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Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Exploring a DNA Sequence for the Three-Dimensional Structure Determination of a Silver(I)-Mediated C-C Base Pair in a
Takenori Dairaku1, Kyoko Furuita2, Hajime Sato3
1a Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku , Sendai , Miyagi , Japan.
Abstract:
Recently, we discovered novel silver(I)-mediated cytosine-cytosine base pair (C-Ag(I)-C) in DNA duplexes. To understand the properties of these base pairs, we searched for a DNA sequence that can be used in NMR structure determination. After extensive sequence optimizations, a non-symmetric 15-base-paired DNA duplex with a single C-Ag(I)-C base pair flanked by 14 A-T base pairs was selected. In spite of its challenging length for NMR measurements (30 independent residues) with small sequence variation, we could assign most non-exchangeable protons (254 out of 270) and imino protons for structure determination.
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