo and in vitro, was proven to be more photostable and thermostable and less toxic to E. coli cells. The discovery of dNaM-dTAT1 represents our first progress for the optimization of this type of bases toward more photostable properties; our data also suggest that less photosensitive unnatural base pairs will be beneficial to build a healthier cellular replication system.

A simple and general approach to generate photoactivatable DNA processing enzymes

DNA processing enzymes, such as DNA polymerases and endonucleases, have found many applications in biotechnology, molecular diagnostics, and synthetic biology, among others. The development of enzymes with controllable activity, such as hot-start or light-activatable versions, has boosted their applications and improved the sensitivity and specificity of the existing ones. However, current approaches to produce controllable enzymes are experimentally demanding to develop and case-specific. Here, we introduce a simple and general method to design light-start DNA processing enzymes. In order to prove its versatility, we applied our method to three DNA polymerases commonly used in biotechnology, including the Phi29 (mesophilic), Taq, and Pfu polymerases, and one restriction enzyme. Light-start enzymes showed suppressed polymerase, exonuclease, and endonuclease activity until they were re-activated by an UV pulse. Finally, we applied our enzymes to common molecular biology assays and showed comparable performance to commercial hot-start enzymes.

Transcription, Reverse Transcription, and Amplification of Backbone-Modified Nucleic Acids with Laboratory-Evolved Thermophilic DNA Polymerases

Backbone-modified nucleic acids are usually more stable enzymatically than their natural counterparts, enabling their broad application as potential diagnostic or therapeutic agents. Moreover, the development of nucleic acids with unnatural backbones has expanded the pool of genetic information carriers and paved the way toward synthetic xenobiology. However, synthesizing these molecules remains very challenging due to the requirement for harsh reaction conditions and the low coupling efficiency during their traditional solid-phase synthesis. Although enzymatic synthesis provides an attractive alternative that also allows the replication and artificial evolution of these molecules, it is crucially dependent on the availability of polymerases capable of synthesizing these backbone-modified nucleotides. Previously, a series of thermostable polymerases that can efficiently synthesize or even amplify backbone-modified DNA or RNA have been evolved through a polymerase evolution method based on phage display. Herein we summarize protocols to use these evolved polymerase mutants to transcribe, reverse transcribe, and PCR amplify backbone-modified nucleic acids. We also outline the polymerase chain transcription method, developed later for the rapid production of RNA or backbone-modified RNA with one of these evolved polymerases, SFM4-3. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Transcription/synthesis of modified DNA/RNA from DNA templates with evolved polymerases SFM4-3 or SFM4-6 Basic Protocol 2: Reverse transcription of modified DNA/RNA with evolved polymerase SFM4-9 Basic Protocol 3: PCR amplification of modified DNA with evolved polymerase SFM4-3 Basic Protocol 4: Polymerase chain transcription for the production of RNA/modified RNA oligonucleotides with evolved polymerase SFM4-3.