title: Design and characterization of symmetric nucleic acids via molecular dynamics simulations.
abstract: Asymmetry (5'→3') associated with each strand of the deoxyribonucleic acid (DNA) is inherent in the sugar-phosphate backbone connectivity and is essential for replication and transcription. We note that this asymmetry is due to one single chemical bond (C3'to C2') in each nucleotide unit, and the absence of this bond results in directionally symmetric nucleic acids. We also discovered that creation of an extra chemical bond (C5'to C2') can lead to a symmetric backbone. Keeping their potential synthetic and therapeutic interest in mind, we designed a few novel symmetric nucleic acids. We investigated their conformational stability and flexibility via detailed all atom explicit solvent 100-ns long molecular dynamics simulations and compared the resulting structures with that of regular B-DNA. Quite interestingly, some of the symmetric nucleic acids retain the overall double helical structure indicating their potential for integration in physiological DNA without causing major structural perturbations.
authors.affiliation: Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.|Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
authors.forename: Pradeep
authors.initials: P
authors.lastname: Pant
authors.affiliation: Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.|Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
authors.forename: Saher
authors.initials: S
authors.lastname: Afshan Shaikh
authors.affiliation: Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.|Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.|Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
authors.forename: B
authors.initials: B
authors.lastname: Jayaram
mesh_terms: D001483:Base Sequence; D059371:DNA, B-Form / Q000138:chemical synthesis / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*
chemical_list: D059371:DNA, B-Form; D009696:Nucleic Acids
keywords: directionality; molecular dynamics; symmetric nucleic acids