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A novel assay to determine the sequence preference and affinity of DNA minor groove binding compounds.

ABSTRACT: Sequence-specific binding in the minor groove of DNA by small molecules is a growing area of research with possible therapeutic relevance. By selectively binding to DNA sequences required by critical transcription factors, these small molecules could potentially modulate the expression levels of disease-causing genes. Precise targeting of a critical transcription factor of a selected gene requires an understanding of the preferred sequence of the DNA binding compound. As new compounds are being synthesized, there is a need to evaluate their DNA recognition profile. We sought to establish a procedure to determine sequence preference of compounds with previously unknown binding properties. A novel procedure for determining the optimal DNA binding sequence of minor groove binding compounds is described here. The assay also allows for determination of the binding affinity to a particular sequence.

SUBMITTER: Thomas R

PROVIDER: S-EPMC373301 | biostudies-literature | 2004

REPOSITORIES: biostudies-literature

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A novel assay to determine the sequence preference and affinity of DNA minor groove binding compounds.

Thomas Rita R Gonzalez Carolyn C Roberts Christopher C Botyanszki Janos J Lou Lillian L Michelotti Emil F EF

Nucleic acids research 20040112 1

Sequence-specific binding in the minor groove of DNA by small molecules is a growing area of research with possible therapeutic relevance. By selectively binding to DNA sequences required by critical transcription factors, these small molecules could potentially modulate the expression levels of disease-causing genes. Precise targeting of a critical transcription factor of a selected gene requires an understanding of the preferred sequence of the DNA binding compound. As new compounds are being ...[more]

PMID: 14718553

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