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Targeting DNA Secondary Structures

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DNA secondary structures containing regions of single-stranded DNA have now been identified in the genomic DNA of a number of prokaryotic and eukaryotic species, including humans. Many of these secondary structures are associated with regions of DNA involved in regulation of transcription: promoters or upstream elements. The secondary structures involved appear likely to be hairpin or cruciform structures that may be recognition sites for binding of transcription factors. In the case of the coliphage N4 virion RNA polymerase, a defined hairpin in the polymerase promoter necessary for binding of the polymerase and regulation of transcription has been shown to be extruded under physiological conditions in plasmid DNA. The presence of single-stranded DNA in the promoters of several species suggests that regulatory hairpins may be involved in transcription of a number of genes. In support of this, hairpin- or cruciform-binding proteins have been identified from several species. These results imply that secondary structures in regulatory regions may be targets for drugs that bind and either block or enhance binding of proteins involved in transcription. In this review, we discuss the evidence for DNA secondary structures, particularly hairpins and cruciforms, in genomic DNA and review the studies to date of development of small molecules that can selectively bind these structures.
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Keywords: DNA Secondary Structures; Drosophila; E coli; E coli DNA gyrase; HIV 1 nucleocapsid protein NC; HIV1 reverse transcripase activity; N4 virion RNA polymerase vRNAP; Prokaryotic; TFIIIA; actinomycin D; bacteriophage N4; biological systems; coliphage N4 virion RNA polymerase; cruciform structures; cruciformn binding proteins; dsDNA; duplex DNA dGGAATTCC2; eukartyotic species; genomic DNA; hairpin; hairpin interactive agents; malaria parasite P falciparum; nuclear factor I NFI; oxytricha nova tolemere binding protein; rRNA promoter; recognition sites; single stranded DNA; ssDNA; telomerase; telomeres; trancription factors; transcription regulation; xenopus kidney cell; zinc finger protein

Document Type: Review Article

Publication date: January 1, 2000

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  • Current Medicinal Chemistry covers all the latest and outstanding developments in medicinal chemistry and rational drug design. Each issue contains a series of timely in-depth reviews written by leaders in the field covering a range of the current topics in medicinal chemistry. Current Medicinal Chemistry is an essential journal for every medicinal chemist who wishes to be kept informed and up-to-date with the latest and most important developments.
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