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Nucleic Acids Symposium Series 2007 51(1):71-72; doi:10.1093/nass/nrm036
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© 2007 Oxford University Press

The base-pairing ability of the base pair-mimic nucleosides

Shu-ichi Nakano1, Kazuya Uenishi2, Masayuki Fujii2,3 and Naoki Sugimoto1,4,*

1Frontier Institute for Biomolecular Engineering Research (FIBER), and
2Molecular Engineering Institute, and
3Department of Environmental and Biological Chemistry, Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka 80-8555, Japan
4Department of Chemistry, Faculty of Science and Engineering, Konan University, 8–9–1 Okamoto, Higashinada–ku, Kobe 658–8501, Japan, and

*Naoki Sugimoto. E-mail: sugimoto{at}konan-u.ac.jp

Abstract

The deoxyadenosine derivative tethering the phenyl group at N6 of deoxyadenosine (Aphe) was previously found to have a property to stack strongly with adjacent nucleotide bases in a DNA duplex. On the other hand, it was also demonstrated that DNA polymerases selectively incorporated dTTP opposite Aphe in a template DNA strand. These observations suggest that the conformation of Aphe in solution differs from that during the DNA polymerase reaction. Here, the chemical modifications of thymine bases in a DNA duplex by KMnO4 and CMCT (1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate) were examined, and it was revealed that the thymine base opposite Aphe was efficiently flipped out of the DNA helix as much as that in a single-stranded DNA.


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