Physico-chemical fingerprinting of RNA genes

Abstract

We advance here a novel concept for characterizing different classes of RNA genes on the basis of physico-chemical properties of DNA sequences. As knowledge-based approaches could yield unsatisfactory outcomes due to limitations of training on available experimental data sets, alternative approaches that utilize properties intrinsic to DNA are needed to supplement training based methods and to eventually provide molecular insights into genome organization. Based on a comprehensive series of molecular dynamics simulations of Ascona B-DNA consortium, we extracted hydrogen bonding, stacking and solvation energies of all combinations of DNA sequences at the dinucleotide level and calculated these properties for different types of RNA genes. Considering ∼7.3 million mRNA, 255 524 tRNA, 40 649 rRNA (different subunits) and 5250 miRNA, 3747 snRNA, gene sequences from 9282 complete genome chromosomes of all prokaryotes and eukaryotes available at NCBI, we observed that physico-chemical properties of different functional units on genomic DNA differ in their signatures.

Towards a universal structural and energetic model for prokaryotic promoters

“…The values for three energy parameters viz. Hydrogen bond energy, stacking energy and solvation energy for the unique ten dinucleotide steps was done as reported in our previous work (27). Profile plotting of sequences: The plotting was performed using MATLAB software.…”

“…Last few decades have witnessed a revolutionary evolution in the analysis of nucleic acids structure (12)(13)(14)(15)(16)(17)(18)(19)(20). We have previously reported that hydrogen bond, stacking and solvation energy show clear signatures of functional densities of DNA sequences (21)(22)(23)(24)(25)(26)(27).…”

“…For the present study, we proceeded with nine backbone, eight inter-base pair (inter-BP), six intra-base pair (intra-BP), five base pair-axis (BP-axis), and three energetic properties adding to a total of thirty one parameters for exploring the genomic regions comprising primary TSSs, of twelve microorganisms (belonging to both kingdoms-archea and eubacteria, of prokaryotes). Numeric values of conformational parameters for the unique di-nucleotides steps were obtained from crystal structures of B-DNA only (from nucleic acid database (NDB) using curves+ (17), while in-house programs were used for energy parameters (27). Here, we report that these parameters provide unique structural and energetic signatures at TSSs.…”

Toward a Universal Structural and Energetic Model for Prokaryotic Promoters

“…The last few decades have witnessed a revolutionary evolution in the analysis of nucleic acids' structure (12)(13)(14)(15)(16)(17)(18)(19)(20). We have previously reported that hydrogen-bond, stacking, and solvation energy show clear signatures of functional densities of DNA sequences (21)(22)(23)(24)(25)(26)(27).…”

“…For our study, we proceeded with nine backbone, eight interbasepair (inter-BP), six intrabasepair (intra-BP), five basepair axis (BP axis), and three energetic properties, adding to a total of 31 parameters, for exploring the genomic regions comprising primary TSSs of 12 microorganisms (belonging to both kingdoms, Archaea and Eubacteria, of prokaryotes). Numeric values of conformational parameters for the unique dinucleotides steps were obtained from crystal structures of B-DNA only (from the Nucleic Acid Database using Curvesþ (17)), whereas in-house programs were used for energy parameters (27). Here, we report that these parameters provide unique structural and energetic signatures at TSSs.…”