Skip Navigation

This Article
Right arrow Print PDF (2658K)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (32)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Vo, T.
Right arrow Articles by Kool, E. T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Vo, T.
Right arrow Articles by Kool, E. T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 1995, Vol. 23, No. 15 2937-2944
© 1995

CHEMISTRY

Targeting pyrimidine single strands by triplex formation: structural optimization of binding

Thuong Vo, Shaouhui Wang and Erich T. Kool*

Department of Chemistry, University of Rochester Rochester, NY 14627, USA

*To Whom correspondence should be addressed

Received April 17, 1995. Accepted June 19, 1995.

Recent reports describe a new strategy for the binding of single-stranded pyrimidine sequences by triple helix formation. In this approach, a double-length purine-rich oligonucleotide binds a target strand, folding back to form an antiparallel pur pur pyr triple helix. We now describe a series of studies in which sequence and structural variations are made in such purine-rich llgands, in an effort to optimize binding properties. Comparison is made between the use of two separate strands and the use of single two-domain ligands; the latter are found to bind more tightly and to aggregate less in media containing Na+ or K+. Placement of mismatched bases in the target shows that sequence selectivity of binding is as high as that for Watson-Crick duplex formation. Variation of the lengths and sequences of loops bridging the binding domains demonstrates that dlnucleotide loops composed of pyrimidines give the highest stability. Oligoethylene glycol-derived loop replacements are shown to give good binding affinity as well. The binding of an RNA target is shown to occur with the same affinity as the binding of DNA. In general, it is found that circular variants bind more tightly than do either separate strands or singly-linked ligands and unlike linear oligomers, the circular compounds do not aggregate to a large extent even in buffers containing 100 mM K+. Such structurally optimized ligands are useful in expanding the number of possible naturally-occurring sequences which can be targeted by triplex formation.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
S. Ivanov, Y. Alekseev, J.-R. Bertrand, C. Malvy, and M. B. Gottikh
Formation of stable triplexes between purine RNA and pyrimidine oligodeoxyxylonucleotides
Nucleic Acids Res., July 15, 2003; 31(14): 4256 - 4263.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. A. Stewart, X. Xu, S. D. Thomas, and D. M. Miller
Acridine-modified, clamp-forming antisense oligonucleotides synergize with cisplatin to inhibit c-Myc expression and B16-F0 tumor progression
Nucleic Acids Res., June 1, 2002; 30(11): 2565 - 2574.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.