Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation.

Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation. Research Abstract Details 

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Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation. Abstract Text:

Rigid spin-labeled nucleoside C, an analog of deoxycytidine that base-pairs with deoxyguanosine, was incorporated into DNA oligomers by chemical synthesis. Thermal denaturation experiments and circular dichroism (CD) measurements showed that C has a negligible effect on DNA duplex stability and conformation. Nucleoside C was incorporated into several positions within single-stranded DNA oligomers that can adopt two hairpin conformations of similar energy, each of which contains a four-base loop. The relative mobility of nucleotides in the alternating C/G hairpin loops, 5'-d(GCGC) and 5'-d(CGCG), was determined by electron paramagnetic resonance (EPR) spectroscopy. The most mobile nucleotide in the loop is the second one from the 5'-end, followed by the third, first and fourth nucleotides, consistent with previous NMR studies of DNA hairpin loops of different sequences. The EPR hairpin data were also corroborated by fluorescence spectroscopy using oligomers containing reduced C (C(f)), which is fluorescent. Furthermore, EPR spectra of duplex DNAs that contained C at the end of the helix showed features that indicated dipolar coupling between two spins. These data are consistent with end-to-end duplex stacking in solution, which was only observed when G was paired to C, but not when C was paired with A, C or T.

Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation. Publishing Authors By Initials

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Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: Nucleic acids research

VOLUME: 36

Page Numbers: 5946-54

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ISSN: 1362-4962

DAY: 19

MONTH: 09

YEAR: 2008

Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation. Information

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LANGUAGE: eng

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Grant and Affiliation Information for Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation.

AFFILIATION: University of Iceland, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland and Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA.

Country: England

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MEDLINETA: Nucleic Acids Res

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