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Nucleosides, Nucleotides & Nucleic Acids Volume 34, 2015 - Issue 12
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Original Articles

Exploring a DNA Sequence for the Three-Dimensional Structure Determination of a Silver(I)-Mediated C-C Base Pair in a DNA Duplex By 1H NMR Spectroscopy

Takenori DairakuGraduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi, Japan
,
Kyoko FuruitaInstitute for Protein Research, Osaka University, Suita, Osaka, Japan
,
Hajime SatoBruker BioSpin K.K., Yokohama, Kanagawa, Japan
,
Yoshinori KondoGraduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi, Japan
,
Chojiro KojimaInstitute for Protein Research, Osaka University, Suita, Osaka, Japan
,
Akira OnoDepartment of Material & Life Chemistry, Kangawa University, Kanagawa-ku, Yokohama, Kanagawa, Japan
&
Yoshiyuki TanakaGraduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi, Japan;Laboratory of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, JapanCorrespondence[email protected]
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Pages 877-900 | Received 25 Aug 2015, Accepted 25 Aug 2015, Published online: 17 Nov 2015
 
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Abstract

Recently, we discovered novel silver(I)-mediated cytosine–cytosine base pair (C–AgI–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–AgI–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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