New Approaches to Drug-DNA Interactions Based on Graphical Representation and Numerical Characterization of DNA Sequences

Ashesh      Nandy; Subhash      C. Basak

Abstract

Graphical representations of DNA sequences is a new field of analysis of the DNA and RNA sequences that have the potential to be of utility in determination of drug-DNA interaction sites and also yield indexation schemes to quantify levels of potency or toxicity of various chemicals and drugs. In this paper we explain the new techniques of analysis and briefly review some of the applications that have been made relevant to the field of drug design and chemical toxicity measures specifically in relation to DNA and RNA sequences. The review concludes with some remarks on the future directions that could be taken in development and applications of this nascent technique.

Keywords: Numerical characterization, Graphical representation, base distribution characteristics, DNA sequence, drug design, drug-DNA interface, chemical toxicity, toxicity indexes, DNA replication, transcription, maintenance, proliferation, non-promoter sequences, thermodynamic, kinetic characteristics of the interactions, structure-activity relationship models, nuclear magnetic resonance, light scattering experiments, computational techniques, screening of new DNA binding drugs, exonuclease digestion, carbazole dications, DNA minor groove, lock-andkey, rational drug design, microRNAs, non-protein-coding RNAs, colon cancer, biomarker research, Quantitative structure-activity relationships (QSAR), quantitative structure-property relationships (QSPR), binding affinities, stable ring-structure, anti-tumour activity, mutant strains, pathogenic organisms, drug-resistant pathogens, The Open Source Drug Discovery (OSDD), genetic, biological information, 3D model, RNA secondary structures, phylogenetic studies, proteomics studies, Cartesian coordinate system, cytosine, nucleotides, “worm” curve, spectrum-like, 2D approach, bio-descriptors, accidental degeneracy, base mutations, exon sequence, beta-globin gene, nucleotide sequences, antibiotics, human diseases, Acute Respiratory Syndrome, coronavirus, generate phylogenetic, multiple alignments, mouse chromosomal sequences, protein serum profiles, interaction, neuraminidase inhibitors, target macromolecule, Ligand, Macromolecule, integrated QSAR, Viral genomes, Phylogenetic relationships, hydrophobic chemical group, polar chemical group, phylogenetic tree, avian flu strains, neuraminidase gene, convex blob linked, hemagglutinin type, influenza genomes, pandemic