title: Probing triplex formation by EPR spectroscopy using a newly synthesized spin label for oligonucleotides.
abstract: Spin labels have been extensively used to study the dynamics of oligonucleotides. Spin labels that are more rigidly attached to a base in an oligonucleotide experience much larger changes in their range of motion than those that are loosely tethered. Thus, their electron paramagnetic resonance spectra show larger changes in response to differences in the mobility of the oligonucleotides to which they are attached. An example of this is 5-(2,2,5,5-tetramethyl-3-ethynylpyrrolidine-1-oxyl)-uridine (1). How ever, the synthesis of this modified DNA base is quite involved and, here, we report the synthesis of a new spin-labeled DNA base, 5-(2,2,6,6-tetramethyl-4-ethynylpiperidyl-3-ene-1-oxyl)-uridine (2). This spin label is readily prepared in half the number of steps required for 1, and yet behaves in a spectroscopically analogous manner to 1 in oligonucleotides. Finally, it is shown here that both spin labels 1 and 2 can be used to detect the formation of both double-stranded and triplex DNA.
authors.affiliation: West Virginia University, Department of Basic Pharmaceutical Sciences, PO Box 9530, Morgantown, WV 26506, USA. pgannett@hsc.wvu.edu
authors.forename: Peter M
authors.initials: PM
authors.lastname: Gannett
authors.forename: Eva
authors.initials: E
authors.lastname: Darian
authors.forename: Jeannine
authors.initials: J
authors.lastname: Powell
authors.forename: Edward M
authors.initials: EM
authors.lastname: Johnson
authors.forename: Claudius
authors.initials: C
authors.lastname: Mundoma
authors.forename: Nancy L
authors.initials: NL
authors.lastname: Greenbaum
authors.forename: Chris M
authors.initials: CM
authors.lastname: Ramsey
authors.forename: Naresh S
authors.initials: NS
authors.lastname: Dalal
authors.forename: David E
authors.initials: DE
authors.lastname: Budil
mesh_terms: D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis* / Q000737:chemistry* / Q000302:isolation & purification; D009943:Organophosphorus Compounds / Q000138:chemical synthesis / Q000737:chemistry; D013113:Spin Labels / Q000138:chemical synthesis*; D013696:Temperature
chemical_list: D009838:Oligodeoxyribonucleotides; D009943:Organophosphorus Compounds; D013113:Spin Labels; C434331:phosphoramidite; C051802:triplex DNA; D004247:DNA