© 2009 Oxford University Press
This article appears in the following Nucleic Acid Symposium Series issue: The 6th International Symposium on Nucleic Acids Chemistry (36th Symposium on Nucleic Acids Chemistry) [View the issue table of contents]
Interaction of silver ion with CG.C+ base triplets in DNA triplex
1Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan and 2PRESTO, Japan Science and Technology Agency, San-bancho Building, 3-5 Sanbancho, Chiyoda-ku, Tokyo 332-0012, Japan
*Corresponding author. E-mail: toshi{at}chem.kumamoto-u.ac.jp
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°C in melting temperature at pH 7. The triplex structure was stable even under weak basic conditions.