Purshotam Sharma

Binding of Gold Nanoclusters with Size-Expanded DNA Bases: A Computational Study of Structural and Electronic Properties

Binding of gold nanoclusters with size-expanded DNA bases, xA, xC, xG, and xT, is studied using quantum chemical methods. Geometries of the neutral xA-Au6, xC-Au6, xG-Au6, and xT-Au6 complexes were fully optimized using the B3LYP density functional method (DFT). The gold clusters around xA and xT adopt triangular geometries, whereas irregular structures are obtained in the case of gold clusters complexed around xC and xG. The lengths of the bonds between atoms in the x-bases increase on gold complexation. The aromatic character of the x-bases also increases on gold complexation except for the five-member rings. A significant charge transfer from the x-base to gold atoms is seen in these complexes. Second-order interactions are observed in addition to direct covalent bonds between gold atoms and x-bases.

Protonation of Base Pairs in RNA: Context Analysis and Quantum Chemical Investigations of Their Geometries and Stabilities

Base pairs involving protonated nucleobases play important roles in mediating global macromolecular conformational changes and in facilitation of catalysis in a variety of functional RNA molecules. Here we present our attempts at understanding the role of such base pairs by detecting possible protonated base pairs in the available RNA crystal structures using BPFind software, in their specific structural contexts, and by the characterization of their geometries, interaction energies, and stabilities using advanced quantum chemical computations. We report occurrences of 18 distinct protonated base pair combinations from a representative data set of RNA crystal structures and propose a theoretical model for one putative base pair combination. Optimization of base pair geometries was carried out at the B3LYP/cc-pVTZ level, and the BSSE corrected interaction energies were calculated at the MP2/aug-cc-pVDZ level of theory. The geometries for each of the base pairs were characterized in terms of H-bonding patterns observed, rmsd values observed on optimization, and base pair geometrical parameters. In addition, the intermolecular interaction in these complexes was also analyzed using Morokuma energy decomposition. The gas phase interaction energies of the base pairs range from -24 to -49 kcal/mol and reveal the dominance of Hartree-Fock component of interaction energy constituting 73% to 98% of the total interaction energy values. On the basis of our combined bioinformatics and quantum chemical analysis of different protonated base pairs, we suggest resolution of structural ambiguities and correlate their geometric and energetic features with their structural and functional roles. In addition, we also examine the suitability of specific base pairs as key elements in molecular switches and as nucleators for higher order structures such as base triplets and quartets.

Quantum Chemical Studies of Structures and Binding in Noncanonical RNA Base pairs: The Trans Watson-Crick:Watson-Crick Family

Abstract The trans Watson-Crick/Watson-Crick family of base pairs represent a geometric class that play important structural and possible functional roles in the ribosome, tRNA, and other functional RNA molecules. They nucleate base triplets and quartets, participate as loop closing terminal base pairs in hair pin motifs and are also responsible for several tertiary interactions that enable sequentially distant regions to interact with each other in RNA molecules. Eleven representative examples spanning nine systems belonging to this geometric family of RNA base pairs, having widely different occurrence statistics in the PDB database, were studied at the HF/6–31G (d, p) level using Morokuma decomposition, Atoms in Molecules as well as Natural Bond Orbital methods in the optimized gas phase geometries and in their crystal structure geometries, respectively. The BSSE and deformation energy corrected interaction energy values for the optimized geometries are compared with the corresponding values in the crystal geometries of the base pairs. For non protonated base pairs in their optimized geometry, these values ranged from −8.19 kcal/mol to −21.84 kcal/mol and compared favorably with those of canonical base pairs. The interaction energies of these base pairs, in their respective crystal geometries, were, however, lesser to varying extents and in one case, that of A:A W:W trans, it was actually found to be positive. The variation in RMSD between the two geometries was also large and ranged from 0.32–2.19 Å. Our analysis shows that the hydrogen bonding characteristics and interaction energies obtained, correlated with the nature and type of hydrogen bonds between base pairs; but the occurrence frequencies, interaction energies, and geometric variabilities were conspicuous by the absence of any apparent correlation. Instead, the nature of local interaction energy hyperspace of different base pairs as inferred from the degree of their respective geometric variability could be correlated with the identities of free and bound hydrogen bond donor/acceptor groups present in interacting bases in conjunction with their tertiary and neighboring group interaction potentials in the global context. It also suggests that the concept of isostericity alone may not always determine covariation potentials for base pairs, particularly for those which may be important for RNA dynamics. These considerations are more important than the absolute values of the interaction energies in their respective optimized geometries in rationalizing their occurrences in functional RNAs. They highlight the importance of revising some of the existing DNA based structure analysis approaches and may have significant implications for RNA structure and dynamics, especially in the context of structure prediction algorithms.

On the role of the cis Hoogsteen:sugar-edge family of base pairs in platforms and triplets-quantum chemical insights into RNA structural biology.

Base pairs belonging to the cis Hoogsteen:sugar-edge (H:S) family play important structural roles in folded RNA molecules. Several of these are present in internal loops, where they are involved in interactions leading to planar dinucleotide platforms which stabilize higher order structures such as base triplets and quartets. We report results of analysis of 30 representative examples spanning 16 possible base pair combinations, with several of them showing multimodality of base pairing geometry. The geometries of 23 of these base pairs were modeled directly from coordinates extracted from RNA crystal structures. The other seven were predicted structures which were modeled on the basis of observed isosteric analogues. After appropriate satisfaction of residual valencies, these structures were relaxed using the B3LYP/6-31G(d,p) method and interaction energies were derived at the RIMP2/aug-cc-pVDZ level of theory. The geometries for each of the studied base pairs have been characterized in terms of the number and nature of H-bonds, rmsd values observed on optimization, base pair geometrical parameters, and sugar pucker analysis. In addition to its evaluation, the nature of intermolecular interaction in these complexes was also analyzed using Morokuma decomposition. The gas phase interaction energies range between -5.2 and -20.6 kcal/mol and, in contrast to the H:S trans base pairs, show enhanced relative importance of the electron correlation component, indicative of the greater role of dispersion energy in stabilization of these base pairs. The rich variety of hydrogen bonding pattern, involving the flexible sugar edge, appears to hold the key to several features of structural motifs, such as planarity and propensity to participate in triplets, observed in this family of base pairs. This work explores these aspects by integrating database analysis, and detailed base pairing geometry analysis at the atomistic level, with ab initio computation of interaction energies. The study, involving alternative classification of base pairs and triplets, provides insights into intrinsic properties of these base pairs and their possible structural and functional roles.

Modeling the noncovalent interactions at the metabolite binding site in purine riboswitches

We present gas phase quantum chemical studies on the metabolite binding interactions in two important purine riboswitches, the adenine and guanine riboswitches, at the B3LYP/6-31G(d,p) level of theory. In order to gain insights into the strucutral basis of their discriminative abilities of regulating gene expression, the structural properties and binding energies for the gas phase optimized geometries of the metabolite bound binding pocket are analyzed and compared with their respective crystal geometries. Kitaura-Morokuma analysis has been carried out to calculate and decompose the interaction energy into various components. NBO and AIM analysis has been carried out to understand the strength and nature of binding of the individual aptamer bases with their respective purine metabolites. The Y74 base, U in case of adenine riboswitch and C in case of guanine riboswitch constitutes the only differentiating element between the two binding pockets. As expected, with W:W cis G:C74 interaction contributing more than 50% of the total binding energy, the interaction energy for metabolite binding as calculated for guanine (-46.43 Kcal/mol) is nearly double compared to the corresponding value for that of adenine (-24.73 Kcal/mol) in the crystal context. Variations in the optimized geometries for different models and comparison of relative contribution to metabolite binding involving four conserved bases reveal the possible role of U47:U51 W:H trans pair in the conformational transition of the riboswitch from the metabolite free to metabolite bound state. Our results are also indicative of significant contributions from stacking and magnesium ion interactions toward cooperativity effects in metabolite recognition.

On the role of Hoogsteen:Hoogsteen interactions in RNA: Ab initio investigations of structures and energies

We use a combination of database analysis and quantum chemical studies to investigate the role of cis and trans Hoogsteen:Hoogsteen (H:H) base pairs and associated higher-order structures in RNA. We add three new examples to the list of previously identified base-pair combinations belonging to these families and, in addition to contextual classification and characterization of their structural and energetic features, we compare their interbase interaction energies and propensities toward participation in triplets and quartets. We find that some base pairs, which are nonplanar in their isolated minimum energy geometries, attain planarity and stability upon triplet formation. A:A H:H trans is the most frequent H:H combination in RNA structures. This base pair occurs at many distinct positions in known rRNA structures, where it helps in the interaction of ribosomal domains in the 50S subunit. It is also present as a part of tertiary interaction in tRNA structures. Although quantum chemical studies suggest an intrinsically nonplanar geometry for this base pair in isolated form, it has the tendency to attain planar geometry in RNA crystal structures by forming higher-order tertiary interactions or in the presence of additional base-phosphate interactions. The tendency of this base pair to form such additional interactions may be helpful in bringing together different segments of RNA, thus making it suitable for the role of facilitator for RNA folding. This also explains the high occurrence frequency of this base pair among all H:H interactions.

Electronic tuning of fluorescent 8-aryl-guanine probes for monitoring DNA duplex–quadruplex exchange

In DNA-based diagnostics, duplex–quadruplex exchange is a common strategy for target detection using fluorescent probes that turn-on during the exchange process. Typical “label” detection platforms use emissive tags that are attached via linkers to the 5′- or 3′-ends of the oligonucleotide. Alternatively, “label-free” strategies employ fluorescent molecules that bind specifically to G-quadruplex structures with enhanced emission. Here, we report the utility of two internal fluorescent 8-aryl-2′-deoxyguanine probes (8-furyl-dG (FurdG) and 8-(4′′-cyanophenyl)-dG (CNPhdG)) for detecting G-quadruplex folding by the 15-mer (5′-GGTTG5G6TG8TGGTTGG) thrombin-binding aptamer (TBA). The 8-aryl-dG probes adopt a syn-conformation and were inserted into G5 (syn), G6 (anti) and G8 (TGT loop) of TBA to study their site-specific impact on duplex and G-quadruplex folding. Our studies show the ability of 8-aryl-dG probes to preferentially stabilize the G-quadruplex structure of TBA at G5 and their acceptance within the TG8T loop despite their syn-preference. Our studies also demonstrate how the choice of 8-aryl substituent can be used to tune probe electronics for turn-on fluorescence in the duplex or G-quadruplex structure. Overall, our studies establish 8-aryl-dG probes as useful tools for DNA-based diagnostics.

A Theoretical Study on Interaction of Small Gold Clusters Aun (n = 4, 6, 8) with xDNA Base Pairs

Abstract xDNA constitutes a novel class of size expanded synthetic nucleic acids in which one of the bases of the base pairs is larger than the natural DNA bases. These expanded bases are called x-bases. In this paper, we investigate the hydrogen bonding characteristics and relevant molecular properties of model complexes (xA…T)-Aun, (xT…A)-Aun, (xG…C)-Aun, and (xC…G)-Aun (n = 4, 6, 8) consisting of xDNA base pairs and gold clusters, in order to study the nature of gold-xDNA binding. We offer detailed characterization of their different aspects, viz., structural, electronic and spectroscopic, effect of gold cluster size, aromaticity, and planarity using quantum mechanics based density functional theory (DFT). Significant charge transfer is seen between the gold clusters and x-base pairs. Gold complexation is found to affect the interbase hydrogen bonding in these complexes. In addition to anchor bonds, X-H…Au type of hydrogen bonding interactions are also found to contribute to the gold-base pair binding in these complexes.

Structural and energetic characterization of the major DNA adduct formed from the food mutagen ochratoxin A in the NarI hotspot sequence: influence of adduct ionization on the conformational preferences and implications for the NER propensity

The nephrotoxic food mutagen ochratoxin A (OTA) produces DNA adducts in rat kidneys, the major lesion being the C8-linked-2′-deoxyguanosine adduct (OTB-dG). Although research on other adducts stresses the importance of understanding the structure of the associated adducted DNA, site-specific incorporation of OTB-dG into DNA has yet to be attempted. The present work uses a robust computational approach to determine the conformational preferences of OTB-dG in three ionization states at three guanine positions in the NarI recognition sequence opposite cytosine. Representative adducted DNA helices were derived from over 2160 ns of simulation and ranked via free energies. For the first time, a close energetic separation between three distinct conformations is highlighted, which indicates OTA-adducted DNA likely adopts a mixture of conformations regardless of the sequence context. Nevertheless, the preferred conformation depends on the flanking bases and ionization state due to deviations in discrete local interactions at the lesion site. The structural characteristics of the lesion thus discerned have profound implications regarding its repair propensity and mutagenic outcomes, and support recent experiments suggesting the induction of double-strand breaks and deletion mutations upon OTA exposure. This combined structural and energetic characterization of the OTB-dG lesion in DNA will encourage future biochemical experiments on this potentially genotoxic lesion.

Structural and biochemical impact of C8-aryl-guanine adducts within the NarI recognition DNA sequence: influence of aryl ring size on targeted and semi-targeted mutagenicity

Chemical mutagens with an aromatic ring system may be enzymatically transformed to afford aryl radical species that preferentially react at the C8-site of 2′-deoxyguanosine (dG). The resulting carbon-linked C8-aryl-dG adduct possesses altered biophysical and genetic coding properties compared to the precursor nucleoside. Described herein are structural and in vitro mutagenicity studies of a series of fluorescent C8-aryl-dG analogues that differ in aryl ring size and are representative of authentic DNA adducts. These structural mimics have been inserted into a hotspot sequence for frameshift mutations, namely, the reiterated G3-position of the NarI sequence within 12mer (NarI(12)) and 22mer (NarI(22)) oligonucleotides. In the NarI(12) duplexes, the C8-aryl-dG adducts display a preference for adopting an anti-conformation opposite C, despite the strong syn preference of the free nucleoside. Using the NarI(22) sequence as a template for DNA synthesis in vitro, mutagenicity of the C8-aryl-dG adducts was assayed with representative high-fidelity replicative versus lesion bypass Y-family DNA polymerases, namely, Escherichia coli pol I Klenow fragment exo− (Kf−) and Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). Our experiments provide a basis for a model involving a two-base slippage and subsequent realignment process to relate the miscoding properties of C-linked C8-aryl-dG adducts with their chemical structures.