title: Oligodeoxynucleotides containing 3-bromo-3-deazaadenine and 7-bromo-7-deazaadenine 2'-deoxynucleosides as chemical probes to investigate DNA-protein interactions.
abstract: We describe the design and proof of concept of a pair of chemical probes for investigating DNA-protein interactions-specifically, the incorporation of 7-bromo-7-deazaadenine and 3-bromo-3-deazaadenine 2'-deoxynucleosides (Br(7)C(7)dA and Br(3)C(3)dA) into oligodeoxynucleotides (ODNs)-and their utility. Whereas the bromo substituent of the Br(7)C(7)dA unit in an ODN duplex acts sterically to inhibit binding with NF-kappaB, which interacts with the duplex in its major groove, the bromo substituent of the Br(3)C(3)dA unit acts sterically to inhibit binding with RNase H, which interacts with the duplex in its minor groove. In addition, the utilization of ODNs containing 7-deazaadenine and 3-deazaadenine 2'-deoxynucleosides (C(7)dA and C(3)dA), together with the pair of chemical probes, afforded valuable information on the requirement for nitrogen atoms located in either the major or minor grooves. Accordingly, we were able to show the utility of ODNs containing Br(7)C(7)dA, Br(3)C(3)dA, C(7)dA, and C(3)dA for the investigation of DNA-protein interactions.
authors.affiliation: Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
authors.forename: Noriaki
authors.initials: N
authors.lastname: Minakawa
authors.forename: Yuri
authors.initials: Y
authors.lastname: Kawano
authors.forename: Shunpei
authors.initials: S
authors.lastname: Murata
authors.forename: Naonori
authors.initials: N
authors.lastname: Inoue
authors.forename: Akira
authors.initials: A
authors.lastname: Matsuda
mesh_terms: D000225:Adenine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D015335:Molecular Probes; D009841:Oligonucleotides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*
chemical_list: D015335:Molecular Probes; D009841:Oligonucleotides; D011506:Proteins; D004247:DNA; D000225:Adenine