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Nucleic Acids Research Advance Access originally published online on November 5, 2008
Nucleic Acids Research 2008 36(22):7009-7018; doi:10.1093/nar/gkn843
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Nucleic Acids Research, 2008, Vol. 36, No. 22 7009-7018
© 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.

Chemistry and Synthetic Biology

Derivatization of DNAs with selenium at 6-position of guanine for function and crystal structure studies

Jozef Salon, Jiansheng Jiang, Jia Sheng, Oksana O. Gerlits and Zhen Huang*

Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA

*To whom correspondence should be addressed. Tel: +1 404 413 5535; Fax: +1 404 413 5505; Email: huang{at}gsu.edu

Received September 16, 2008. Accepted October 14, 2008.

To investigate nucleic acid base pairing and stacking via atom-specific mutagenesis and crystallography, we have synthesized for the first time the 6-Se-deoxyguanosine phosphoramidite and incorporated it into DNAs via solid-phase synthesis with a coupling yield over 97%. We found that the UV absorption of the Se-DNAs red-shifts over 100 nm to 360 nm ({varepsilon} = 2.3 x 104 M–1 cm–1), the Se-DNAs are yellow colored, and this Se modification is relatively stable in water and at elevated temperature. Moreover, we successfully crystallized a ternary complex of the Se-G-DNA, RNA and RNase H. The crystal structure determination and analysis reveal that the overall structures of the native and Se-modified nucleic acid duplexes are very similar, the selenium atom participates in a Se-mediated hydrogen bond (Se ... H–N), and the SeG and C form a base pair similar to the natural G–C pair though the Se-modification causes the base-pair to shift (approximately 0.3 Å). Our biophysical and structural studies provide new insights into the nucleic acid flexibility, duplex recognition and stability. Furthermore, this novel selenium modification of nucleic acids can be used to investigate chemogenetics and structure of nucleic acids and their protein complexes.


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