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We have prepared oligonucleotides containing the novel base analogue 2'-aminoethoxy,5-propargylamino-U in place of thymidine and examined their ability to form intermolecular and intramolecular triple helices by DNase I footprinting and thermal melting studies. The results were compared with those for oligonucleotides containing 5-propargylamino-dU and 2'-aminoethoxy-T. We find that the bis-substituted derivative produces a large increase in triplex stability, much greater than that produced by either of the monosubstituted analogues, which are roughly equipotent with each other. Intermolecular triplexes with 9-mer oligonucleotides containing three or four base modifications generate footprints at submicromolar concentrations even at pH 7.5, in contrast to the unmodified oligonucleotide, which failed to produce a footprint at pH 5.0, even at 30 microM. UV- and fluorescence melting studies with intramolecular triplexes confirmed that the bis-modified base produces a much greater increase in T(m) than either modification alone.

Type

Journal article

Journal

Biochemistry

Publication Date

11/06/2002

Volume

41

Pages

7224 - 7231

Keywords

Azo Compounds, DNA, DNA Footprinting, Deoxyribonuclease I, Deoxyuridine, Fluorescein, Nucleic Acid Conformation, Nucleic Acid Denaturation, Oligonucleotides, Pargyline, Propylamines, Spectrometry, Fluorescence, Ultraviolet Rays