Beyond DAD: proposing a one-letter code for nucleobase-mediated molecular recognition

Nucleobase binding is a fundamental molecular recognition event central to modern biological and bioinspired supramolecular research. Underpinning this recognition is a deceptively simple hydrogen-bonding code, primarily based on the canonical nucleobases in DNA and RNA. Inspired by these biotic structures, chemists and biologists have designed abiotic hydrogen-bonding motifs that can interact with, augment, and reshape native molecular recognition, for applications ranging from genetic code expansion and nucleic acid recognition to supramolecular materials utilizing mono- and bifacial nucleobases. However, as the number of nucleobase-inspired motifs expands, the absence of a standard vocabulary to describe hydrogen bond (HB) patterns has led to a haphazard mixture of shorthand descriptors that are confusing and inconsistent. Alternative notations that specify individual HB sites (such as DAD for donor-acceptor-donor) are cumbersome for biological and supramolecular constructs that contain many such patterns. This situation creates a barrier to sharing and interpreting nucleobase-related research across sub-disciplines, hindering collaboration and innovation. In this perspective, we aim to initiate discourse on this issue by considering what would be needed to formulate a concise one-letter code for the HB patterns associated with synthetic nucleobases. We first summarize some of the issues caused by the current absence of a consistent naming scheme. Subsequently, we discuss some key considerations in designing a coherent naming system. Finally, we leverage chemical rationale and pedagogical mnemonic considerations to propose a succinct and intuitive one-letter code for supramolecular two- and three-HB motifs. We hope that this discussion will spark conversations within our interdisciplinary community, thereby facilitating collaboration and easing communication among researchers engaged in synthetic nucleobase design.

Macromolecular Information Transfer

Macromolecular information transfer can be defined as the process by which a coded monomer sequence is communicated from one macromolecule to another. In such a transfer process, the information sequence can be kept identical, transformed into a complementary sequence or even translated into a different molecular language. Such mechanisms are crucial in biology and take place in DNA→DNA replication, DNA→RNA transcription and RNA→protein translation. In fact, there would be no life on Earth without macromolecular information transfer. Mimicking such processes with synthetic macromolecules would also be of major scientific relevance because it would open up new avenues for technological applications (e.g. data storage and processing) but also for the creation of artificial life. In this important context, this minireview summarizes recent research about information transfer in synthetic oligomers and polymers. Medium- and long-term perspectives are also discussed.

Evaluating the effect of ionic strength on PNA:DNA duplex formation kinetics

Peptide nucleic acid (PNA) is a unique synthetic nucleic acid analog that has been adopted for use in many biological applications. These applications rely upon the robust Franklin-Watson-Crick base pairing provided by PNA, particularly at lower ionic strengths. However, our understanding of the relationship between the kinetics of PNA:DNA hybridization and ionic strength is incomplete. Here we measured the kinetics of association and dissociation of PNA with DNA across a range of ionic strengths and temperatures at single-molecule resolution using total internal reflection fluorescence imaging. Unlike DNA:DNA duplexes, PNA:DNA duplexes are more stable at lower ionic strength, and we demonstrate that this is due to a higher association rate. While the dissociation rate of PNA:DNA duplexes is largely insensitive to ionic strength, it is significantly lower than that of DNA:DNA duplexes having the same number and sequence of base pairing interactions. The temperature dependence of PNA:DNA kinetic rate constants indicate a significant enthalpy barrier to duplex dissociation, and to a lesser extent, duplex formation. This investigation into the kinetics of PNA:DNA hybridization provides a framework towards better understanding and design of PNA sequences for future applications.

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.

Redesigning the Genetic Polymers of Life

Genomes can be viewed as constantly updated memory systems where information propagated in cells is refined over time by natural selection. This process, commonly known as heredity and evolution, has been the sole domain of DNA since the origin of prokaryotes. Now, some 3.5 billion years later, the pendulum of discovery has swung in a new direction, with carefully trained practitioners enabling the replication and evolution of "xeno-nucleic acids" or "XNAs"-synthetic genetic polymers in which the natural sugar found in DNA and RNA has been replaced with a different type of sugar moiety. XNAs have attracted significant attention as new polymers for synthetic biology, biotechnology, and medicine because of their unique physicochemical properties that may include increased biological stability, enhanced chemical stability, altered helical geometry, or even elevated thermodynamics of Watson-Crick base pairing.This Account describes our contribution to the field of synthetic biology, where chemical synthesis and polymerase engineering have allowed my lab and others to extend the concepts of heredity and evolution to synthetic genetic polymers with backbone structures that are distinct from those found in nature. I will begin with a discussion of α-l-threofuranosyl nucleic acid (TNA), a specific type of XNA that was chosen as a model system to represent any XNA system. I will then proceed to discuss advances in organic chemistry that were made to enable the synthesis of gram quantities of TNA phosphoramidites and nucleoside triphosphates, the monomers used for solid-phase and polymerase-mediated TNA synthesis, respectively. Next, I will recount our development of droplet-based optical sorting (DrOPS), a single-cell microfluidic technique that was established to evolve XNA polymerases in the laboratory. This section will conclude with structural insights that have been gained by solving X-ray crystal structures of a laboratory-evolved TNA polymerase and a natural DNA polymerase that functions with general reverse transcriptase activity on XNA templates.The final passage of this Account will examine the role that XNAs have played in synthetic biology by highlighting examples in which engineered polymerases have enabled the evolution of biologically stable affinity reagents (aptamers) and catalysts (XNAzymes) as well as the storage and retrieval of binary information encoded in electronic word and picture file formats. Because these examples provide only a glimpse of what the future may have in store for XNA, I will conclude the Account with my thoughts on how synthetic genetic polymers could help drive new innovations in synthetic biology and molecular medicine.

The proto-Nucleic Acid Builder: a software tool for constructing nucleic acid analogs

The helical structures of DNA and RNA were originally revealed by experimental data. Likewise, the development of programs for modeling these natural polymers was guided by known structures. These nucleic acid polymers represent only two members of a potentially vast class of polymers with similar structural features, but that differ from DNA and RNA in the backbone or nucleobases. Xeno nucleic acids (XNAs) incorporate alternative backbones that affect the conformational, chemical, and thermodynamic properties of XNAs. Given the vast chemical space of possible XNAs, computational modeling of alternative nucleic acids can accelerate the search for plausible nucleic acid analogs and guide their rational design. Additionally, a tool for the modeling of nucleic acids could help reveal what nucleic acid polymers may have existed before RNA in the early evolution of life. To aid the development of novel XNA polymers and the search for possible pre-RNA candidates, this article presents the proto-Nucleic Acid Builder (https://github.com/GT-NucleicAcids/pnab), an open-source program for modeling nucleic acid analogs with alternative backbones and nucleobases. The torsion-driven conformation search procedure implemented here predicts structures with good accuracy compared to experimental structures, and correctly demonstrates the correlation between the helical structure and the backbone conformation in DNA and RNA.

Recent advances in understanding oligonucleotide aptamers and their applications as therapeutic agents

The innovative discovery of aptamers was based on target-specific treatment in clinical diagnostics and therapeutics. Aptamers are synthetic, single-stranded oligonucleotides, simply described as chemical antibodies, which can bind to diverse targets with high specificity and affinity. Aptamers are synthesized by the SELEX technique, and possess distinctive properties as small size (10-50 kDa), higher stability, easy manufacture and less immunogenicity. These oligonucleotides are easily degraded by nucleases, so require some important modifications like capping and incorporation of modified nucleotides. RNA aptamers can be modified chemically on 2' positions using -NH3, -F, -deoxy, or -OMe groups to enhance their nuclease resistance. Aptamers have been employed for multiple purposes, as direct drugs or aptamer-drug conjugates targeted against different diseased cells. Different aptamer-conjugated nanovehicles (e.g., micelles, liposomes, silica nano-shells) have been designed to transport diverse anticancer-drugs like doxorubicin and cisplatin in bulk to minimize systemic cytotoxicity. Some drug-loaded nanovehicles (up to 97% loading capacity) and conjugated with specific aptamer resulted in more than 60% tumor inhibition as compared to unconjugated drug-loaded nanovehicles which showed only 31% cancer inhibition. In addition, aptamers have been widely used in basic research, food safety, environmental monitoring, clinical diagnostics and therapeutics. Different FDA-approved RNA and DNA aptamers are now available in the market, used for the treatment of diverse diseases, especially cancer. These aptamers include Macugen, Pegaptanib, etc. Despite a good progress in aptamer use, the present-day chemotherapeutics and drug targeting systems still face great challenges. Here in this review article, we are discussing nucleic acid aptamers, preparation, role in the transportation of different nanoparticle vehicles and their applications as therapeutic agents.

Solid-Phase Synthesis of Sequence-Defined Informational Oligomers

Genetic biopolymers utilize defined sequences and monomer-specific molecular recognition to store and transfer information. Synthetic polymers that mimic these attributes using reversible covalent chemistry for base-pairing pose unique synthetic challenges. Here, we describe a solid-phase synthesis methodology for the efficient construction of ethynyl benzene oligomers with specific sequences of aniline and benzaldehyde subunits. Handling these oligomers is complicated by the fact that they often exhibit multiple conformations because of intra- or intermolecular pairing. We describe conditions that allow the dynamic behavior of these oligomers to be controlled so that they may be manipulated and characterized without needing to mask the recognition units with protecting groups.

Synthetic Biology: A Solution for Tackling Nanomaterial Challenges

Bioengineers have mastered practical techniques for tuning a biomaterial's properties with only limited information on the relationship between the material's structure and function. These techniques have been quintessential to engineering proteins, which are most often riddled with ill-defined structure-function relationships. In this Perspective, we review bioengineering approaches aimed at overcoming the elusive protein structure-function relation. We extend these principles to engineering synthetic nanomaterials, specifically applying the underlying theory to optical sensors based on single-stranded DNA-wrapped single-walled carbon nanotubes (ssDNA-SWCNTs). Bioengineering techniques such as directed evolution, computational design, and noncanonical synthesis are reviewed in the broader context of nanomaterials engineering. We further provide an order-of-magnitude analysis of empirical approaches that rely on random or guided searches for designing new nanomaterials. The underlying concepts presented in these approaches can be further extended to a broad range of engineering fields confronted with empirical design strategies, including catalysis, metal-organic frameworks (MOFs), pharmaceutical dosing, and optimization algorithms.

Peptide nucleic acids harness dual information codes in a single molecule

Nature encodes the information required for life in two fundamental biopolymers: nucleic acids and proteins. Peptide nucleic acid (PNA), a synthetic analog comprised of nucleobases arrayed along a pseudopeptide backbone, has the ability to combine the power of nucleic acids to encode information with the versatility of amino acids to encode structure and function. Historically, PNA has been perceived as a simple nucleic acid mimic having desirable properties such as high biostability and strong affinity for complementary nucleic acids. In this feature article, we aim to adjust this perception by highlighting the ability of PNA to act as a peptide mimic and showing the largely untapped potential to encode information in the amino acid sequence. First, we provide an introduction to PNA and discuss the use of conjugation to impart tunable properties to the biopolymer. Next, we describe the integration of functional groups directly into the PNA backbone to impart specific physical properties. Lastly, we highlight the use of these integrated amino acid side chains to encode peptide-like sequences in the PNA backbone, imparting novel activity and function and demonstrating the ability of PNA to simultaneously mimic both a peptide and a nucleic acid.

Non-covalent Methods of Engineering Optical Sensors Based on Single-Walled Carbon Nanotubes

Optical sensors based on single-walled carbon nanotubes (SWCNTs) demonstrate tradeoffs that limit their use in in vivo and in vitro environments. Sensor characteristics are primarily governed by the non-covalent wrapping used to suspend the hydrophobic SWCNTs in aqueous solutions, and we herein review the advantages and disadvantages of several of these different wrappings. Sensors based on surfactant wrappings can show enhanced quantum efficiency, high stability, scalability, and diminished selectivity. Conversely, sensors based on synthetic and bio-polymer wrappings tend to show lower quantum efficiency, stability, and scalability, while demonstrating improved selectivity. Major efforts have focused on optimizing sensors based on DNA wrappings, which have intermediate properties that can be improved through synthetic modifications. Although SWCNT sensors have, to date, been mainly engineered using empirical approaches, herein we highlight alternative techniques based on iterative screening that offer a more guided approach to tuning sensor properties. These more rational techniques can yield new combinations that incorporate the advantages of the diverse nanotube wrappings available to create high performance optical sensors.

Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development

Aptamers are short single-stranded nucleic acid sequences capable of binding to target molecules in a way similar to antibodies. Due to various advantages such as prolonged shelf life, low batch to batch variation, low/no immunogenicity, freedom to incorporate chemical modification for enhanced stability and targeting capacity, aptamers quickly found their potential in diverse applications ranging from therapy, drug delivery, diagnosis, and functional genomics to bio-sensing. Aptamers are generated by a process called SELEX. However, the current overall success rate of SELEX is far from being satisfactory, and still presents a major obstacle for aptamer-based research and application. The need for an efficient selection strategy consisting of defined procedures to deal with a wide variety of targets is significantly important. In this work, by analyzing key aspects of SELEX including initial library design, target preparation, PCR optimization, and single strand DNA separation, we provide a comprehensive analysis of individual steps to facilitate researchers intending to develop personalized protocols to address many of the obstacles in SELEX. In addition, this review provides suggestions and opinions for future aptamer development procedures to address the concerns on key SELEX steps, and post-SELEX modifications.

Recent Developments in Solid-Phase Strategies towards Synthetic, Sequence-Defined Macromolecules

Sequence-control in synthetic polymers is an important contemporary research area because it provides the opportunity to create completely novel materials for structure-function studies. This is especially relevant for biomimetic polymers, bioactive and information security materials. The level of control is strongly dependent and inherent upon the polymerization technique utilized. Today, the most established method yielding monodispersity and monomer sequence-definition is solid-phase synthesis. This Focus Review highlights recent advances in solid-phase strategies to access synthetic, sequence-defined macromolecules. Alternatives strategies towards sequence-defined macromolecules are also briefly summarized.

How do hydrophobic nucleobases differ from natural DNA nucleobases? Comparison of structural features and duplex properties from QM calculations and MD simulations

Computational (DFT and MD simulation) methods are employed to systematically characterize the structural and energetic properties of five hydrophobic nucleobases (FEMO, MMO2, NaM, 5SICS and TPT3) that constitute four unnatural base pairs (FEMO:5SICS, MMO2:5SICS, NaM:5SICS and TPT3:NaM). These hydrophobic bases have been recently shown to be replicated when present between natural bases in DNA duplexes, with the highest replication fidelity and efficiency occuring for the TPT3:NaM pair. Our QM calculations suggest that the preferred (anti) glycosidic orientations of nucleosides containing hydrophobic bases are similar to the natural DNA nucleosides despite differences in their chemical structures. However, due to the inability to form interbase hydrogen bonds, hydrophobic base pairs intrinsically prefer nonplanar, distorted geometries, many of which are stabilized through π-π stacking interactions. Furthermore, the intrinsic stacking potential between a hydrophobic and a natural base is similar to that between two natural bases, indicating that the strength of stacking interactions in DNA duplexes containing hydrophobic bases is likely comparable to natural DNA. However, in contrast to the isolated base-pair geometries, our MD simulations suggest that the hydrophobic base pairs adopt variable geometries within DNA, which range from stacked (5SICS:FEMO) to nearly planar (5SICS:NaM and SICS:MMO2) to planar (TPT3:NaM). As a result, the duplex structural features at the site of modification depend on the identity of the hydrophobic base pair, where the TPT3:NaM pair causes the least structural changes compared to natural DNA. Overall, the structural insight obtained from our calculations on DNA containing hydrophobic base pairs explains the experimentally-observed higher fidelity and efficiency during replication of TPT3:NaM compared to other hydrophobic nucleobase pairs. By providing valuable structural information that explains the intrinsic and duplex properties of this class of unnatural nucleobases, the present work may aid the future design of improved hydrophobic analogues.

Recent advances in the synthesis of functional materials by engineered and recombinant living cells

At the interface of materials science and synthetic biology, several concepts were recently developed for the production of functional materials by living cells. Selected recent strategies for this are highlighted here with a focus on bioactive, electronic and fluorescent materials.