Experimental Measurement of Aromatic Stacking Affinities in the Context of Duplex DNA

N-Si Heterolysis by Chiral (BOX)Cu(OTf)2 Catalysts for the Synthesis of Indole and Carbazole Glycosides

Chiral Cu(II) bisoxazolines have been shown to catalyze the coupling of acetyl-protected carbohydrates with N-silylated indoles to give the corresponding N-glycosides. Preliminary mechanistic experiments indicated that catalysis occurs through formation of a Cu-indolide complex with concomitant formation of TMS-OTf which together activate the sugar and deliver the indole nucleophile.

Effect of hydrophilicity-imparting substituents on exciton delocalization in squaraine dye aggregates covalently templated to DNA Holliday junctions

Molecular aggregates exhibit emergent properties, including the collective sharing of electronic excitation energy known as exciton delocalization, that can be leveraged in applications such as quantum computing, optical information processing, and light harvesting. In a previous study, we found unexpectedly large excitonic interactions (quantified by the excitonic hopping parameter Jm,n) in DNA-templated aggregates of squaraine (SQ) dyes with hydrophilic-imparting sulfo and butylsulfo substituents. Here, we characterize DNA Holliday junction (DNA-HJ) templated aggregates of an expanded set of SQs and evaluate their optical properties in the context of structural heterogeneity. Specifically, we characterized the orientation of and Jm,n between dyes in dimer aggregates of non-chlorinated and chlorinated SQs. Three new chlorinated SQs that feature a varying number of butylsulfo substituents were synthesized and attached to a DNA-HJ via a covalent linker to form adjacent and transverse dimers. Various characteristics of the dye, including its hydrophilicity (in terms of log Po/w) and surface area, and of the substituents, including their local bulkiness and electron withdrawing capacity, were quantified computationally. The orientation of and Jm,n between the dyes were estimated using a model based on Kühn-Renger-May theory to fit the absorption and circular dichroism spectra. The results suggested that adjacent dimer aggregates of all the non-chlorinated and of the most hydrophilic chlorinated SQ dyes exhibit heterogeneity; that is, they form a mixture of dimers subpopulations. A key finding of this work is that dyes with a higher hydrophilicity (lower log Po/w) formed dimers with smaller Jm,n and large center-to-center dye distance (Rm,n). Also, the results revealed that the position of the dye in the DNA-HJ template, that is, adjacent or transverse, impacted Jm,n. Lastly, we found that Jm,n between symmetrically substituted dyes was reduced by increasing the local bulkiness of the substituent. This work provides insights into how to maintain strong excitonic coupling and identifies challenges associated with heterogeneity, which will help to improve control of these dye aggregates and move forward their potential application as quantum information systems.

Versatile DNA Balances via Adjacent Base Stacking for Homogeneous Assay of Energy Parameters, Small Molecules, And Ribonuclease

Homogeneous assays often obviate any separation and washing steps, thus minimizing the risks of contamination and false positive. DNA toehold exchange is a homogeneous, reversible process whose thermodynamic properties can be finely tuned for various assay applications. However, the developed probes often rely on direct interactions of analytes with DNA strands involved in toehold exchange, limiting the versatility of probe design. Here, the coaxial adjacent stacking between one auxiliary strand and another invading strand offers a favorable ΔG to shift one DNA balance, while the auxiliary strand is independent of the DNA balance itself. Therefore, such a DNA balance allowed fine tuning of the equilibrium via adjustment of the auxiliary strand alone. The energy contribution of base stacking can be quantified in a homogeneous solution based on the difference in the equilibrium constant. Besides, the proof of concept for DNA balance allows effective assay of a small molecule or ribonuclease in a homogeneous solution. This novel DNA balance via adjacent base stacking provides an interesting alternative to homogeneously assay various analytes.

Synthesis and Behavior of DNA Oligomers Containing the Ambiguous Z-Nucleobase 5-Aminoimidazole-4-carboxamide

5-Amino-1-β-D-ribofuranosylimidazole-4-carboxamide 5'-monophosphate (ZMP) is a central intermediate in de novo purine nucleotide biosynthesis. Its nucleobase moiety, 5-aminoimidazole-4-carboxamide (Z-base), is considered an ambiguous base that can pair with any canonical base owing to the rotatable nature of its 5-carboxamide group. This idea of ambiguous base pairing due to free rotation of the carboxamide has been applied to designing mutagenic antiviral nucleosides, such as ribavirin and T-705. However, the ambiguous base-pairing ability of Z-base has not been elucidated, because the synthesis of Z-base-containing oligomers is problematic. Herein, we propose a practical method for the synthesis of Z-base-containing DNA oligomers based on the ring-opening reaction of an N¹-dinitrophenylhypoxanthine (Hxa^DNP) base. Thermal denaturation studies of the resulting oligomers revealed that the Z-base behaves physiologically as an A-like nucleobase, preferentially forming pairs with T. We tested the behavior of Z-base-containing DNA oligomers in enzyme-catalyzed reactions: in single nucleotide insertion, Klenow fragment DNA polymerase recognized Z-base as an A-like analog and incorporated dTTP as a complementary nucleotide to Z-base in the DNA template; in PCR amplification, Taq DNA polymerase similarly incorporated dTTP as a complementary nucleotide to Z-base. Our findings will contribute to the development of new mutagenic antiviral nucleoside analogs.

Toward Force Fields with Improved Base Stacking Descriptions

Recent DNA force fields indicate good performance in describing flexibility and structural stability of double-stranded B-DNA. However, it is not clear how accurately base stacking interactions are represented that are critical for simulating structure formation processes and conformational changes. Based on the equilibrium nucleoside association and base pair nicking, we find that the recent Tumuc1 force field improves the description of base stacking compared to previous state-of-the-art force fields. Nevertheless, base pair stacking is still overstabilized compared to experiment. We propose a rapid method to reweight calculated free energies of stacking upon force field modifications in order to generate improved parameters. A decrease of the Lennard-Jones attraction between nucleo-bases alone appears insufficient; however, adjustments in the partial charge distribution on base atoms could help to further improve the force field description of base stacking.

Hoogsteen triplexes stabilized through ethynyl-linked pyrene-indole synthesized by high-temperature Sonogashira coupling

The low binding affinity of unmodified triplex-forming oligonucleotides (TFO) is the main drawback to their promising utilization in gene therapy. In the present study, we have synthesized DNA intercalator 5-(pyren-1-ylethynyl)indole Y, known as twisted intercalating nucleic acid (TINA), by a Cu-mediated Sonogashira palladium-catalyzed coupling reaction of 1-ethynylpyrene with 5-iodoindole at a high temperature under anaerobic conditions. Coupling with indole C-5 was far more preferable in obtaining stable TINA-indole than enamine site C-3, as neither hydration of the triple bond to ketones nor competitive Glaser-type homocoupling of acetylenes was observed. The insertion of the new TINA monomer Y as a bulge in the middle or at the 5'-end of the oligodeoxynucleotide sequence via a flexible butane-1,2-diol linker showed extraordinary binding potential, resulting in excellent thermal stabilization of Hoogsteen-type triplex- and duplex-deoxyribonucleic acid (DNA) structures which was detected by thermal denaturation studies and supported by circular dichroism (CD). Molecular dynamics AMBER* revealed the lowest energy conformation in which a pyrenyl residue of the TINA monomer Y stacks in the dsDNA part, while an indolyl unit intercalates between the nucleobases of the TFO pattern. Overall the torsionally rigid conjugated TINA system with a decent twisting of 15.1° around acetylene is confirmed here as a requirement for the best fit inside the intercalation site of the triplex, resulting in high TFO-dsDNA affinity.

Adenine oligomer directed synthesis of chiral gold nanoparticles

Precise control of morphology and optical response of 3-dimensional chiral nanoparticles remain as a significant challenge. This work demonstrates chiral gold nanoparticle synthesis using single-stranded oligonucleotide as a chiral shape modifier. The homo-oligonucleotide composed of Adenine nucleobase specifically show a distinct chirality development with a dissymmetric factor up to g ~ 0.04 at visible wavelength, whereas other nucleobases show no development of chirality. The synthesized nanoparticle shows a counter-clockwise rotation of generated chiral arms with approximately 200 nm edge length. The molecular dynamics and density functional theory simulations reveal that Adenine shows the highest enantioselective interaction with Au(321)R/S facet in terms of binding orientation and affinity. This is attributed to the formation of sequence-specific intra-strand hydrogen bonding between nucleobases. We also found that different sequence programming of Adenine-and Cytosine-based oligomers result in chiral gold nanoparticles' morphological and optical change. These results extend our understanding of the biomolecule-directed synthesis of chiral gold nanoparticles to sequence programmable deoxyribonucleic acid and provides a foundation for programmable synthesis of chiral gold nanoparticles.

Label-free detection of ssDNA base insertion and deletion mutations by surface-enhanced Raman spectroscopy

Surface-enhanced Raman spectroscopy (SERS), as a label-free, highly sensitive analytical method, has become an important tool for providing substance fingerprints. In this study, silver nanoparticles containing thiosulfate ions and calcium ions (Ag@SCNPs) have been used as an enhanced substrate to eliminate the interference of impurities on DNA signals. Intrinsic structural information on single-strand DNA (ssDNA) was directly obtained through SERS. The improved enhancement system was used to explore the base-stacking rules of ssDNA in a solution environment. For the first time, single-base insertion mutations and deletion mutations, as well as their exact mutation sites, were identified, and Raman spectra with high stability, repeatability, and high signal-to-noise ratio were obtained. The method is simple, fast, and accurate, and the detection process is nondestructive. It has potential to be applied in the fields of medical diagnosis and genetics research.

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.

Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties

Synthesis of the novel thiophenyl carbazole phosphoramidite DNA building block 5 was accomplished in four steps using a Suzuki-Miyaura cross-coupling reaction from the core carbazole and it was seamlessly accommodated into a 9-mer DNA-based oligonucleotide by incorporation at the flanking 5'-end in combination with a central insertion of an LNA-T nucleotide. The carbazole-containing oligonucleotide was combined in different duplex hybrids, which were characterized by thermal denaturation, circular dichroism and fluorescence studies. The carbazole monomer modulates the duplex stability in various ways. Thus, monomer Z increased the thermal stability of the 9-mer towards the complementary 9-mer/15-mer DNA duplex by 4.2 °C. Furthermore, indications of its intercalation into the duplex were obtained by modeling studies and robust decreases in fluorescence emission intensities upon duplex formation. In contrast, no clear intercalating tendency was corroborated for monomer Z within the DNA/RNA hybrid duplex as indicated by moderate quenching of the fluorescence and similar duplex thermal stabilities relative to the corresponding control duplex. The recognition efficiencies of the carbazole modified oligonucleotide toward single nucleotide mismatches were studied with two 15-mer model targets (DNA and RNA). For both systems, mismatches positioned at the juxtaposition of the carbazole monomer showed pronounced deceases in thermal denaturation temperature. Steady-state fluorescence emission studies of all mismatched duplexes with incorporation of Z monomer typically displayed efficient fluorescence quenching.

Trinucleotide Base Pair Stacking Free Energy for Understanding TF-DNA Recognition and the Functions of SNPs

Single nucleotide polymorphisms (SNPs) affect base pair stacking, which is the primary factor for maintaining the stability of DNA. However, the mechanism of how SNPs lead to phenotype variations is still unclear. In this work, we connected SNPs and base pair stacking by a 3-mer base pair stacking free energy matrix. The SNPs with large base pair stacking free energy differences led to phenotype variations. A molecular dynamics (MD) simulation was then applied. Our results showed that base pair stacking played an important role in the transcription factor (TF)-DNA interaction. Changes in DNA structure mainly originate from TF-DNA interactions, and with the increased base pair stacking free energy, the structure of DNA approaches its free type, although its binding affinity was increased by the SNP. In addition, quantitative models using base pair stacking features revealed that base pair stacking can be used to predict TF binding specificity. As such, our work combined knowledge from bioinformatics and structural biology and provided a new understanding of the relationship between SNPs and phenotype variations. The 3-mer base pair stacking free energy matrix is useful in high-throughput screening of SNPs and predicting TF-DNA binding affinity.

Structural Manipulation of the Conjugated Phenyl Moiety in 3-Phenylbenzofulvene Monomers: Effects on Spontaneous Polymerization

Spontaneous polymerization is an intriguing phenomenon in which pure monomers begin their polymerization without initiators or catalysts. Previously, 3-phenylbenzofulvene monomers were found to polymerize spontaneously after solvent removal. Here, eight new 3-substituted benzofulvene monomers 1a⁻h were synthesized in order to investigate the effects of differently substituted aromatic rings in position 3 of the benzofulvene scaffold on spontaneous polymerization. The newly synthesized monomers maintained the tendency toward spontaneous polymerization. However, monomer 1a, bearing an ortho-methoxy substituted phenyl, polymerized hardly, thus producing low polymerization yields, inhomogeneous structure, and low molecular weight of the obtained polymeric material. This result suggested the importance of the presence of hydrogen atoms in the 2'-position to achieve productive interactions among the monomers in the recognition step preluding the spontaneous polymerization and among the monomeric units in the polybenzofulvene backbones. Moreover, this study paves the way to modify the pendant rings in position 3 of the indene scaffold to synthesize new polybenzofulvene derivatives variously decorated.

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.

In-Gene Quantification of O(6)-Methylguanine with Elongated Nucleoside Analogues on Gold Nanoprobes

Exposure of DNA to chemicals can result in the formation of DNA adducts, a molecular initiating event in genotoxin-induced carcinogenesis. O(6)-Methylguanine (O(6)-MeG) is a highly mutagenic DNA adduct that forms in human genomic DNA upon reaction with methylating agents of dietary, environmental, or endogenous origin. In this work, we report the design and synthesis of novel non-natural nucleoside analogues 1'-β-[1-naphtho[2,3-d]imidazol-2(3H)-one)]-2'-deoxy-d-ribofuranose and 1'-β-[1-naphtho[2,3-d]imidazole]-2'-deoxy-d-ribofuranose and their use for quantifying O(6)-MeG within mutational hotspots of the human KRAS gene. The novel nucleoside analogues were incorporated into oligonucleotides conjugated to gold nanoparticles to comprise a DNA hybridization probe system for detecting O(6)-MeG in a sequence-specific manner on the basis of colorimetric readout of the nanoparticles. The concept described herein is unique in utilizing new nucleoside analogues with elongated hydrophobic surfaces to successfully measure in-gene abundance of O(6)-MeG in mixtures with competing unmodified DNA.

Free energy analysis and mechanism of base pair stacking in nicked DNA

The equilibrium of stacked and unstacked base pairs is of central importance for all nucleic acid structure formation processes. The stacking equilibrium is influenced by intramolecular interactions between nucleosides but also by interactions with the solvent. Realistic simulations on nucleic acid structure formation and flexibility require an accurate description of the stacking geometry and stability and its sequence dependence. Free energy simulations have been conducted on a series of double stranded DNA molecules with a central strand break (nick) in one strand. The change in free energy upon unstacking was calculated for all ten possible base pair steps using umbrella sampling along a center-of-mass separation coordinate and including a comparison of different water models. Comparison to experimental studies indicates qualitative agreement of the stability order but a general overestimation of base pair stacking interactions in the simulations. A significant dependence of calculated nucleobase stacking free energies on the employed water model was observed with the tendency of stacking free energies being more accurately reproduced by more complex water models. The simulation studies also suggest a mechanism of stacking/unstacking that involves significant motions perpendicular to the reaction coordinate and indicate that the equilibrium nicked base pair step may slightly differ from regular B-DNA geometry in a sequence-dependent manner.

Stabilization of duplex DNA and RNA by dangling ends studied by free energy simulations

Single unpaired nucleotides at the end of double-stranded nucleic acids, termed dangling ends, can contribute to duplex stability. Umbrella sampling free energy simulations of dangling cytosine and guanine nucleotides at the end of duplex and single stranded RNA and DNA molecules have been used to investigate the molecular origin of dangling end effects. In unrestraint simulations, the dangling end nucleotides stayed close to placements observed in experimental structures. Calculated free energy contributions associated with the presence of dangling nucleotides were in reasonable agreement with experiment predicting the general trend of a more stabilizing effect of purine vs. pyrimidine dangling ends. In addition, the calculations indicate a more significant stabilizing effect of dangling ends at the 5'-end vs. 3'-end in case of DNA and the opposite trend in case of RNA. Both electrostatic and van der Waals interactions contribute to the duplex stabilizing effect of dangling end nucleotides. The free energy simulation scheme could also be used to design dangling end nucleotides that result in enhanced duplex stabilization.

Elastic Energy Partitioning in DNA Deformation and Binding to Proteins

We study the elasticity of DNA based on local principal axes of bending identified from over 0.9-μs all-atom molecular dynamics simulations of DNA oligos. The calculated order parameters describe motion of DNA as an elastic rod. In 10 possible dinucleotide steps, bending about the two principal axes is anisotropic yet linearly elastic. Twist about the centroid axis is largely decoupled from bending, but DNA tends to overtwist for unbending beyond the typical range of thermal motion, which is consistent with experimentally observed twist-stretch coupling. The calculated elastic stiffness of dinucleotide steps yield sequence-dependent persistence lengths consistent with previous single-molecule experiments, which is further analyzed by performing coarse-grained simulations of DNA. Flexibility maps of oligos constructed from simulation also match with those from the precalculated stiffness of dinucleotide steps. These support the premise that base pair interaction at the dinucleotide-level is mainly responsible for the elasticity of DNA. Furthermore, we analyze 1381 crystal structures of protein-DNA complexes. In most structures, DNAs are mildly deformed and twist takes the highest portion of the total elastic energy. By contrast, in structures with the elastic energy per dinucleotide step greater than about 4.16 kBT (kBT: thermal energy), the major bending becomes dominant. The extensional energy of dinucleotide steps takes at most 35% of the total elastic energy except for structures containing highly deformed DNAs where linear elasticity breaks down. Such partitioning between different deformational modes provides quantitative insights into the conformational dynamics of DNA as well as its interaction with other molecules and surfaces.

Synthesis of new C-5-triazolyl-functionalized thymidine analogs and their ability to engage in aromatic stacking in DNA : DNA and DNA : RNA duplexes

Stacking interactions of substituted triazoles in the major groove were studied, and with a polar uracil, increased duplex stabilities were found.

Conformational features of benzo-homologated yDNA duplexes by molecular dynamics simulation

yDNA is a base-modified nucleic acid duplex containing size-expanded nucleobases. Base-modified nucleic acids could expand the genetic alphabet and thereby enhance the functional potential of DNA. Unrestrained 100 ns MD simulations were performed in explicit solvent on the yDNA NMR sequence [5'(yA T yA yA T yA T T yA T)₂ ] and two modeled yDNA duplexes, [5'(yC yC G yC yC G G yC G G)₂ ] and [(yT5' G yT A yC yG C yA yG T3')•(yA5' C T C yG C G yT A yC A3')]. The force field parameters for the yDNA bases were derived in consistent with the well-established AMBER force field. Our results show that DNA backbone can withstand the stretched size of the bases retaining the Watson-Crick base pairing in the duplexes. The duplexes retained their double helical structure throughout the simulations accommodating the strain due to expanded bases in the backbone torsion angles, sugar pucker and helical parameters. The effect of the benzo-expansion is clearly reflected in the extended C1'-C1' distances and enlarged groove widths. The size expanded base modification leads to reduction in base pair twist resulting in larger overlapping area between the stacked bases, enhancing inter and intra strand stacking interactions in yDNA in comparison with BDNA. This geometry could favour enhanced interactions with the groove binders and DNA binding proteins., 2016. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 55-64, 2016.

Applying Thymine Isostere 2,4-Difluoro-5-Methylbenzene as a NMR Assignment Tool and Probe of Homopyrimidine/Homopurine Tract Structural Dynamics

Proton assignment of nuclear magnetic resonance (NMR) spectra of homopyrimidine/homopurine tract oligonucleotides becomes extremely challenging with increasing helical length due to severe cross-peak overlap. As an alternative to the more standard practice of (15)N and (13)C labeling of oligonucleotides, here, we describe a method for assignment of highly redundant DNA sequences that uses single-site substitution of the thymine isostere 2,4-difluoro-5-methylbenzene (dF). The impact of this approach in facilitating the assignment of intractable spectra and analyzing oligonucleotide structure and dynamics is demonstrated using A-tract and TATA box DNA and two polypurine tract-containing RNA:DNA hybrids derived from HIV-1 and the Saccharomyces cerevisiae long-terminal repeat-containing retrotransposon Ty3. Only resonances proximal to the site of dF substitution exhibit sizable chemical shift changes, providing spectral dispersion while still allowing chemical shift mapping of resonances from unaffected residues distal to the site of modification directly back to the unmodified sequence. It is further illustrated that dF incorporation can subtly alter the conformation and dynamics of homopyrimidine/homopurine tract oligonucleotides, and how these NMR observations can be correlated, in the cases of the TATA box DNA, with modulation in the TATA box-binding protein interaction using an orthogonal gel assay.

Effect of preorganization on the affinity of synthetic DNA binding motifs for nucleotide ligands

Triplexes with a gap in the purine strand have been shown to bind adenosine or guanosine derivatives through a combination of Watson-Crick and Hoogsteen base pairing. Rigidifying the binding site should be advantageous for affinity. Here we report that clamps delimiting the binding site have a modest effect on affinity, while bridging the gap of the purine strand can strongly increase affinity for ATP, cAMP, and FAD. The lowest dissociation constants were measured for two-strand triple helical motifs with a propylene bridge or an abasic nucleoside analog, with Kd values as low as 30 nM for cAMP in the latter case. Taken together, our data suggest that improving preorganization through covalent bridges increases the affinity for nucleotide ligands. But, a bulky bridge may also block one of two alternative binding modes for the adenine base. The results may help to design new receptors, switches, or storage motifs for purine-containing ligands.

Imidazolo-dC metal-mediated base pairs: purine nucleosides capture two Ag(+) ions and form a duplex with the stability of a covalent DNA cross-link

8-Phenylimidazolo-dC ((ph) ImidC, 2) forms metal-mediated DNA base pairs by entrapping two silver ions. To this end, the fluorescent "purine" 2'-deoxyribonucleoside 2 has been synthesised and converted into the phosphoramidite 6. Owing to the ease of nucleobase deprotonation, the new Ag(+) -mediated base pair containing a "purine" skeleton is much stronger than that derived from the pyrrolo- [3,4-d]pyrimidine system ((ph) PyrdC, 1). The silver-mediated (ph) ImidC-(ph) ImidC base pair fits well into the DNA double helix and has the stability of a covalent cross-link. The formation of such artificial metal base pairs might not be limited to DNA but may be applicable to other nucleic acids such as RNA, PNA and GNA as well as other biopolymers.

Design and synthesis of triazolyl-donor/acceptor unnatural nucleosides and oligonucleotide probes containing triazolyl-phenanthrene nucleoside

In the context of abasic DNA or DNA duplex stabilization, several unnatural nucleosidic/non-nucleosidic base surrogates have been reported. Toward this end, we have designed and synthesized triazolyl-aromatic donor chomophores as unnatural nucleoside analogs. These modifications display markedly higher thermal stabilization of abasic DNA duplex in comparison to the stabilization offered by other nucleoside/non-nucleoside base surrogates reported in the literature. The same oligonucleotide probe containing triazolylphenanthrene nucleotide also offers very good stability of the self-pair duplex via π-π stacking interaction and hetero-pair duplex via charge transfer interaction when paired against triazolyl acceptor aromatic nucleoside. Moreover, the probe in the reverse sequence containing triazolylphenanthrene nucleotide has shown FRET efficiency in a chimeric DNA duplex. The triazolyl nucleotides would expectedly show stability toward exonuclease activity. This unit describes protocols for chemical synthesis of unnatural triazolyl nucleosides and one oligonucleotide probe. The unit also provides a summary of various thermal and photophysical applications of triazolylphenantherene-containing oligonucleotides.

Efficient functionalization of oligonucleotides by new achiral nonnucleosidic monomers

A novel synthetic strategy has been designed for preparation of achiral nonnucleosidic phosphoramidite monomers for automated solid-phase oligonucleotide synthesis. It is based on O-DMTr-protected 4-(2-hydroxyethyl)-morpholine-2,3-dione as the key compound and a family of building blocks obtained by its ring-opening by primary aliphatic amines. A series of nonnucleosidic phosphoramidites containing various side-chain functionalities was synthesized, and corresponding oligodeoxyribonucleotides incorporating modified units in single or multiple positions along the chain were prepared.

Probing the Protein-Nanoparticle Interface: The Role of Aromatic Substitution Pattern on Affinity

A new class of cationic gold nanoparticles has been synthesized bearing benzyl moieties featuring -NO₂ and -OMe groups to investigate the regioisomeric control of aromatic nanoparticle-protein recognition. In general, nanoparticles bearing electron withdrawing group demonstrated higher binding affinities towards green fluorescent protein (GFP) compared to electron-donating groups. Significantly, a ~7.5 and ~4.3 fold increase in binding with GFP was observed for -NO2 groups in meta- and para-position respectively, while ortho-substitution showed similar binding compared to the unsubstituted ring. These findings demonstrated that nanoparticle-protein interaction can be controlled by the tuning the spatial orientation and the relative electronic properties of the aromatic substituents. This improved biomolecular recognition provides opportunities for enhanced biosensing and functional protein delivery to the cells.

Temperature-dependent self-assembly of adenine derivative on HOPG

Temperature-dependent self-assembly formed by the adsorption of the nucleobase adenine derivative on a graphite surface were investigated by in situ scanning tunneling microscopy (STM). The high-resolution STM images reveal two types of structures, α phase and β phase, which are mainly driven by either hydrogen bonding or aromatic π-π interactions between adenine bases, respectively, as well as the interactions of alkyl chains. α-Phase structures can be transformed into β-phase structures by increasing temperature. The reverse is true for decreasing temperature. This reflects structural stabilities resulting from the different interactions. Density functional theory (DFT) calculations were performed to characterize possible arrangements of adjacent adenine moieties systematically in terms of binding energies and structural properties. Via a systematic search algorithm, all possible network structures were determined on a microscopic level. In this way, it is possible to rationalize the structural parameters as found in the STM images.

Backbone-base interactions critical to quantum stabilization of transfer RNA anticodon structure

Transfer RNA (tRNA) anticodons adopt a highly ordered 3'-stack without significant base overlap. Density functional theory at the M06-2X/6-31+G(d,p) level in combination with natural bond orbital analysis was utilized to calculate the intramolecular interactions within the tRNA anticodon that are responsible for stabilizing the stair-stepped conformation. Ten tRNA X-ray crystal structures were obtained from the PDB databank and were trimmed to include only the anticodon bases. Hydrogenic positions were added and optimized for the structures in the stair-stepped conformation. The sugar-phosphate backbone has been retained for these calculations, revealing the role it plays in RNA structural stability. It was found that electrostatic interactions between the sugar-phosphate backbone and the base provide the most stability, rather than the traditionally studied interbase stacking. Base-stacking interactions, though present, were weak and inconsistent. Aqueous solvation was found to have little effect on the intramolecular interactions.

Thermodynamic and structural analysis of DNA damage architectures related to replication

Damaged DNA, generated by the abstraction of one of five hydrogen atoms from the 2′-deoxyribose ring of the nucleic acid, can contain a variety of lesions, some of which compromise physiological processes. Recently, DNA damage, resulting from the formation of a C3′-thymidinyl radical in DNA oligomers, was found to be dependent on nucleic acid structure. Architectures relevant to DNA replication were observed to generate larger amounts of strand-break and 1-(2′-deoxy-β-D-threo-pentofuranosyl)thymidine formation than that observed for duplex DNA. To understand how this damage can affect the integrity of DNA, the impact of C3′-thymidinyl radical derived lesions on DNA stability and structure was characterized using biophysical methods. DNA architectures evaluated include duplex DNA (dsDNA), single 3′ or 5′-overhangs (OvHgs), and forks. Thermal melting analysis and differential scanning calorimetry measurements indicate that an individual 3′-OvHg is more destabilizing than a 5′-OvHg. The presence of a terminal 3′ or 5′ phosphate decreases the ΔG₂₅ to the same extent, while the effect of the phosphate at the ss-dsDNA junction of OvHgs is dependent on sequence. Additionally, the effect of 1-(2′-deoxy-β-D-threo-pentofuranosyl)thymidine is found to depend on DNA architecture and proximity to the 3′ end of the damaged strand.

M1.3--a small scaffold for DNA origami

The DNA origami method produces programmable nanoscale objects that form when one long scaffold strand hybridizes to numerous oligonucleotide staple strands. One scaffold strand is dominating the field: M13mp18, a bacteriophage-derived vector 7249 nucleotides in length. The full-length M13 is typically folded by using over 200 staple oligonucleotides. Here we report the convenient preparation of a 704 nt fragment dubbed "M1.3" as a linear or cyclic scaffold and the assembly of small origami structures with just 15-24 staple strands. A typical M1.3 origami is large enough to be visualized by TEM, but small enough to show a cooperativity in its assembly and thermal denaturation that is reminiscent of oligonucleotide duplexes. Due to its medium size, M1.3 origami with globally modified staples is affordable. As a proof of principle, two origami structures with globally 5'-capped staples were prepared and were shown to give higher UV-melting points than the corresponding assembly with unmodified DNA. M1.3 has the size of a gene, not a genome, and may function as a model for gene-based nanostructures. Small origami with M1.3 as a scaffold may serve as a workbench for chemical, physical, and biological experiments.

Biophysical and RNA Interference Inhibitory Properties of Oligonucleotides Carrying Tetrathiafulvalene Groups at Terminal Positions

Oligonucleotide conjugates carrying a single functionalized tetrathiafulvalene (TTF) unit linked through a threoninol molecule to the 3′ or 5′ ends were synthesized together with their complementary oligonucleotides carrying a TTF, pyrene, or pentafluorophenyl group. TTF-oligonucleotide conjugates formed duplexes with higher thermal stability than the corresponding unmodified oligonucleotides and pyrene- and pentafluorophenyl-modified oligonucleotides. TTF-modified oligonucleotides are able to bind to citrate-stabilized gold nanoparticles (AuNPs) and produce stable gold AuNPs functionalized with oligonucleotides. Finally, TTF-oligoribonucleotides have been synthesized to produce siRNA duplexes carrying TTF units. The presence of the TTF molecule is compatible with the RNA interference mechanism for gene inhibition.

The steric hypothesis for DNA replication and fluorine hydrogen bonding revisited in light of structural data

In DNA, bases pair in a molecular interaction that is both highly predictable and exquisitely specific. Therefore researchers have generally believed that the insertion of the matching nucleotide opposite a template base by DNA polymerases (pols) required Watson-Crick (W-C) hydrogen bond formation. However pioneering work by Kool and co-workers using hydrophobic base analogs such as the thymine (T) isostere 2,4-difluorotoluene (F) showed that shape rather than H-bonding served as the primary source of specificity in DNA replication by certain pols. This steric hypothesis for DNA replication has gained popularity, perhaps discouraging further experimental studies to address potential limitations of this new idea. The idea that shape trumps H-bonding in terms of pol selectivity largely hinges on the belief that fluorine is a poor H-bond acceptor. However, the shape complementarity model was embraced in the absence of any detailed structural data for match (F:A) and mismatch pairs (F:G, F:C, F:T) in DNA duplexes or at active sites of pols. Although the F and T nucleosides are roughly isosteric, it is unclear whether F:A and T:A pairs exhibit similar geometries. If the F:A pair is devoid of H-bonding, it will be notably wider than a T:A pair. Because shape and size and H-bonding are intimately related, it may not be possible to separate these two properties. Thus the geometries of an isolated F:A pair in water may differ considerably from an F:A pair embedded in a stretch of duplex DNA, at the tight active site of an A-family replicative pol, or within the spacious active site of a Y-family translesion pol. The shape complementarity model may have more significance for pol accuracy than efficiency: this model appears to be most relevant for replicative pols that use specific residues to probe the identity of the nascent base pair from the minor groove side. However, researchers have not fully considered the importance of such interactions that include H-bonds compared with W-C H-bonds in terms of pol fidelity and the shape complementarity model. This Account revisits the steric hypothesis for DNA replication in light of recent structural data and discusses the role of fluorine as an H-bond acceptor. Over the last 5 years, crystal structures have emerged for nucleic acid duplexes with F paired opposite to natural bases or located at the active sites of DNA pols. These data permit a more nuanced understanding of the role of shape in DNA replication and the capacity of fluorine to form H-bonds. These studies and additional research involving RNA or other fluorine-containing nucleoside analogs within duplexes indicate that fluorine engages in H-bonding in many cases. Although T and F are isosteric at the nucleoside level, replacement of a natural base by F in pairs often changes their shapes and sizes, and dF in DNA behaves differently from rF in RNA. Similarly, the pairing geometries observed for F and T opposite dATP, dGTP, dTTP, or dCTP and their H-bonding patterns at the active site of a replicative pol differ considerably.

A universal nucleoside with strong two-band switchable fluorescence and sensitivity to the environment for investigating DNA interactions

With the aim of developing a new tool to investigate DNA interactions, a nucleoside analogue incorporating a 3-hydroxychromone (3HC) fluorophore as a nucleobase mimic was synthesized and incorporated into oligonucleotide chains. In comparison with existing fluorescent nucleoside analogues, this dye features exceptional environmental sensitivity switching between two well-resolved fluorescence bands. In labeled DNA, this nucleoside analogue does not alter the duplex conformation and exhibits a high fluorescence quantum yield. This probe is up to 50-fold brighter than 2-aminopurine, the fluorescent nucleoside standard. Moreover, the dual emission is highly sensitive to the polarity of the environment; thus, a strong shielding effect of the flanking bases from water was observed. With this nucleoside, the effect of a viral chaperone protein on DNA base stacking was site-selectively monitored.

Apolar carbohydrates as DNA capping agents

Mono- and disaccharides have been shown to stack on top of DNA duplexes stabilizing sequences with terminal C-G base pairs. Here we present an apolar version of glucose and cellobiose as new capping agents that stack on DNA increasing considerably its stability with respect to their natural polyhydroxylated mono- and disaccharide DNA conjugates.

Measurement and theory of hydrogen bonding contribution to isosteric DNA base pairs

We address the recent debate surrounding the ability of 2,4-difluorotoluene (F), a low-polarity mimic of thymine (T), to form a hydrogen-bonded complex with adenine in DNA. The hydrogen bonding ability of F has been characterized as small to zero in various experimental studies, and moderate to small in computational studies. However, recent X-ray crystallographic studies of difluorotoluene in DNA/RNA have indicated, based on interatomic distances, possible hydrogen bonding interactions between F and natural bases in nucleic acid duplexes and in a DNA polymerase active site. Since F is widely used to measure electrostatic contributions to pairing and replication, it is important to quantify the impact of this isostere on DNA stability. Here, we studied the pairing stability and selectivity of this compound and a closely related variant, dichlorotoluene deoxyriboside (L), in DNA, using both experimental and computational approaches. We measured the thermodynamics of duplex formation in three sequence contexts and with all possible pairing partners by thermal melting studies using the van't Hoff approach, and for selected cases by isothermal titration calorimetry (ITC). Experimental results showed that internal F-A pairing in DNA is destabilizing by 3.8 kcal/mol (van't Hoff, 37 °C) as compared with T-A pairing. At the end of a duplex, base-base interactions are considerably smaller; however, the net F-A interaction remains repulsive while T-A pairing is attractive. As for selectivity, F is found to be slightly selective for adenine over C, G, T by 0.5 kcal mol, as compared with thymine's selectivity of 2.4 kcal/mol. Interestingly, dichlorotoluene in DNA is slightly less destabilizing and slightly more selective than F, despite the lack of strongly electronegative fluorine atoms. Experimental data were complemented by computational results, evaluated at the M06-2X/6-31+G(d) and MP2/cc-pVTZ levels of theory. These computations suggest that the pairing energy of F to A is ~28% of that of T-A, and most of this interaction does not arise from the F···HN interaction, but rather from the CH···N interaction. The nucleobase analogue shows no inherent selectivity for adenine over other bases, and L-A pairing energies are slightly weaker than for F-A. Overall, the results are consistent with a small favorable noncovalent interaction of F with A offset by a large desolvation cost for the polar partner. We discuss the findings in light of recent structural studies and of DNA replication experiments involving these analogues.

A 5'-cap for DNA probes binding RNA target strands

Detecting short RNA strands with high fidelity at any of the bases of their sequence, including the termini, can be challenging, since fraying, wobbling, and refolding all compete with canonical base pairing. We performed a search for 5'-substituents of oligodeoxynucleotides that increase base pairing fidelity at the terminus of duplexes with RNA target strands. From a total of over 70 caps, differing in stacking moiety and linker, a phosphodiester-linked sequence of the residues of L-prolinol, glycine, and oxolinic acid, dubbed ogOA, was identified as a 5'-cap that stabilizes any of the four canonical base pairs, with ΔT(m) values of up to +13.1 °C for an octamer. At the same time, the cap increases discrimination against any of the 12 possible terminal mismatches, including mismatches that are more stable than their perfectly matched counterparts in the control duplex, such as A:A. A probe with the cap also showed increased selectivity in the detection of two closely related microRNAs, let7c and let7a, with a ΔT(m) value of 9.2 °C. Melting curves also yielded thermodynamic data that shed light on the uniformity of molecular recognition in the sequence space of DNA:DNA and DNA:RNA duplexes. Hybridization probes with fidelity-enhancing caps should find applications in the individual and parallel detection of biologically active RNA species.

Use of nucleic Acid analogs for the study of nucleic Acid interactions

Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.