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PubMed · 1418737

Strong binding of single-stranded DNA by stem-loop oligonucleotides.

D J D'Souza·E T Kool
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Abstract

We report that oligodeoxynucleotides which form stem-loop hairpin structures and which have pyrimidine-rich loops can form strong complexes with complementary single-stranded DNA sequences. Stem-loop oligonucleotides were constructed with a 25-nt T-rich loop and with variable Watson-Crick stems. The complexes of these oligomers with the sequence dA8 were studied by thermal denaturation. Evidence is presented that the complexes are one-to-one, bimolecular complexes in which the pyrimidine loop bases comprise the outer strands in a pyr.pur.pyr triplex, in effect chelating the purine strand in the center of the loop. Melting temperatures for the loop complexes are shown to be up to 29 degrees C higher than Watson-Crick duplex of the same length. It is shown that the presence of a stem increases stability of the triplex relative to an analogous oligomer without a stem. The effect of stem length on the stability of such a complex is examined. Such hairpin oligomers represent a new approach to the sequence-specific binding of single-stranded RNA and DNA. In addition, the finding raises the possibility that such a complex may exist in natural RNA folded sequences.

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Base SequenceDNA, Single-StrandedHot TemperatureMolecular Sequence DataNucleic Acid ConformationNucleic Acid DenaturationOligodeoxyribonucleotidesJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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D J D'Souza, E T Kool. 1992. Strong binding of single-stranded DNA by stem-loop oligonucleotides.. https://doi.org/10.1080/07391102.1992.10508634

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