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Nucleic Acids Res Suppl. 2002;(2):175-6.

Molecular dynamics investigation of the double stranded oligonucleotide d(AT)6d(AT)6.

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Department of Applied Chemistry, Faculty of Engineering, Kyushu University, Fukuoka 812-8581, Japan.


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.

[Indexed for MEDLINE]

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