Geometry and energetics of DNA basepairs and triplets from first principles quantum molecular relaxations

Density-functional tight-binding: basic concepts and applications to molecules and clusters

The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.

Cooperative vibrational properties of hydrogen bonds in Watson–Crick DNA base pairs

For the AT pair, Symst and Strech peaks further shift toward the red, giving the H-bonds an amplified effect (orange arrows).

PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition

The pseudo oligonucleotide composition, or pseudo K-tuple nucleotide composition (PseKNC), can be used to represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides. Therefore, the PseKNC approach may hold very high potential for enhancing the power in dealing with many problems in computational genomics and genome sequence analysis. However, dealing with different DNA or RNA problems may need different kinds of PseKNC. Here, we present a flexible and user-friendly web server for PseKNC (at http://lin.uestc.edu.cn/pseknc/default.aspx) by which users can easily generate many different modes of PseKNC according to their need by selecting various parameters and physicochemical properties. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to generate their desired PseKNC without the need to follow the complicated mathematical equations, which are presented in this article just for the integrity of PseKNC formulation and its development. It is anticipated that the PseKNC web server will become a very useful tool in computational genomics and genome sequence analysis.

Targeting duplex DNA with chimeric α,β-triplex-forming oligonucleotides

Triplex-directed DNA recognition is strictly limited by polypurine sequences. In an attempt to address this problem with synthetic biology tools, we designed a panel of short chimeric α,β-triplex-forming oligonucleotides (TFOs) and studied their interaction with fluorescently labelled duplex hairpins using various techniques. The hybridization of hairpin with an array of chimeric probes suggests that recognition of double-stranded DNA follows complicated rules combining reversed Hoogsteen and non-canonical homologous hydrogen bonding. In the presence of magnesium ions, chimeric TFOs are able to form highly stable α,β-triplexes, as indicated by native gel-electrophoresis, on-array thermal denaturation and fluorescence-quenching experiments. CD spectra of chimeric triplexes exhibited features typically observed for anti-parallel purine triplexes with a GA or GT third strand. The high potential of chimeric α,β-TFOs in targeting double-stranded DNA was demonstrated in the EcoRI endonuclease protection assay. In this paper, we report, for the first time, the recognition of base pair inversions in a duplex by chimeric TFOs containing α-thymidine and α-deoxyguanosine.

Self Consistent-Charge Density-Functional Tight-Binding Method for Simulations of Biological Molecules

We apply a self-consistent charge tight-binding scheme to biomolecules. This method has been shown to give a reliable description of reaction energies, geometries and vibrational frequencies of small organic molecules. We discuss the performance of this method for model peptides and non-bonding interactions in biologically relevant molecular complexes. A comparison with semi-empirical methods and ab initio calculations will be given for DNA base pair H-bonding and stacking interactions.

Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: application to polycyclic aromatic hydrocarbon clusters

The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.

Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum

A method is presented to computationally identify core promoters in the Plasmodium falciparum genome using only DNA physicochemical properties.

Little is known about the structure and distinguishing features of core promoters in Plasmodium falciparum. In this work, we describe the first method to computationally identify core promoters in this AT-rich genome. This prediction algorithm uses solely DNA physicochemical properties as descriptors. Our results add to a growing body of evidence that a physicochemical code for eukaryotic genomes plays a crucial role in core promoter recognition.

Study of the hydrogen bond in different orientations of adenine-thymine base pairs: an ab initio study

In order to gain deeper insight into structure, charge distribution, and energies of A-T base pairs, we have performed quantum chemical ab initio and density functional calculations at the HF (Hartree-Fock) and B3LYP levels with 3-21G*, 6-31G*, 6-31G**, and 6-31++G** basis sets. The calculated donor-acceptor atom distances in the Watson-Crick A-T base pair are in good agreement with the experimental mean values obtained from an analysis of 21 high resolution DNA structures. In addition, for further correction of interaction energies between adenine and thymine, the basis set superposition error (BSSE) associated with the hydrogen bond energy has been computed via the counterpoise method using the individual bases as fragments. In the Watson-Crick A-T base pair there is a good agreement between theory and experimental results. The distances for (N2...H23-N19), (N8-H13...O24), and (C1...O18) are 2.84, 2.94, and 3.63 A, respectively, at B3LYP/6-31G** level, which is in good agreement with experimental results (2.82, 2.98, and 3.52 A). Interaction energy of the Watson-Crick A-T base pair is -13.90 and -10.24 kcal/mol at B3LYP/6-31G** and HF/6-31G** levels, respectively. The interaction energy of model (9) A-T base pair is larger than others, -18.28 and -17.26 kcal/mol, and for model (2) is the smallest value, -13.53 and -13.03 kcal/mol, at B3LYP/6-31G** and B3LYP/6-31++G** levels, respectively. The computed B3LYP/6-31G** bond enthalpies for Watson-Crick A-T pairs of -14.4 kcal/mol agree well with the experimental results of -12.1 kcal/mol deviating by as little as -2.3 kcal/mol. The BSSE of some cases is large (9.85 kcal/mol) and some is quite small (0.6 kcal/mol).

Hydrogen-bonded trimers of DNA bases and their interaction with metal cations: ab initio quantum-chemical and empirical potential study

Neutral (G.GC, A.AT, G.AT, T.AT, and C(imino).GC) and protonated (CH+.GC and AH+.GC) hydrogen-bonded trimers of nucleic acid bases were characterized by ab initio methods with the inclusion of electron correlation. In addition, the influence of metal cations on the third-strand binding in Purine-Purine-Pyrimidine (Pu.PuPy) reverse-Hoogsteen triplets has been studied. The ab initio calculations were compared with those from recently introduced force fields (AMBER4.1, CHARMM23, and CFF95). The three-body term in neutral trimers is mostly negligible, and the use of empirical potentials is justified. The only exception is the neutral G.GC Hoogsteen trimer with a three-body term of -4 kcal/mol. Protonated trimers are stabilized by molecular ion-molecular dipole attraction and the interaction within the complex is nonadditive, with the three-body term on the order of -3 kcal/mol. There is a significant induction interaction between the third-strand protonated base and guanine. The calculations indicate an enhancement of the third-strand binding in the G.GC reverse-Hoogsteen trimer due to-metal cation coordination to the N7/O6 position of the third-strand guanine. Interactions between metal cations and complexes of DNA bases are in general highly non-additive; the three-body term is above-10 kcal/mol in a complex of a divalent cation (Ca2+) with the GG reverse-Hoogsteen pair. The pairwise additive empirical potentials qualitatively underestimate the binding energy between cation and base.