title: Conformational feasibility of a DNA hairpin with one-base loop.
abstract: Molecular dynamics calculations and energy minimizations have been used to provide a conformational rationale for a DNA hairpin (5'-d-C1A2G3C4T5G6C7T8G9) with one-base (T5) loop. The loop forms a "closed" structure in which the base, T5 of the loop, is turned towards the center of the loop. The base, T5, is partially stacked upon G6 at the 3'-side of the loop. The bases flanking T5, C4 and C6 are held together by usual Watson-Crick base-pairing with a high buckle angle of 25.78 degrees. The Cl'-C1' distance for the base-pairs in the stem of the hairpin are as expected in the case of a B-DNA conformation.
authors.affiliation: Chemical Physics Group, Tata Institute of Fundemental Research, Bombay, India.
authors.forename: S R
authors.initials: SR
authors.lastname: Bhaumik
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D005240:Feasibility Studies; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D009838:Oligodeoxyribonucleotides; D004247:DNA