Conformational diversity versus nucleic acid triplex stability, a combinatorial study

Bernal-Méndez, E.; Leumann, Christian (2001). Conformational diversity versus nucleic acid triplex stability, a combinatorial study. Journal of biological chemistry, 276(38), pp. 35320-35327. American Society for Biochemistry and Molecular Biology 10.1074/jbc.M105794200

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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

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP)

UniBE Contributor:

Leumann, Christian


500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry




American Society for Biochemistry and Molecular Biology




Christian Leumann

Date Deposited:

19 May 2015 12:59

Last Modified:

05 Dec 2022 14:47

Publisher DOI:


PubMed ID:


Uncontrolled Keywords:

ACID backbone base bases combinatorial DNA double duplex DUPLEXES helix methods motif oligonucleotide Oligonucleotides parallel physicochemical stability sugar Temperature triple triple helix Triplex




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