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Nucleic Acids Symposium Series 2000 44(1):261-262; doi:10.1093/nass/44.1.261
© 2000 by Oxford University Press
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Unnatural base pairs between 2-amino-6-(2-thienyl)purine and the complementary bases

Ichiro Hirao1, Tsuyoshi Fujiwara1, Michiko Kimoto2, Tsuneo Mitsui1, Taeko Okuni1, Takashi Ohtsuki3 and Shigeyuki Yokoyama1,2,3

1 Yokoyama CytoLogic Project, ERATO, JST, c/o RIKEN 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan, 2 Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, 3 Genomic Sciences Center, RIKEN 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan

The unnatural base, 2-amino-6-(2-thienyl)purine (designated as s), instead of 2-amino-6-(N,N-dimethylamino)purine (designated as x), was designed in order to improve the specificity and efficiency of the base pairing with pyridin-2-one (designated as y). DNA fragments containing s were chemically synthesized, and the thermal stability and the enzymatic reactions involving the s-y pairing were examined. Thermal denaturation experiments showed that the DNA duplex (12-mer) containing the s-y pair was more stable than that containing the x-y pair. The incorporation of dyTP was also more advantageous to the s-y pairing than the x-y pairing in single-nucleotide insertion experiments using the Klenow fragment of Escherichia coli DNA polymerase I.


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