Interaction of silver ion with CG.C+ base triplets in DNA triplex.

Abstract

When designing ligands for specific sequences in DNA duplexes, triple helix formation is a useful recognition motif, because base triplet formation is based on the simple rule of complementary Hoogsteen hydrogen bonding, CG.C(+) and TA.T. However the triplexes containing CG.C(+) triplets form only in a weak acidic solution, because cytosines in third strand need to be protonated to satisfy its complementarity to CG base-pairs. A simple and easy method to stabilize the DNA triplex using Ag(+) was reported. A silver ion displaces the N3 proton of cytosine in Hoogsteen base-pairing to form a base triplet, CG.CAg(+). By the addition of an equimolar amount of Ag(+), the third strand 15 mer sequence containing five cytosines was stabilized by ca. 30 degrees C in melting temperature at pH 7. The triplex structure was stable even under weak basic conditions.