Conformational diversity versus nucleic acid triplex stability, a combinatorial study

DOI
Publisher DOI
PubMed ID
11441024
Abstract
The stability of a triple helix formed between a DNA duplex and an incoming oligonucleotide strand strongly depends on the solvent conditions and on intrinsic chemical and conformational factors. Attempts to increase triple helix stability in the past included chemical modification of the backbone, sugar ring, and bases in the third strand. However, the predictive power of such modifications is still rather poor. We therefore developed a method that allows for rapid screening of conformationally diverse third strand oligonucleotides for triplex stability in the parallel pairing motif to a given DNA double helix sequence. Combinatorial libraries of oligonucleotides of the requisite (fixed) base composition and length that vary in their sugar unit (ribose or deoxyribose) at each position were generated. After affinity chromatography against their corresponding immobilized DNA target duplex, utilizing a temperature gradient as the selection criterion, the oligonucleotides forming the most stable triple helices were selected and characterized by physicochemical methods. Thus, a series of oligonucleotides were identified that allowed us to define basic rules for triple helix stability in this conformationally diverse system. It was found that ribocytidines in the third strand increase triplex stability relative to deoxyribocytidines independently of the neighboring bases and position along the strand. However, remarkable sequence-dependent differences in stability were found for (deoxy)thymidines and uridines
Date Issued
2001
Publication Type
Article
Subject(s)
Subjects
ACID
backbone
base
bases
combinatorial
DNA
double
duplex
DUPLEXES
helix
methods
motif
oligonucleotide
Oligonucleotides
parallel
physicochemical
stability
sugar
Temperature
triple
triple helix
Triplex
Language(s)
en
Author(s)
Bernal-Méndez, E.
Additional Credits
Journal
Journal of biological chemistry
Publisher
American Society for Biochemistry and Molecular Biology
ISSN
0021-9258
Access(Rights)
restricted
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