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Nucleic Acids Research Advance Access originally published online on February 5, 2008
Nucleic Acids Research 2008 36(6):1805-1812; doi:10.1093/nar/gkn011
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Nucleic Acids Research, 2008, Vol. 36, No. 6 1805-1812
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Unexpected A-form formation of 4'-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance

Akimasa Matsugami1, Takako Ohyama1, Masashi Inada1, Naonori Inoue2, Noriaki Minakawa2, Akira Matsuda2 and Masato Katahira1,3,*

1Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, 2Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812 and 3JST, PRESTO, Japan

*To whom correspondence should be addressed. Tel: +81 45 508 7213; Fax: +81 45 508 7361; Email: katahira{at}tsurumi.yokohama-cu.ac.jp

Received November 28, 2007. Revised January 8, 2008. Accepted January 8, 2008.

Fully modified 4'-thioDNA, an oligonucleotide only comprising 2'-deoxy-4'-thionucleosides, exhibited resistance to an endonuclease, in addition to preferable hybridization with RNA. Therefore, 4'-thioDNA is promising for application as a functional oligonucleotide. Fully modified 4'-thioDNA was found to behave like an RNA molecule, but no details of its structure beyond the results of circular dichroism analysis are available. Here, we have determined the structure of fully modified 4'-thioDNA with the sequence of d(CGCGAATTCGCG) by NMR. Most sugars take on the C3'-endo conformation. The major groove is narrow and deep, while the minor groove is wide and shallow. Thus, fully modified 4'-thioDNA takes on the A-form characteristic of RNA, both locally and globally. The only structure reported for 4'-thioDNA showed that partially modified 4'-thioDNA that contained some 2'-deoxy-4'-thionucleosides took on the B-form in the crystalline form. We have determined the structure of 4'-thioDNA in solution for the first time, and demonstrated unexpected differences between the two structures. The origin of the formation of the A-form is discussed. The remarkable biochemical properties reported for fully modified 4'-thioDNA, including nuclease-resistance, are rationalized in the light of the elucidated structure.


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