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Molecular dynamics investigation of the double stranded oligonucleotide d(AT)6d(AT)6
Satoshi Fujii1, Noriaki Okimoto, Toshikazu Ebisuzaki
1Department of Applied Chemistry, Faculty of Engineering, Kyushu University, Fukuoka 812-8581, Japan.
Nucleic Acids Research. Supplement (2001)
|August 9, 2003
Abstract:
Molecular dynamics simulation of double stranded 12-meric oligonucleotide carrying an A and T alternating sequence, d(AT)6d(AT)6, over 1 ns was carried out under low NaCl conditions by using AMBER 6. It was found that the d(AT)6d(AT)6 was stabilized in the D-type structure which is an intermediate structure between A- and B-type ones and this result was in agreement with the previous report.