Competition between the purine and pyrimidine triple helix motifs in an oligonucleotide system

Triple helices are classified into two groups according to the composition and orientation of the third strand, namely the pyrimidine motif and the purine motif. These motifs constitute two separate fields of research. It was proposed, based on the alternative design rules, that the two motifs can in fact lead to competing structures. An oligonucleotide system has been designed to demonstrate this competition. Systematic variation of its components give insight into the requirements for optimal binding of a third strand. A palindromic, homopyrimidine oligonucleotide of 22 bases was designed to form an overlapping 9-base, Watson-Crick (WC), duplex with a partly complementary 22-base purine-rich oligonucleotide. This leaves two free 3' extensions under conditions when only the duplex is stable. If the conditions, however, favour triplex formation the pyrimidine tail can compete with the purine-rich tail as third strand for the duplex forming Hoogsteen or reverse-Hoogsteen hydrogen bonding respectively with the purines in the WC double strand. The underlying triplexes and core duplex were synthesised and characterised as controls.

Grantor dc:publisher.institution

Department of Molecular and Cell Biology

Year dc:date.issued

1998

Author dc:creator

• Mills, Martin George

Advisor dc:contributor.advisor

• Klump, Horst

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/11427/17946

OAI identifier oai:identifier

oai:open.uct.ac.za:11427/17946