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Nucleic Acids Research, 2002, Vol. 30, No. 3 749-758
© 2002 Oxford University Press

The high binding affinity of phosphorothioate-modified oligomers for Ff gene 5 protein is moderated by the addition of C-5 propyne or 2'-O-methyl modifications

Tung-Chung Mou and Donald M. Gray*

Department of Molecular and Cell Biology, Mail Stop FO31, The University of Texas at Dallas, PO Box 830688, Richardson, TX 75083-0688, USA

One of the problems that hamper the use of antisense DNAs as effective drugs is the non-specific binding of chemically-modified oligonucleotides to cellular proteins. We previously showed that the affinity of a model ssDNA-binding protein, the Ff gene 5 protein (g5p), was >300-fold higher for phosphorothioate-modified DNA (S-DNA) than for unmodified dA36, consistent with the propensity of S-DNA to bind indiscriminately to proteins. The current work shows that g5p binding is also sensitive to sugar and pyrimidine modifications used in antisense oligomers. Binding affinities of g5p for 10 36mer oligomers were quantitated using solution circular dichroism measurements. The oligomers contained C-5-propyne (prC), 2'-O-methyl (2'-O-Me) or 2'-OH (RNA) groups, alone or combined with the phosphorothioate modification. In agreement with reported increases in antisense activity, the addition of prC or 2'-O-Me modifications substantially reduced the affinity of oligomers for g5p by ~2-fold compared with the same DNA oligomer sequences containing only phosphorothioate linkages. That is, such modifications moderated the propensity of the phosphorothioate group to bind tightly to the g5p. The Ff g5p could be a useful model protein for assessing non-specific binding effects of antisense oligomer modifications.

* To whom correspondence should be addressed. Tel: +1 972 883 2513; Fax: +1 972 883 2409; Email: dongray{at}utdallas.edu


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B. H. Yoo, E. Bochkareva, A. Bochkarev, T.-C. Mou, and D. M. Gray
2'-O-methyl-modified phosphorothioate antisense oligonucleotides have reduced non-specific effects in vitro
Nucleic Acids Res., April 2, 2004; 32(6): 2008 - 2016.
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