title: The models of proton assisted and the unassisted formation of CGC base triplets.
abstract: The triple helix is formed by combining a double and a single strand DNAs in low pH and dissociates in high pH. Under such conditions, protonation of cytosine in the single strand is necessary for triplex formation where cytosine-guanine-cytosine (CGC+) base triplet stabilizes the triple helix. The mechanism of CGC+ triplet formation from guanine-cytosine (GC) and a protonated cytosine (C+) shows the importance of N3 proton. Similarly in the case of CGC (unprotonated) triplet, the donor acceptor H-bond at N3 hydrogen of the cytosine analog (C) initiates the interaction with GC. The correspondence between the two models of triplets, CGC+ and CGC, unambiguously assigned that protonation at N3 cytosine in low pH to be the first step in triplet formation, but a donor acceptor triplet (CGC) can be designed without involving a proton in the Hoogsteen H-bond. Further, the bases of cytosine analogue also show the capability of forming Watson Crick (WC) H-bonds with guanine.
authors.affiliation: Chemistry Department, Gauhati University, Guwahati-781014, India. chitrani@satyam.net.in
authors.forename: Chitrani
authors.initials: C
authors.lastname: Medhi
mesh_terms: D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D011522:Protons
chemical_list: D011522:Protons; D004247:DNA