Replacing the nucleobases in DNA with designer molecules

Exploring the molecular aspect and updating evolutionary approaches to the DNA polymerase enzymes for biotechnological needs: A comprehensive review

DNA polymerases are essential enzymes that play a key role in living organisms, as they participate in the synthesis and maintenance of the DNA molecule. The intrinsic properties of these enzymes have been widely observed and studied to understand their functions, activities, and behavior, which has allowed their natural power in DNA synthesis to be exploited in modern biotechnology, to the point of making them true pillars of the field. In this context, the laboratory evolution of these enzymes, either by directed evolution or rational design, has led to the generation of a wide range of new DNA polymerases with novel properties, suitable for a variety of biotechnological needs. In this review, we examine DNA polymerases at the molecular level, their biotechnological use, and their evolutionary methods in relation to the novel properties sought, providing a chronological selection of evolved DNA polymerases cited in the literature that we consider to be of great interest. To our knowledge, this work is the first to bring together the molecular, functional and evolutionary aspects of the DNA polymerase enzyme. We believe it will be of great interest to researchers whose aim is to produce new lines of evolved DNA polymerases.

Palladium-Catalyzed Regio- and Stereoselective Glycosylation of Azole Heterocycles Enables Access to Diverse Heterocyclic N-Glycosides

An efficient and practical glycosylation platform for synthesizing N-glycosides by leveraging palladium catalysis is disclosed. This approach enables facile access to diverse heterocyclic N-glycosides with excellent regio- and stereoselectivities and high site selectivity of multiple N atoms. The reaction exhibits a broad substrate scope (65 examples), high functional group tolerance, and easy scalability. Its synthetic utility is demonstrated through late-stage functionalization of pharmaceutically relevant molecules and various diastereoselective transformations of the glycoside products. Overall, our method provides a handy tool for efficient and stereocontrolled synthesis of valuable N-glycosylated heterocycles.

Boronic Acid-Catalyzed Regio- and Stereoselective N-Glycosylations of Purines and Other Azole Heterocycles: Access to Nucleoside Analogues

In the presence of an arylboronic acid catalyst, azole-type heterocycles, including purines, tetrazoles, triazoles, indazoles, and benzo-fused congeners, undergo regio- and stereoselective N-glycosylations with furanosyl and pyranosyl trichloroacetimidate donors. The protocol, which does not require stoichiometric activators, specialized leaving groups, or drying agents, provides access to nucleoside analogues and enables late-stage N-glycosylation of azole-containing pharmaceutical agents. A mechanism involving simultaneous activation of the glycosyl donor and acceptor by the organoboron catalyst has been proposed, supported by kinetic analysis and computational modeling.

BN-Phenanthrene- and BN-Pyrene-Based Fluorescent Uridine Analogues

Two unprecedented fluorescent nucleosides that feature BN-doped polycyclic aromatic hydrocarbons are presented. One of them, having a BN-modified phenanthrene moiety incorporated, shows blue fluorescence but suffers from poor stability under aqueous conditions. The other nucleoside comprises an internally BN-doped pyrene as the chromophore. It shows green fluorescence in various solvents and is stable under aqueous and alkaline conditions.

Cobalt-assisted route to rare carbocyclic C-ribonucleosides

(Re)emerging RNA viruses have been major threats to public health in the past years, and from the few drugs available, nucleoside analogues are still at the cornerstone of the antiviral therapy. Among them, the synthesis of carbocyclic C-nucleosides is suffering from long syntheses and poor yields. Herein we report a concise stereoselective synthesis of rare carbocyclic C-nucleosides (11a-l) bearing non-canonical nucleobases through a cobalt-assisted-route as key step starting from the optically pure (-)-cyclopentenone 1. This approach paves the route for novel carbocyclic C-nucleoside discovery.

Keeping the chromophores crossed: evidence for null exciton splitting

Fundamental understanding of the supramolecular assemblies of organic chromophores and the development of design strategies have seen endless ripples of interest owing to their exciting photophysical properties and optoelectronic applications. The independent discovery of dye aggregates by Jelley and Scheibe was the commencement of the remarkable advancement in the field of aggregate photophysics. Subsequent research warranted an exceptional model for defining the exciton interactions in aggregates, proposed by Davydov, Kasha and co-workers, independently, based on the long-range Coulombic coupling. Fascinatingly, the orthogonally cross-stacked molecular transition dipole arrangement was foretold by Kasha to possess null exciton interaction leading to spectroscopically uncoupled molecular assembly, which lacked an experimental signature for decades. There have been several attempts to identify and probe atypical molecular aggregates for decoding their optical behaviour. Herein, we discuss the recent efforts in experimentally verifying the unusual exciton interactions supported with quantum chemical computations, primarily focusing on the less explored null exciton splitting. Exciton engineering can be realized through synthetic modifications that can additionally offer control over the assorted non-covalent interactions for orchestrating precise supramolecular assembly, along with molecular editing. The task of attaining a minimal excitonic coupling through an orthogonally cross-stacked crystalline architecture envisaged to offer a monomer-like optical behaviour was first reported in 1,7-dibromoperylene-3,4,9,10-tetracarboxylic tetrabutylester (PTE-Br2). The attempt to stitch molecules covalently in an orthogonal fashion to possess null excitonic character culminated in a spiro-conjugated perylenediimide dimer exhibiting a monomer-like spectroscopic signature. The computational and experimental efforts to map the emergent properties of the cross-stacked architecture are also discussed here. Using the null aggregates formed by the interference effects between CT-mediated and Coulombic couplings in the molecular array is another strategy for achieving monomer-like spectroscopic properties in molecular assemblies. Moreover, identifying supramolecular assemblies with precise angle-dependent properties can have implications in functional material design, and this review can provide insights into the uncharted realm of null exciton splitting.

Syntheses of Pyrimidine-Modified Seleno-DNAs as Stable Antisense Molecules

Chemically modified antisense oligonucleotides (ASO) currently in pre-clinical and clinical experiments mainly focus on the 2'-position derivatizations to enhance stability and targeting affinity. Considering the possible incompatibility of 2'-modifications with RNase H stimulation and activity, we have hypothesized that the atom specific modifications on nucleobases can retain the complex structure and RNase H activity, while enhancing ASO's binding affinity, specificity, and stability against nucleases. Herein we report a novel strategy to explore our hypothesis by synthesizing the deoxynucleoside phosphoramidite building block with the seleno-modification at 5-position of thymidine, as well as its Se-oligonucleotides. Via X-ray crystal structural study, we found that the Se-modification was located in the major groove of nucleic acid duplex and didn't cause the thermal and structural perturbations. Surprisingly, our nucleobase-modified Se-DNAs were exceptionally resistant to nuclease digestion, while compatible with RNase H activity. This affords a novel avenue for potential antisense modification in the form of Se-antisense oligonucleotides (Se-ASO).

Recognition-Encoded Synthetic Information Molecules

ConspectusNucleic acids represent a unique class of highly programmable molecules, where the sequence of monomer units incorporated into the polymer chain can be read through duplex formation with a complementary oligomer. It should be possible to encode information in synthetic oligomers as a sequence of different monomer units in the same way that the four different bases program information into DNA and RNA. In this Account, we describe our efforts to develop synthetic duplex-forming oligomers composed of sequences of two complementary recognition units that can base-pair in organic solvents through formation of a single H-bond, and we outline some general guidelines for the design of new sequence-selective recognition systems.The design strategy has focused on three interchangeable modules that control recognition, synthesis, and backbone geometry. For a single H-bond to be effective as a base-pairing interaction, very polar recognition units, such as phosphine oxide and phenol, are required. Reliable base-pairing in organic solvents requires a nonpolar backbone, so that the only polar functional groups present are the donor and acceptor sites on the two recognition units. This criterion limits the range of functional groups that can be produced in the synthesis of oligomers. In addition, the chemistry used for polymerization should be orthogonal to the recognition units. Several compatible high yielding coupling chemistries that are suitable for the synthesis of recognition-encoded polymers are explored. Finally, the conformational properties of the backbone module play an important role in determining the supramolecular assembly pathways that are accessible to mixed sequence oligomers.Almost all complementary homo-oligomers will form duplexes provided the product of the association constant for formation of a base-pair and the effective molarity for the intramolecular base-pairing interactions that zip up the duplex is significantly greater than one. For these systems, the structure of the backbone does not play a major role, and the effective molarities for duplex formation tend to fall in the range 10-100 mM for both rigid and flexible backbones. For mixed sequences, intramolecular H-bonding interactions lead to folding. The competition between folding and duplex formation depends critically on the conformational properties of the backbone, and high-fidelity sequence-selective duplex formation is only observed for backbones that are sufficiently rigid to prevent short-range folding between bases that are close in sequence. The final section of the Account highlights the prospects for functional properties, other than duplex formation, that might be encoded with sequence.

Disclosing the Role of C4-Oxo Substitution in the Photochemistry of DNA and RNA Pyrimidine Monomers: Formation of Photoproducts from the Vibrationally Excited Ground State

Oxo and amino substituted purines and pyrimidines have been suggested as protonucleobases participating in ancient pre-RNA forms. Considering electromagnetic radiation as a key environmental selection pressure on early Earth, the investigation of the photophysics of modified nucleobases is crucial to determine their viability as nucleobases' ancestors and to understand the factors that rule the photostability of natural nucleobases. In this Letter, we combine femtosecond transient absorption spectroscopy and quantum mechanical simulations to reveal the photochemistry of 4-pyrimidinone, a close relative of uracil. Irradiation of 4-pyrimidinone with ultraviolet radiation populates the S₁(ππ*) state, which decays to the vibrationally excited ground state in a few hundred femtoseconds. Analysis of the postirradiated sample in water reveals the formation of a 6-hydroxy-5H-photohydrate and 3-(N-(iminomethyl)imino)propanoic acid as the primary photoproducts. 3-(N-(Iminomethyl)imino)propanoic acid originates from the hydrolysis of an unstable ketene species generated from the C4-N3 photofragmentation of the pyrimidine core.

Efficient synthesis of novel indolizine C-nucleoside analogues via coupling of sugar alkynes, pyridines and α-bromo carbonyl compounds in one pot

The synthesis of novel indolizine C-nucleoside analogues has been achieved by the three-component coupling reaction of sugar alkynes, pyridines and α-bromo carbonyl compounds in one pot. The corresponding products are obtained in good to excellent yields. 49 examples have been given. The synthetic method is convenient, practical and efficient. It is suitable for various substrates including structurally diversified sugar alkynes with sensitive groups. The sugar alkynes include pyranosides, furanosides, and acyclic sugars. A plausible mechanism for the formation of indolizine C-nucleoside analogues has been elucidated.

Direct and selective metal-free N6-arylation of adenosine residues for simple fluorescence labeling of DNA and RNA

We have developed an unprecedented transition metal-free approach for the direct fluorescence turn-on labeling of natural oligonucleotides through selective N6-arylation of adenosine moieties. This method allows the simple and direct fluorescence labeling of natural unmodified DNA and RNA, but is dependent on the secondary structure, favoring single-stranded structures.

Recent progress in the applications of amino–yne click chemistry

This mini-review summarizes the recent research studies on the application of the amino–yne click reaction in surface immobilization, construction of drug delivery systems, preparation of hydrogel materials and synthesis of functional polymers.

Unnatural bases for recognition of noncoding nucleic acid interfaces

The notion of using synthetic heterocycles instead of the native bases to interface with DNA and RNA has been explored for nearly 60 years. Unnatural bases compatible with the DNA/RNA coding interface have the potential to expand the genetic code and co-opt the machinery of biology to access new macromolecular function; accordingly, this body of research is core to synthetic biology. While much of the literature on artificial bases focuses on code expansion, there is a significant and growing effort on docking synthetic heterocycles to noncoding nucleic acid interfaces; this approach seeks to illuminate major processes of nucleic acids, including regulation of transcription, translation, transport, and transcript lifetimes. These major avenues of research at the coding and noncoding interfaces have in common fundamental principles in molecular recognition. Herein, we provide an overview of foundational literature in biophysics of base recognition and unnatural bases in coding to provide context for the developing area of targeting noncoding nucleic acid interfaces with synthetic bases, with a focus on systems developed through iterative design and biophysical study.

Building better polymerases: Engineering the replication of expanded genetic alphabets

DNA polymerases are today used throughout scientific research, biotechnology, and medicine, in part for their ability to interact with unnatural forms of DNA created by synthetic biologists. Here especially, natural DNA polymerases often do not have the "performance specifications" needed for transformative technologies. This creates a need for science-guided rational (or semi-rational) engineering to identify variants that replicate unnatural base pairs (UBPs), unnatural backbones, tags, or other evolutionarily novel features of unnatural DNA. In this review, we provide a brief overview of the chemistry and properties of replicative DNA polymerases and their evolved variants, focusing on the Klenow fragment of Taq DNA polymerase (Klentaq). We describe comparative structural, enzymatic, and molecular dynamics studies of WT and Klentaq variants, complexed with natural or noncanonical substrates. Combining these methods provides insight into how specific amino acid substitutions distant from the active site in a Klentaq DNA polymerase variant (ZP Klentaq) contribute to its ability to replicate UBPs with improved efficiency compared with Klentaq. This approach can therefore serve to guide any future rational engineering of replicative DNA polymerases.

Can modified DNA base pairs with chalcogen bonding expand the genetic alphabet? A combined quantum chemical and molecular dynamics simulation study

A comprehensive (DFT and MD) computational study is presented with the goal to design and analyze model chalcogen-bonded modified nucleobase pairs that replace one (i.e., A_XY:T, G:C_XY, G_XY:C) or two (G_XY:C_X'Y', X/X' = S, Se and Y/Y' = F, Cl, Br) Watson-Crick (WC) hydrogen bonds of the canonical A:T or G:C pair with chalcogen bond(s). DFT calculations on 18 base pair combinations that replace one WC hydrogen bond with a chalcogen bond reveal that the bases favorably interact in the gas phase (binding strengths up to -140 kJ mol^-1) and water (up to -85 kJ mol^-1). Although the remaining hydrogen bond(s) exhibits similar characteristics to those in the canonical base pairs, the structural features of the (Y-XO) chalcogen bond(s) change significantly with the identity of X and Y. The 36 doubly-substituted (G_XY:C_X'Y') base pairs have structural deviations from canonical G:C similar to those of the singly-substituted modifications (G:C_XY or G_XY:C). Furthermore, despite the replacement of two strong hydrogen bonds with chalcogen bonds, some G_XY:C_X'Y' pairs possess comparable binding energies (up to -132 kJ mol^-1 in the gas phase and up to -92 kJ mol^-1 in water) to the most stable G:C_XY or G_XY:C pairs, as well as canonical G:C. More importantly, G:C-modified pairs containing X = Se (high polarizability) and Y = F (high electronegativity) are the most stable, with comparable or slightly larger (by up to 13 kJ mol^-1) binding energies than G:C. Further characterization of the chalcogen bonding in all modified base pairs (AIM, NBO and NCI analyses) reveals that the differences in the binding energies of modified base pairs are mainly dictated by the differences in the strengths of their chalcogen bonds. Finally, MD simulations on DNA oligonucleotides containing the most stable chalcogen-bonded base pair from each of the four classifications (A_XY:T, G:C_XY, G_XY:C and G_XY:C_X'Y') reveal that the singly-modified G:C pairs best retain the local helical structure and pairing stability to a greater extent than the modified A:T pair. Overall, our study identifies two (G:C_SeF and G_SeF:C) promising pairs that retain chalcogen bonding in DNA and should be synthesized and further explored in terms of their potential to expand the genetic alphabet.

Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet

Evolution has yielded biopolymers that are constructed from exactly four building blocks and are able to support Darwinian evolution. Synthetic biology aims to extend this alphabet, and we recently showed that 8-letter (hachimoji) DNA can support rule-based information encoding. One source of replicative error in non-natural DNA-like systems, however, is the occurrence of alternative tautomeric forms, which pair differently. Unfortunately, little is known about how structural modifications impact free-energy differences between tautomers of the non-natural nucleobases used in the hachimoji expanded genetic alphabet. Determining experimental tautomer ratios is technically difficult, and so, strategies for improving hachimoji DNA replication efficiency will benefit from accurate computational predictions of equilibrium tautomeric ratios. We now report that high-level quantum-chemical calculations in aqueous solution by the embedded cluster reference interaction site model, benchmarked against free-energy molecular simulations for solvation thermodynamics, provide useful quantitative information on the tautomer ratios of both Watson-Crick and hachimoji nucleobases. In agreement with previous computational studies, all four Watson-Crick nucleobases adopt essentially only one tautomer in water. This is not the case, however, for non-natural nucleobases and their analogues. For example, although the enols of isoguanine and a series of related purines are not populated in water, these heterocycles possess N₁-H and N₃-H keto tautomers that are similar in energy, thereby adversely impacting accurate nucleobase pairing. These robust computational strategies offer a firm basis for improving experimental measurements of tautomeric ratios, which are currently limited to studying molecules that exist only as two tautomers in solution.

Building better enzymes: Molecular basis of improved non-natural nucleobase incorporation by an evolved DNA polymerase

Obtaining semisynthetic microorganisms that exploit the information density of "hachimoji" DNA requires access to engineered DNA polymerases. A KlenTaq variant has been reported that incorporates the "hachimoji" P:Z nucleobase pair with a similar efficiency to that seen for Watson-Crick nucleobase incorporation by the wild type (WT) KlenTaq DNA polymerase. The variant polymerase differs from WT KlenTaq by only four amino acid substitutions, none of which are located within the active site. We now report molecular dynamics (MD) simulations on a series of binary complexes aimed at elucidating the contributions of the four amino acid substitutions to altered catalytic activity. These simulations suggest that WT KlenTaq is insufficiently flexible to be able to bind AEGIS DNA correctly, leading to the loss of key protein/DNA interactions needed to position the binary complex for efficient incorporation of the "hachimoji" Z nucleobase. In addition, we test literature hypotheses about the functional roles of each amino acid substitution and provide a molecular description of how individual residue changes contribute to the improved activity of the KlenTaq variant. We demonstrate that MD simulations have a clear role to play in systematically screening DNA polymerase variants capable of incorporating different types of nonnatural nucleobases thereby limiting the number that need to be characterized by experiment. It is now possible to build DNA molecules containing nonnatural nucleobase pairs in addition to A:T and G:C. Exploiting this development in synthetic biology requires engineered DNA polymerases that can replicate nonnatural nucleobase pairs. Computational studies on a DNA polymerase variant reveal how amino acid substitutions outside of the active site yield an enzyme that replicates nonnatural nucleobase pairs with high efficiency. This work will facilitate efforts to obtain bacteria possessing an expanded genetic alphabet.

Role of the backbone of nucleic acids in the stability of Hg2+-mediated canonical base pairs and thymine–thymine mispair: a DFT study

Metal-mediated base pairs have attracted attention in nucleic acid research and molecular devices. Herein, we report a systematic computational study on Hg²⁺-mediated base pairs with canonical and TT mispair dimers. The computed results revealed that the model _DTT_D (thymine–thymine with DNA backbone) mispair is more energetically favored than the canonical base pairs. The _DTTTT_D mispair dimer is more energetically stable by ∼36.0 kcal mol⁻¹ than the corresponding canonical _DATGC_D base pairs. The Hg⋯Hg metallophilic interaction was observed with the _DTTTT_D mispair and not the canonical base pairs. The _DATGC_D (adenine: thymine, guanine: cytosine) base pairs were significantly perturbed upon interaction with the mercury ion; however, the TTTT mispairs were aligned upon interaction with the Hg²⁺ ion. The _DTTTT_D mispair adopts a B-type conformation with proper alignment of its nucleobases along the axis. The MESP calculations showed a larger V_min value for the interacting nitrogen centers of the thymine nucleobase, supporting its stronger binding with the Hg²⁺ ion compared to the other nucleobases. The role of the backbone is crucial in nucleic acids to determine many useful properties, and PNAs have been exploited extensively in the literature. Thus, this study was further extended to metal-mediated PNA-containing dimer mispairs such as _DTTTT_P (thymine–thymine dimer model with hybrid DNA and PNA backbone) and _PTTTT_P (thymine–thymine dimer model with PNA backbone). The calculated results showed that the _PTTTT_P PNA mispair is thermodynamically more stable than the canonical dimers. The enthalpy calculated for _DTTTT_D and _PTTTT_P at the B3LYP-D3/6-31G* level of theory showed that _PTTTT_P is ∼3.0 kcal mol⁻¹ more stable than _DTTTT_D. The metallophilic interaction of Hg²⁺ ions in the _PTTTT_P mispair was not observed; however, the metal ions interact with the nitrogen of the thymine bases, presumably enhancing the stability of this mispair by strong electrostatic interactions. These interactions arise due to the P-type conformations of PNAs, which lack metallophilic interactions between the metal ions and can adopt a wider and more unwounded helix. The interaction of the mispair dimers with the explicit water molecules also showed a similar stability trend to that observed with the implicit solvation model. The metallophilic interaction (Hg⋯Hg) was found to be conserved in _DTTTT_D. The AIM analysis performed for these dimers revealed that the interactions are primarily electrostatic in nature. The UV-vis absorption spectra of the mispair systems calculated at the B3LYP-D3/6-31G* level of theory using the TD-DFT method in the aqueous phase suggested that the absorption maximum is located at a longer wavelength in the case of _PTTTT_P compared to the corresponding _DTTTT_D and can be a signature to identify the formation of metal-mediated nucleic acid systems.

Hg²⁺-mediated PNA–PNA mispair duplex (_PTTTT_P) is more energetically favoured compared to DNA–DNA mispair duplex (_DTTTT_D).

Distinct Crystalline Aromatic Structural Motifs: Identification, Classification, and Implications

Spatial noncovalent helical organization of nucleobases in DNA and radial organization of chromophores in natural light-harvesting systems are fascinating yet enigmatic. Understanding the numerous weak interactions that drive the formation of elegant supramolecular architectures in native natural systems and developing bioinspired design strategies have seen a surge of interest in recent decades. Self-assembly of functional chromophores in the crystalline phase is a definitive strategy to identify novel molecule-molecule interactions, in particular, atom-atom interactions, and to understand the synergistic nature of noncovalent interactions that stabilizes the supramolecular organization. This Account narrates our recent efforts in developing desirable supramolecular motifs employing weak interaction-based strategies and our observation of deviations from the common motifs chartered in aromatic systems. Modulation of long-range aromatic interactions through chemical modifications (acylation, benzoylation, haloacylation, and alkylation of chromophores) to attain a preferred stacking (herringbone, lamellar, or columnar) is presented. Particular attention has been given to attaining lamellar or columnar packing possessing potential interchromophoric electronic coupling mediated high charge mobility. Supramolecular arrangements of noncovalently or covalently associated donor-acceptor systems that open up additional possibilities of packing modes (segregated, mixed etc.) are explored. Our persistent efforts yielded distinct twisted-segregated and alternate distichous stacks for the nonparallel covalently linked donor-acceptor systems that favor a long-lived photoinduced charge-separated state. We further move on to discuss the unconventional packing motifs that were identified recently. The highly sought-after Greek cross (+) stacking of chromophores in crystalline phase and an elegant crystalline radial arrangement of chromophores are examined. The Greek cross (+) stacked architecture exhibits monomer-like emission characteristics owing to the absence of exciton coupling across the orthogonally stacked chromophores. Crystalline helical chromophore assembly is yet another emerging motif with far-reaching applications in domains ranging from asymmetric catalysis to chiral smart materials and has been accounted here by citing certain phenomenal examples from literature. Thus, this Account demonstrates that identifying and classifying new structural motifs based on topological aspects, such as interchromophoric orientation (cross) and extended chromophore arrangement in the crystal lattice (radial, helical, etc.), are crucial since such fundamental characteristics dictate the properties emerging out of the corresponding motifs. Encouraged from ours and others' works, we propose the addition of new aromatic supramolecular structural motifs, namely, cross-stacked, helical, and radial arrangements, in order to expand the classification. We believe that identifying new emergent property-based supramolecular motifs and investigating the methods to achieve the desired motif will eventually have implications in fundamental crystal engineering, supramolecular chemistry, and biomimetic design of functional materials.

Artificial Sandwich Base for Monitoring Single-Nucleobase Changes and Charge-Transfer Rates in DNA

Developing a convenient method to discriminate among different types of DNA nucleotides within a target sequence of the human genome is extremely challenging. We herein report an artificial ferrocene-base (Fe-base) that was synthesized and incorporated into different loci of a DNA strand. The Fe-base replacement on a nucleobase can interact with DNA bases and efficiently discriminate among A, T, G, and C DNA bases of the complementary locus on the basis of interacting electrochemical properties. Furthermore, cyclic-voltammetry (CV) studies demonstrated the electrochemical stability of DNA strands incorporated with Fe-bases and the reversibility of the incorporation. Square-wave voltammetry (SWV) was performed to measure current changes between Fe-bases and bases of interest in the DNA duplex. The changes in the charge-transfer rates appeared to be correlated with the position of the Fe-base in the DNA strand, allowing rapid and efficient sensing of single-nucleobase changes in DNA and showing promise for the design of Fe-oligomer chip technology as a tool for DNA sequencing.

Why do A·T and G·C self-sort? Hückel aromaticity as a driving force for electronic complementarity in base pairing

Computations reveal that the potential for aromaticity gain and loss in nucleobases play key roles in modulating base pairing strengths.

H-Bonded Duplexes based on a Phenylacetylene Backbone

Complementary phenylacetylene oligomers equipped with phenol and phosphine oxide recognition sites form stable multiply H-bonded duplexes in toluene solution. Oligomers were prepared by Sonogashira coupling of diiodobenzene and bis-acetylene building blocks in the presence of monoacetylene chain terminators. The product mixtures were separated by reverse phase preparative high-pressure liquid chromatography to give a series of pure oligomers up to seven recognition units in length. Duplex formation between length complementary homo-oligomers was demonstrated by 31P NMR denaturation experiments using dimethyl sulfoxide as a competing H-bond acceptor. The denaturation experiments were used to determine the association constants for duplex formation, which increase by nearly 2 orders of magnitude for every phenol-phosphine oxide base-pair added. These experiments show that the phenylacetylene backbone supports formation of extended duplexes with multiple cooperative intermolecular H-bonding interactions, and together with previous studies on the mixed sequence phenylacetylene 2-mer, suggest that this supramolecular architecture is a promising candidate for the development of synthetic information molecules that parallel the properties of nucleic acids.

Studies of Impending Oligonucleotide Therapeutics in Simulated Biofluids

Synthetic oligonucleotides, their complexes and conjugates with other biomolecules represent valuable research tools and therapeutic agents. In spite of growing applications in basic research and clinical science, only few studies have addressed the issue of such compounds' stability in biological media. Herein, we studied the stability of two therapeutically relevant oligonucleotide probes in simulated biofluids; the 21 nucleotide-long DNA/locked nucleic acid oligonucleotide ON targeted toward cancer-associated BRAF V600E mutation, and a longer DNA analog (TTC) originating from BRAF gene. We found that stability of peptide-oligonucleotide conjugates (POCs) in human serum (HS) was superior compared with the naked or complexed 21mer oligonucleotide, whereas stability of POCs in simulated gastric juice (GJ) was dependent on the peptide sequence. Addition of pepstatin A in general increased the stability of oligonucleotides after 24 h digestion in HS and simulated GJ. Similarly, complexation with optimal amounts of histone proteins was found to rescue oligonucleotide stability after 24 h digestion in hydrochloric acid.

Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers

Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.

Fluorescent excimers and exciplexes of the purine base derivative 8-phenylethynyl-guanine in DNA hairpins

The ground- and excited-state electronic interactions between the nucleobase analog 8-(4'-phenylethynyl)deoxyguanosine, EG, with natural nucleobases and 7-deazaguanine, as well as between adjacent EG base analogs, have been characterized using a combination of steady-state spectroscopy and time-resolved fluorescence, absorption, and stimulated Raman spectroscopies. The properties of the nucleoside EG-H2 are only weakly perturbed upon incorporation into synthetic DNA hairpins in which thymine, cytosine or adenine are the bases flanking EG. Incorporation of the nucleoside to be adjacent to guanine or deazaguanine results in the formation of short-lived (40-80 ps) exciplexes, the charge transfer character of which increases as the oxidation potential of the donor decreases. Hairpins possessing two or three adjacent EG base analogs display exciton-coupled circular dichroism in the ground state and form long-lived fluorescent excited states upon electronic excitation. Incorporation of EG into the helical scaffold of the DNA hairpins places it adjacent to its neighboring nucleobases or a second EG, thus providing the close proximity required for the formation of exciplex or excimer intermediates upon geometric relaxation of the short-lived EG excited state. The three time-resolved spectroscopic methods employed permit both the characterization of the several intermediates and the kinetics of their formation and decay.

2-Methoxypyridine as a Thymidine Mimic in Watson-Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability, and NMR Structural Studies

The development of nucleic acid base-pair analogues that use new modes of molecular recognition is important both for fundamental research and practical applications. The goal of this study was to evaluate 2-methoxypyridine as a cationic thymidine mimic in the A-T base pair. The hypothesis was that including protonation in the Watson-Crick base pairing scheme would enhance the thermal stability of the DNA double helix without compromising the sequence selectivity. DNA and peptide nucleic acid (PNA) sequences containing the new 2-methoxypyridine nucleobase (P) were synthesized and studied by using UV thermal melting and NMR spectroscopy. Introduction of P nucleobase caused a loss of thermal stability of ≈10 °C in DNA-DNA duplexes and ≈20 °C in PNA-DNA duplexes over a range of mildly acidic to neutral pH. Despite the decrease in thermal stability, the NMR structural studies showed that P-A formed the expected protonated base pair at pH 4.3. Our study demonstrates the feasibility of cationic unnatural base pairs; however, future optimization of such analogues will be required.

Fluorescent nucleobases as tools for studying DNA and RNA

Understanding the diversity of dynamic structures and functions of DNA and RNA in biology requires tools that can selectively and intimately probe these biomolecules. Synthetic fluorescent nucleobases that can be incorporated into nucleic acids alongside their natural counterparts have emerged as a powerful class of molecular reporters of location and environment. They are enabling new basic insights into DNA and RNA, and are facilitating a broad range of new technologies with chemical, biological and biomedical applications. In this Review, we will present a brief history of the development of fluorescent nucleobases and explore their utility as tools for addressing questions in biophysics, biochemistry and biology of nucleic acids. We provide chemical insights into the two main classes of these compounds: canonical and non-canonical nucleobases. A point-by-point discussion of the advantages and disadvantages of both types of fluorescent nucleobases is made, along with a perspective into the future challenges and outlook for this burgeoning field.

Sequence-Selective Formation of Synthetic H-Bonded Duplexes

Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (102 to 105 M-1). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor-acceptor sequences are avoided.

Toward an Expanded Genome: Structural and Computational Characterization of an Artificially Expanded Genetic Information System

Although the fundamental properties of DNA as first proposed by Watson and Crick in 1953 provided a basic understanding of how duplex DNA was organized and might be replicated, it was not until the first crystal structures of DNA (Z-DNA in 1979, B-DNA in 1980, and A-DNA in 1982) that the true complexity of the molecule began to be appreciated. Many crystal structures of oligonucleotides have since shed light on the helical forms that "Watson-Crick" DNA can adopt, their associated groove widths, and the properties of the nucleobase pairs and their interactions in all three helical forms. Additional understanding of the properties of Watson-Crick DNA has been provided by computational studies employing a variety of theoretical methods. Together with these studies devoted to understanding Watson-Crick DNA, recent efforts to expand the genetic alphabet have founded a new field in synthetic biology. One of these efforts, the artificially expanded genetic information system (AEGIS) developed by Steven Benner and co-workers, takes advantage of orthogonal hydrogen bonding to produce DNA comprised of six nucleobase pairs, of which the most extensively studied is referred to as P:Z with P being 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one) and Z being 6-amino-5-nitro-2(1H)-pyridone. P:Z forms three edge-on hydrogen bonds that differ from standard Watson-Crick pairs in the arrangement of acceptors and donor groups; P presents acceptor, acceptor, donor, and Z presents donor, donor, acceptor. Z is unique among the AEGIS nucleobases in having a nitro group present in the major groove. PZ-containing DNA has been exploited in a number of clinical applications and is being used to develop receptors and catalysts. Ultimately, the grand challenge will be to create a semisynthetic organism with an expanded genome. Furthermore, just as our understanding of the properties of natural DNA have benefited from structural and computational characterization, so too will our understanding of artificial DNA. This Account focuses on the structural and biophysical properties of AEGIS DNA containing P:Z pairs. We begin with the fundamental properties of P:Z nucleobase pairs, including their electrostatic potential and hydrogen-bonding energies, as elucidated by quantum mechanical calculations. We then examine the impact of including multiple consecutive P:Z pairs into duplex DNA providing an opportunity to investigate stacking interactions between P:Z pairs. The self-complementary 5'-CTTATPPTAZZATAAG was crystallized in B-form using the host-guest system along with analogous natural sequences including Gs or As. Use of the host-guest system to characterize B-DNA obviates a number of limitations on the structural characterization of sequences of interest; these include the ability to crystallize the desired sequences and to distinguish structural effects imparted by the lattice constraints from those inherent in the sequence itself. On the other hand, 3/6ZP, 5'-CTTATPPPZZZATAAG, was crystallized in A-form in a DNA-only lattice allowing a comparative analysis of P:Z pairs in two of the biologically relevant helical forms: A- and B-DNA. Computational studies on the 3/6ZP sequence starting in A-form provide additional evidence for a more energetically favorable stacking interaction, which we term the "slide" conformer, observed in the A-form crystal structure; this unusual stacking interaction plays a major role in altering the conformational dynamics observed for the PZ-containing duplex as compared to a GC-containing "control" duplex in long time scale molecular dynamics simulations. This combined use of structural and computational strategies paves the way for obtaining a detailed description of artificial DNA, both in how it differs from Watson-Crick DNA and in the rational discovery of proteins, such as endonucleases, transcription factors, and polymerases, which can specifically manipulate DNA containing AEGIS nucleobase pairs.

Photochemical Reactivity of dTPT3: A Crucial Nucleobase Derivative in the Development of Semisynthetic Organisms

In 2017, the Romesberg group successfully developed the dTPT3·dNaM unnatural base pair to create a semisynthetic organism with enhanced genetic fidelity and the ability to store additional genetic information indefinitely. It is also desirable that the newly developed genetic material remains stable upon exposure to radiation. However, the photochemical properties of dTPT3 are presently unknown. In this contribution, excitation of dTPT3 with near-visible radiation is shown to efficiently populate a reactive triplet state in high yield and on a sub-1 ps time scale; a state that is able to survive for up to a few microseconds in aqueous solution. The triplet state can also generate singlet oxygen in ca. 30% yield, suggesting that dTPT3 can act as a pervasive photosensitizer to accelerate oxidatively generated damage within DNA and to other biological molecules within cells.

Synthesis and Excellent Duplex Stability of Oligonucleotides Containing 2'-Amino-LNA Functionalized with Galactose Units

A convenient method for the preparation of oligonucleotides containing internally-attached galactose and triantennary galactose units has been developed based on click chemistry between 2′-N-alkyne 2′-amino-LNA nucleosides and azido-functionalized galactosyl building blocks. The synthesized oligonucleotides show excellent binding affinity and selectivity towards complementary DNA/RNA strands with an increase in the melting temperature of up to +23.5 °C for triply-modified variants.

Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 μs molecular dynamics simulations

Z

Little is known about the influence of multiple consecutive 'non-standard' ( , 6-amino-5-nitro-2(1H)-pyridone, and , 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one) nucleobase pairs on the structural parameters of duplex DNA. nucleobase pairs follow standard rules for Watson-Crick base pairing but have rearranged hydrogen bonding donor and acceptor groups. Using the X-ray crystal structure as a starting point, we have modeled the motions of a DNA duplex built from a self-complementary oligonucleotide (5΄-CTTATPPPZZZATAAG-3΄) in water over a period of 50 μs and calculated DNA local parameters, step parameters, helix parameters, and major/minor groove widths to examine how the presence of multiple, consecutive nucleobase pairs might impact helical structure. In these simulations, the -containing DNA duplex exhibits a significantly wider major groove and greater average values of stagger, slide, rise, twist and h-rise than observed for a 'control' oligonucleotide in which nucleobase pairs are replaced by . The molecular origins of these structural changes are likely associated with at least two differences between and . First, the electrostatic properties of differ from in terms of density distribution and dipole moment. Second, differences are seen in the base stacking of pairs in dinucleotide steps, arising from energetically favorable stacking of the nitro group in with π-electrons of the adjacent base.

A Single Deoxynucleoside Kinase Variant from Drosophila melanogaster Synthesizes Monophosphates of Nucleosides That Are Components of an Expanded Genetic System

Deoxynucleoside kinase from D. melanogaster (DmdNK) has broad specificity; although it catalyzes the phosphorylation of natural pyrimidine more efficiently than natural purine nucleosides, it accepts all four 2'-deoxynucleosides and many analogues, using ATP as a phosphate donor to give the corresponding deoxynucleoside monophosphates. Here, we show that replacing a single amino acid (glutamine 81 by glutamate) in DmdNK creates a variant that also catalyzes the phosphorylation of nucleosides that form part of an artificially expanded genetic information system (AEGIS). By shuffling hydrogen bonding groups on the nucleobases, AEGIS adds potentially as many as four additional nucleobase pairs to the genetic "alphabet". Specifically, we show that DmdNK Q81E creates the monophosphates from the AEGIS nucleosides dP, dZ, dX, and dK (respectively 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one, dP; 6-amino-3-(1'-β-d-2'-deoxyribofuranosyl)-5-nitro-1H-pyridin-2-one, dZ; 8-(1'β-d-2'-deoxy-ribofuranosyl)imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione, dX; and 2,4-diamino-5-(1'-β-d-2'-deoxyribofuranosyl)-pyrimidine, dK). Using a coupled enzyme assay, in vitro kinetic parameters were obtained for three of these nucleosides (dP, dX, and dK; the UV absorbance of dZ made it impossible to get its precise kinetic parameters). Thus, DmdNK Q81E appears to be a suitable enzyme to catalyze the first step in the biosynthesis of AEGIS 2'-deoxynucleoside triphosphates in vitro and, perhaps, in vivo, in a cell able to manage plasmids containing AEGIS DNA.

Homochiral oligomers with highly flexible backbones form stable H-bonded duplexes

Two homochiral building blocks featuring a protected thiol, an alkene and a H-bond recognition unit (phenol or phosphine oxide) have been prepared. Iterative photochemical thiol-ene coupling reactions were used to synthesize oligomers containing 1-4 phosphine oxide and 1-4 phenol recognition sites. Length-complementary H-bond donor and H-bond acceptor oligomers were found to form stable duplexes in toluene. NMR titrations and thermal denaturation experiments show that the association constant and the enthalpy of duplex formation increase significantly for every additional H-bonding unit added to the chain. There is an order of magnitude increase in stability for each additional H-bonding interaction at room temperature indicating that all of the H-bonding sites are fully bound to their complements in the duplexes. The backbone of the thiol-ene duplexes is a highly flexible alkane chain, but this conformational flexibility does not have a negative impact on binding affinity. The average effective molarity for the intramolecular H-bonding interactions that zip up the duplexes is 18 mM. This value is somewhat higher than the EM of 14 mM found for a related family of duplexes, which have the same recognition units but a more rigid backbone prepared using reductive amination chemistry. The flexible thiol-ene AAAA·DDDD duplex is an order of magnitude more stable than the rigid reductive amination AAAA·DDDD duplex. The backbone of the thiol-ene system retains much of its conformational flexibility in the duplex, and these results show that highly flexible molecules can make very stable complexes, provided there is no significant restriction of degrees of freedom on complexation.

Copper carbenes alkylate guanine chemoselectively through a substrate directed reaction

Cu(i) carbenes derived from α-diazocarbonyl compounds lead to selective alkylation of the O6 position in guanine (O6-G) in mono- and oligonucleotides. Only purine-type lactam oxygens are targeted - other types of amides or lactams are poorly reactive under conditions that give smooth alkylation of guanine. Mechanistic studies point to N7G as a directing group that controls selectivity. Given the importance of O6-G adducts in biology and biotechnology we expect that Cu(i)-catalyzed O6-G alkylation will be a broadly used synthetic tool. While the propensity for transition metals to increase redox damage is well-appreciated, our results suggest that transition metals might also increase the vulnerability of nucleic acids to alkylation damage.