Design and Applications of Noncanonical DNA Base Pairs

Molecular elements: novel approaches for molecular building

Classically, a molecular element (ME) is a pure substance composed of two or more atoms of the same element. However, MEs, in the context of this review, can be any molecules as elements bonded together into the backbone of synthetic oligonucleotides (ONs) with designed sequences and functions, including natural A, T, C, G, U, and unnatural bases. The use of MEs can facilitate the synthesis of designer molecules and smart materials. In particular, we discuss the landmarks associated with DNA structure and related technologies, as well as the extensive application of ONs, the ideal type of molecules for intervention therapy aimed at correcting disease-causing genetic errors (indels). It is herein concluded that the discovery of ON therapeutics and the fabrication of designer molecules or nanostructures depend on the ME concept that we previously published. Accordingly, ME will be our focal point as we discuss related research directions and perspectives in making molecules and materials. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.

Self-assembly of rylene-decorated guanine ribbons on graphene surface for optoelectronic applications: a theoretical study

We are witnessing a change of paradigm from the conventional top-down to the bottom-up fabrication of nanodevices and particularly optoelectronic devices. A promising example of the bottom-up approach is self-assembling of molecules into layers with predictable and reproducible structural, electronic and optical properties. Nucleobases possess extraordinary ability to self-assembly into one-, two-, and three-dimensional structures. Optical properties of nucleotides are not suitable for wider application to optoelectronics and photovoltaics due to their large optical band gap, which is in contrast to rylene-based dyes that have been intensively investigated in organic optoelectronics. However, these lack the self-assembly capability of nucleobases. Combinations of covalently decorated guanine molecules with rylene type chromophores present 'the best of the both worlds'. Due to the large size of such compounds and its flexible nature their self-assemblies have not been fully understood yet. Here, we use a theoretical approach to study the structural, energetic and optical properties of rylene-based dye decorated guanine (GPDI), as self-assembled on a graphene sheet. Particularly we utilize the density-functional based tight-binding method to study atomic structure of these systems including the potential energy surface of GPDI and stability and organization of single- and multilayered GPDIs on graphene sheet. Using density-functional theory (DFT) we employ the energy decomposition analysis to gain a deeper insight into the contributions of different moieties to stability of GPDI films. Using time dependent DFT we analyze optical properties of these systems. We find that atomically thin films consisting of only a few molecular layers with large surface areas are more favorable than isolated thick islands. Our study of excited states indicates existence of charge separated states similar to ones found in the well-studied hydrogen bonded organic frameworks. The self-assembly characterized with a large homogeneous coverage and long-living charge-separated states provide the great potential for optoelectronic applications.

A unified computational view of DNA duplex, triplex, quadruplex and their donor-acceptor interactions

DNA can assume various structures as a result of interactions at atomic and molecular levels (e.g., hydrogen bonds, π–π stacking interactions, and electrostatic potentials), so understanding of the consequences of these interactions could guide development of ways to produce elaborate programmable DNA for applications in bio- and nanotechnology. We conducted advanced ab initio calculations to investigate nucleobase model structures by componentizing their donor-acceptor interactions. By unifying computational conditions, we compared the independent interactions of DNA duplexes, triplexes, and quadruplexes, which led us to evaluate a stability trend among Watson–Crick and Hoogsteen base pairing, stacking, and even ion binding. For a realistic solution-like environment, the influence of water molecules was carefully considered, and the potassium-ion preference of G-quadruplex was first analyzed at an ab initio level by considering both base-base and ion-water interactions. We devised new structure factors including hydrogen bond length, glycosidic vector angle, and twist angle, which were highly effective for comparison between computationally-predicted and experimentally-determined structures; we clarified the function of phosphate backbone during nucleobase ordering. The simulated tendency of net interaction energies agreed well with that of real world, and this agreement validates the potential of ab initio study to guide programming of complicated DNA constructs.

Protonation of Cytosine-Rich Telomeric DNA Fragments by Carboxylated Carbon Nanotubes: Insights from Computational Studies

In this work, we studied, using computational methods, the protonation reactions of telomeric DNA fragments being due to interaction with carboxylated carbon nanotubes. The applied computational methodology is divided into two stages. (i) Using classical molecular dynamics, we generated states in which carboxyl groups are brought to the vicinity of nitrogen atoms within the cytosine rings belonging to the DNA duplex. (ii) From these states, we selected two systems for systematic quantum chemical studies aimed at the analysis of proton-transfer reactions between the carboxyl groups and nitrogen atoms within the cytosine rings. Results of molecular dynamics calculations led to the conclusion that sidewall-functionalized carbon nanotubes deliver carboxyl groups slightly more effectively than the on-tip-functionalized ones. The latter can provide carboxyl groups in various arrangements and more diverse quality of approach of carboxyl groups to the cytosines; however, the differences between various arrangements of carboxyl groups are still not big. It was generally observed that narrow nanotubes can access the cytosine pocket easier than wider ones. Quantum chemical calculations led however to the conclusion that a direct proton transfer from the carboxyl group to the nitrogen atom within the cytosine ring is impossible under normal conditions. Precisely, we detected either very high activation barrier for the proton-transfer reaction or instability of the reaction product, i.e., its spontaneous decomposition toward reaction substrates.

Studies on the structure and chirality of A-motif in adenosine monophosphate nucleotide metal coordination complexes

Structure and chirality of A-motif.

Hydrophobic unnatural base pairs show a Watson-Crick pairing in micro-second molecular dynamics simulations

Two unnatural hydrophobic nucleotides, d5SICS (2,6-dimethyl-2H-isoquiniline-1-thione) and dNaM (2-methoxy-3-methylnaphthalene), were previously replicated in vivo by a modified E. coli strand, however, a consistent structure for their pairing in terms of specific and selective directional interactions remains elusive, as data from spectroscopy experiments and simulations are inconsistent. The proposed d5SICS-dNaM pairing has been suggested to be a stacked configuration as suggested by NMR data; simulations have failed to reproduce this configuration and a Watson-Crick like pairing is observed. Previously, we focused on reproducing the d5SICS-dNaM Unnatural Base Pair (UBP) paring using an older (bsc0) AMBER force field, which was not able to correctly reproduce the experimental data. We present our efforts to reproduce the experimental pairing using the current version of the AMBER DNA force fields (OL15 and bsc1), two water models (OPC and TIP3P) and external electrostatic stabilization by Mg²⁺ ions. Opposite to previously reported simulations, a Watson-Crick-like pairing with no hydrogen bonds persists throughout all our results. Despite our efforts to replicate the reported stacked conformation, we cannot confirm its plausibility nor obtain a consistent structure that is independent of the neighboring nucleotides. Communicated by Ramaswamy H. Sarma.

The investigation of the G-quadruplex aptamer selectivity to Pb2+ ion: a joint molecular dynamics simulation and density functional theory study

The aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb²⁺ in comparison with some ions. The Free Energy Landscape (FEL) analysis indicates that Pb²⁺ has remained inside the aptamer during the MD simulation, while the other ions have left it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energies prove that the conformational stability of the aptamer is the highest in the presence of Pb²⁺. According to the compaction parameters, the greatest compressed ion-aptamer complex, and hence, the highest ion-aptamer interaction have been induced in the presence of Pb²⁺. The contact maps clarify the closer contacts between the nucleotides of the aptamer in the presence of Pb²⁺. The density functional theory (DFT) results show that Pb²⁺ forms the most stable complex with the aptamer, which is consistent with the MD results. The QM calculations reveal that the N-H bonds and the O…H distances are the longest and the shortest, respectively, in the presence of Pb²⁺. The obtained results verify that the strongest hydrogen bonds (HBs), and hence, the most compressed aptamer structure are induced by Pb²⁺. Besides, atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm the results.Communicated by Ramaswamy H. Sarma.

Charge-dipole interactions in G-quadruplex thrombin-binding aptamer

DNAs form various structures through hydrogen-bonding, base-stacking and electrostatic interactions. Although these noncovalent interactions are known to be cooperative in stabilizing a G-quadruplex (G4) structure of DNA, we find from all-atom molecular dynamics simulations that the electrostatic charge-dipole interaction is competitive with both hydrogen-bonding and base-stacking interactions. For the thrombin-binding aptamer (TBA) forming a chair-type antiparallel G4 structure, we have examined effects of an intercalating metal ion [K+, Sr2+, Mn+: an ion having a charge of n+ (n = 1-4) with the ionic radius of K+] on structural properties and noncovalent interactions. When K+ in the TBA·K+ complex is replaced with Sr2+, guanine dipoles in the two G-tetrads are realigned toward the central metal ion, thereby distorting the planar G4 geometry. Replacing K+ with Sr2+ significantly enhances the charge-dipole interaction but substantially reduces the number of hydrogen bonds in the G-tetrads. In the case of TBA·Mn+ complexes, as the charge n increases, the charge-dipole interaction increases but both of the hydrogen-bonding and base-stacking interactions decrease. These results suggest that the charge-dipole interaction realigning guanine dipoles in the G-tetrads is not cooperative but competitive with both hydrogen-bonding and base-stacking interactions favoring the planar G-tetrad geometry. Obviously, the charge state of an intercalating metal ion is as important as the ionic radius in forming a stable G4 structure. Thus, a delicate balance between these competing noncovalent interactions makes the chair-type antiparallel G4 structure of TBA selective for intercalating metal ions.

On the misincorporation of nucleotides opposite mutagenic cyclic 1,N2-propanoguanine: A computational investigation

The misincorporation properties of exocyclic DNA adduct, cyclic 1,N²-propanoguanine with nucleobases have been investigated using DFT and DFT-D methods. Number of possible and stable mispairing conformations of cyclic 1,N²-propanoguanine with A,T,G and C have been considered for our investigation. The single point energy calculations have been carried out at the M06/6-311++G**, ωB97XD/6-311++G** and MP2/6-311++G** levels on corresponding optimized geometries. The reaction enthalpy values were employed at the M06/6-31 + G* and ωB97XD/6-31 + G* levels. The energies have been compared among the cyclic 1,N²-propanoguanine adduct with nucleobases to find the most stable conformer. The CPCM model was utilized on account of solvent phase and overall polarizability. The computed binding energies follow the order as CPr-Gua-G(2)(-23.2 kcal/mol) > CPr-Gua-C(1) (-16.1 kcal/mol) > CPr-Gua-A(2)(-10.6 kcal/mol) > CPr-Gua-T(2)(-9.6 kcal/mol) in the gas phase at M06 level, which indicates the guanine and cytosine are favorable for mispairing with the cyclic 1,N²-propanoguanine adduct. The obtained results using computational tools are in good agreement with the experimental observation.

pH-Control in Aptamer-Based Diagnostics, Therapeutics, and Analytical Applications

Aptamer binding has been used effectively for diagnostics, in-vivo targeting of therapeutics, and the construction and control of nanomachines. Nanostructures that respond to pH by releasing or changing affinity to a target have also been used for in vivo delivery, and in the construction of sensors and re-usable nanomachines. There are many applications that use aptamers together with pH-responsive materials, notably the targeted delivery of chemotherapeutics. However, the number of reported applications that directly use pH to control aptamer binding is small. In this review, we first discuss the use of aptamers with pH-responsive nanostructures for chemotherapeutic and other applications. We then discuss applications that use pH to denature or otherwise disrupt the binding of aptamers. Finally, we discuss motifs using non-canonical nucleic acid base pairing that can shift conformation in response to pH, followed by an overview of engineered pH-controlled aptamers designed using those motifs.

Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA

We develop a robust coarse-grained model for single- and double-stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking, hydrogen bond, and electrostatic interactions as well as bond-stretching and bond angle potentials that account for the polymeric nature of DNA. The choices of force constants for stretching and the bending potentials were guided by a Boltzmann inversion procedure using a large representative set of DNA structures extracted from the Protein Data Bank. Some of the parameters in the stacking interactions were calculated using a learning procedure, which ensured that the experimentally measured melting temperatures of dimers are faithfully reproduced. Without any further adjustments, the calculations based on the TIS model reproduce the experimentally measured salt and sequence-dependence of the size of single-stranded DNA (ssDNA), as well as the persistence lengths of poly(dA) and poly(dT) chains. Interestingly, upon application of mechanical force, the extension of poly(dA) exhibits a plateau, which we trace to the formation of stacked helical domains. In contrast, the force-extension curve (FEC) of poly(dT) is entropic in origin and could be described by a standard polymer model. We also show that the persistence length of double-stranded DNA, formed from two complementary ssDNAs, is consistent with the prediction based on the worm-like chain. The persistence length, which decreases with increasing salt concentration, is in accord with the Odijk-Skolnick-Fixman theory intended for stiff polyelectrolyte chains near the rod limit. Our model predicts the melting temperatures of DNA hairpins with excellent accuracy, and we are able to recover the experimentally known sequence-specific trends. The range of applications, which did not require adjusting any parameter after the initial construction based solely on PDB structures and melting profiles of dimers, attests to the transferability and robustness of the TIS model for ssDNA and dsDNA.

Theoretical study of gas and solvent phase stability and molecular adsorption of noncanonical guanine bases on graphene

The gas and solvent phase stability of noncanonical (Gua)_n nucleobases is investigated in the framework of dispersion-corrected density functional theory (DFT). The calculated results strongly support the high tendency for the dimerization of (Gua)_n bases in both gas and solvent phases. An interplay between intermolecular and bifurcated H-bonds is suggested to govern the stability of (Gua)_n bases which bears a correlation with the description of dispersion correction terms employed in the DFT calculations. For example, a higher polarity is predicted for (Gua)_n bases by the dispersion-corrected DFT in contrast to the non-polar nature of (Gua)₃ and (Gua)₄ predicted by the hybrid meta-GGA calculations. This distinct variation becomes significant under physiological conditions as polar (Gua)_n is likely to exhibit greater stabilization in the gas phase compared to solvated (Gua)_n. Graphene acting as a substrate induces modification in base configurations via maximization of π-orbital overlap between the base and substrate. In solvent, the substrate-induced effects are further heightened with lowering of the dipole moments of (Gua)_n as also displayed by the corresponding isosurface of the electrostatic potential. The graphene-induced stability in both gas and solvent phases appears to fulfill one of the prerequisite criteria for molecular self-assembly. The DFT results therefore provide atomistic insights into the stability and molecular assembly of free-standing noncanonical (Gua)_n nucleobases which can be extended to understanding the self-assembly process of functional biomolecules on 2D materials for potential biosensing applications.

Theoretical study on photo-induced processes of 1-methyl-3-(N-(1,8-naphthalimidyl)ethyl)imidazolium halide species: an application of constrained density functional theory

1-Methyl-3-(N-(1,8-naphthalimidyl)ethyl)imidazolium (MNEI) has potential as a versatile sensor that can measure the electronegativity of anions based on the fluorescence intensity upon irradiation. To clarify the factors that determine the fluorescence intensity, constrained density functional theory (CDFT) was applied to explore the electron transfer (ET) states of MNEI halide species (MNEI-X; X = F, Cl, Br, I). According to the CDFT potential energy surface, intra-molecular ET (S_M1) states on MNEI are responsible for the intensity of absorption and fluorescence spectra. However, inter-molecular ET (S_ET) states between MNEI and X are certainly responsible for fluorescence quenching. Hence, the energetic difference between the S_M1 state and the S_ET state (ΔE_{M1_ET}) is a crucial factor that determines the fluorescence intensity in the spectra of MNEI-X complexes. ΔE_{M1_ET} decreases as the electronegativity of X decreases (i.e., F > Cl > Br > I). This explains the fluorescence intensity of MNEI-X.

Consequences of Mg2+ binding on the geometry and stability of RNA base pairs

Quantum chemical calculations reveal the role of magnesium in stabilizing the geometries of intrinsically unstable RNA base pairs.

Structure and Electronic Properties of Unnatural Base Pairs: The Role of Dispersion Interactions

Recent reports of the successful incorporation of unnatural base pairs (UBPs), such as d5SICS-dNaM, in the gene sequence and replication with DNA is an important milestone in synthetic biology. Followed by this, several other UBPs, such as dTPT3-dNaM, dTPT3-dFIMO, dTPT3-IMO, dTPT3-FEMO, FTPT3-NaM, FTPT3-FIMO, FTPT3-IMO, and FTPT3-FEMO, have demonstrated similar or better retention and fidelity inside cells. Of these base pairs, dNaM-dTPT3 has been optimized to be a better fit inside a pAIO plasmid. Based on both implicit and explicit dispersion-corrected density functional theory (DFT) calculations, we show that although this set of UBPs is significantly diverse in elemental and structural configuration, the members do share a common trait of favoring a slipped parallel stacked dimer arrangement. Unlike the natural bases (A, T, G, C, and U), this set of UBPs has a negligible affinity for a Watson-Crick (WC)-type planar structure because they are invariably more stable within slipped parallel stacked orientations. We also observed that all the UBPs have either similar or higher binding energies with the natural bases in similar stacked orientations. When arranged between two natural base pairs, the UBPs exhibited a binding energy similar to that of three-base sequences of natural bases. Our computational data show that the most promising base pairs are 5SICS-NaM, TPT3-NaM, and TPT3-FEMO. These results are consistent with recent progress on experimental research into UBPs along with our previous calculations on the d5SICS-dNaM pair and, therefore, strengthen the hypothesis that hydrogen bonding might not be absolutely essential and that interbase stacking dispersion interactions play a key role in the stabilization of genetic materials.

Visible-Light-Mediated Excited State Relaxation in Semi-Synthetic Genetic Alphabet: d5SICS and dNaM

The excited state dynamics of an unnatural base pair (UBP) d5SICS/dNaM were investigated by accurate ab-initio calculations. Time-dependent density functional and high-level multireference calculations (MS-CASPT2) were performed to elucidate the excitation of this UBP and its excited state relaxation mechanism. After excitation to the bright state S₂ (ππ*), it decays to the S₁ state and then undergoes efficient intersystem crossing to the triplet manifold. The presence of sulfur atom in d5SICS leads to strong spin-orbit coupling (SOC) and a small energy gap that facilitates intersystem crossing from S₁ (n_s π*) to T₂ (ππ*) followed by internal conversion to T₁ state. Similarly in dNaM, the deactivation pathway follows analogous trends. CASPT2 calculations suggest that the S₁ (ππ*) state is a dark state below the accessible S₂ (ππ*) bright state. During the ultrafast deactivation, it exhibits bond length inversion. From S₁ state, significant SOC leads the population transfer to T₃ due to a smaller energy gap. Henceforth, fast internal conversion occurs from T₃ to T₂ followed by T₁ . From time-dependent trajectory surface hopping dynamics, it is found that excited state relaxation occurs on a sub-picosecond timescale in d5SICS and dNaM. Our findings strongly suggest that there is enough energy available in triplet state of UBP to generate reactive oxygen species and induce phototoxicity with respect to cellular DNA.

Computational studies on the interactions of glycine amino acid with graphene, h-BN and h-SiC monolayers

In the present work, the adsorption of glycine amino acid and its zwitterionic form onto three different hexagonal sheets, namely graphene, boron-nitride (h-BN) and silicon carbide (h-SiC), has been investigated within the framework of density functional theory (DFT) calculations.

Theoretical understanding of two-photon-induced fluorescence of isomorphic nucleoside analogs

We use ab initio Density Functional Theory (DFT) and Time-dependent DFT (TDDFT) calculations for a detailed understanding of one-photon absorption (1PA) and two-photon absorption (2PA) cross sections of eight different nucleoside analogs. The results are compared and contrasted with the available experimental data. Our calculated results show that the low energy peaks in the absorption spectra mainly arise because of the π-π* electronic transition of the nucleoside analogs. The emission spectra of the nucleoside analogs are also calculated using TDDFT methods. The calculated absorption and emission spectra in the presence of a solvent follow the same trend as those found experimentally. Our results demonstrate that the nucleoside analogs show significantly different electronic and optical properties, although their bonding aspects towards Watson-Crick base pairing remain the same. We also derive the microscopic details of the origin of nonlinear optical properties of the nucleoside analogs.

First-principles investigation of the lattice vibrational properties of inorganic double helical XY (X = Li, Na, K, Rb, Cs; Y = P, As, Sb)

The vibrational frequencies of the newly discovered inorganic double helical compounds XY (X = Li, Na, K, Rb, Cs; Y = P, As, Sb) are sensitive to either cation or anion or both of them.

Wobble↔Watson-Crick tautomeric transitions in the homo-purine DNA mismatches: a key to the intimate mechanisms of the spontaneous transversions

The intrinsic capability of the homo-purine DNA base mispairs to perform wobble↔Watson-Crick/Topal-Fresco tautomeric transitions via the sequential intrapair double proton transfer was discovered for the first time using QM (MP2/DFT) and QTAIM methodologies that are crucial for understanding the microstructural mechanisms of the spontaneous transversions.

DNA Structural Correlation in Short and Long Ranges

Recent single-molecule measurements have revealed the DNA allostery in protein/DNA binding. MD simulations showed that this allosteric effect is associated with the deformation properties of DNA. In this study, we used MD simulations to further investigate the mechanism of DNA structural correlation, its dependence on DNA sequence, and the chemical modification of the bases. Besides a random sequence, poly d(AT) and poly d(GC) are also used as simpler model systems, which show the different bending and twisting flexibilities. The base-stacking interactions and the methyl group on the 5-carbon site of thymine causes local structures and flexibility to be very different for the two model systems, which further lead to obviously different tendencies of the conformational deformations, including the long-range allosteric effects.

The effects of tautomerization and protonation on the adenine-cytosine mismatches: a density functional theory study

In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine-cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs.

How many tautomerization pathways connect Watson-Crick-like G*·T DNA base mispair and wobble mismatches?

In this study, we have theoretically demonstrated the intrinsic ability of the wobble G·T(w)/G*·T*(w)/G·T(w1)/G·T(w2) and Watson-Crick-like G*·T(WC) DNA base mispairs to interconvert into each other via the DPT tautomerization. We have established that among all these transitions, only one single G·T(w) ↔ G*·T(WC) pathway is eligible from a biological perspective. It involves short-lived intermediate - the G·T*(WC) base mispair - and is governed by the planar, highly stable, and zwitterionic [Formula: see text] transition state stabilized by the participation of the unique pattern of the five intermolecular O6(+)H⋯O4(-), O6(+)H⋯N3(-), N1(+)H⋯N3(-), N1(+)H⋯O2(-), and N2(+)H⋯O2(-) H-bonds. This non-dissociative G·T(w) ↔ G*·T(WC) tautomerization occurs without opening of the pair: Bases within mispair remain connected by 14 different patterns of the specific intermolecular interactions that successively change each other along the IRC. Novel kinetically controlled mechanism of the thermodynamically non-equilibrium spontaneous point GT/TG incorporation errors has been suggested. The mutagenic effect of the analogues of the nucleotide bases, in particular 5-bromouracil, can be attributed to the decreasing of the barrier of the acquisition by the wobble pair containing these compounds of the enzymatically competent Watson-Crick's geometry via the intrapair mutagenic tautomerization directly in the essentially hydrophobic recognition pocket of the replication DNA-polymerase machinery. Proposed approaches are able to explain experimental data, namely growth of the rate of the spontaneous point incorporation errors during DNA biosynthesis with increasing temperature.

Feasibility of occurrence of different types of protonated base pairs in RNA: a quantum chemical study

Protonated nucleobases have significant roles in facilitating catalytic functions of RNA, and in stabilizing different structural motifs. Reported pKa values of nucleobase protonation suggest that the population of neutral nucleobases is 10(3)-10(4) times higher than that of protonated nucleobases under physiological conditions (pH ∼ 7.4). Therefore, a molecular level understanding of various putative roles of protonated nucleobases cannot be achieved without addressing the question of how their occurrence propensities and stabilities are related to the free energy costs associated with the process of protonation under physiological conditions. With water as the proton donor, we use advanced QM methods to evaluate the site specific protonation propensities of nucleobases in terms of their associated free energy changes (ΔGprot). Quantitative follow up on the energetics of base pair formation and database search for evaluating their occurrence frequencies, reveal a lack of correlation between base pair stability and occurrence propensities on the one hand, and ease of protonation on the other. For example, although N7 protonated adenine (ΔGprot = 40.0 kcal mol(-1)) is found to participate in stable base pairing, base pairs involving N7 protonated guanine (ΔGprot = 36.8 kcal mol(-1)), on geometry optimization, converge to a minima where guanine transfers its extra proton to its partner base. Such observations, along with examples of weak base pairs involving N3 protonation of cytosine (ΔGprot = 37.0 kcal mol(-1)) are rationalized by analysing the protonation induced charge redistributions which are found to significantly influence, both positively and negatively, the hydrogen bonding potentials of different functional sites of individual nucleobases. Protonation induced charge redistribution is also found to strongly influence (i) the aromatic character of the rings of the participating bases and (ii) hydrogen bonding potential of the free edges of the protonated base pair. Comprehensive analysis of a non-redundant RNA crystal structure dataset further reveals that, while availability of stabilization possibilities determine the feasibility of occurrence of protonated bases, their occurrence context and specific functional roles are important factors determining their occurrence propensities.

Watson–Crick base pairing, electronic and photophysical properties of triazole modified adenine analogues: a computational study

Triazole adenine nucleobase analogues show fluorescence in the UV-Vis region and form Watson–Crick base pairing with thymine nucleobases.

Understanding the binding interaction of imidazole with ZnO nanomaterials and clusters

The order of binding energy values for imidazole adsorbed ZnO clusters through the preferred azomethine nitrogen site is imidazole–Zn₄O₄ (R) > imidazole–Zn₃O₃ > imidazole–Zn₄O₄ (W) > imidazole–Zn₂O₂.

Surface enhanced vibrational spectroscopy and first-principles study of l-cysteine adsorption on noble trimetallic Au/Pt@Rh clusters

First-principles study of l-cysteine adsorption on noble trimetallic Au/Pt@Rh clusters has been discussed in the light of SEIRS and theoretical surface complex calculation.

Thermodynamically feasible photoelectron transfer from bioactive π-expanded imidazole luminophores to ZnO nanocrystals

The chemical affinity between the nitrogen atom of the imidazole and the zinc ion on the surface of the nano oxide may be a reason for strong interaction of the ligand on nanoparticles causing the enhancement.

Why does substitution of thymine by 6-ethynylpyridone increase the thermostability of DNA double helices?

Efficiency of 6-ethynylpyridone (E), a potential thymine (T) analogue, which forms high-fidelity base pairs with adenine (A) and gives rise to stabler DNA duplexes, with stability comparable to those containing canonical cytosine(C):guanine(G) base pairs, has been reported recently. Estimates of the interaction energies, involving geometry optimization at the DFT level (including middle range dispersion interactions) followed by single point energy calculation at MP2 level, in excellent correlation with the experimentally observed trends, show that E binds more strongly and more discriminately with A than T does. Detailed analysis reveals that the increase in base-base interaction arises out of conjugation of acetylenic π electrons with the ring π system of E, which results in not only an extra stabilizing C-H···π interaction in the EA pair, but also a strengthening of the conventional hydrogen bonds. However, the computed base-base interaction energy for the EA pair was found to be much less than that of the canonical CG pair, implying that the difference in the TA versus EA base pairing interaction alone cannot explain the large experimentally observed increase in the thermostability of DNA duplexes, where a TA pair is replaced with an EA pair. Our computations show that the conjugation of acetylenic π electrons with the ring π system also possibly plays a role in increasing the stacking potential of the EA pair, which in turn can explain its marked influence in the enhancement of duplex stability.

Experimental and first-principles study of guanine adsorption on ZnO clusters

Electronic structure for interaction of guanine with Zn₂O₂ cluster and the most preferred N1-site to form a stable G–Zn₂O₂ model.