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Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe.

ABSTRACT: This protocol describes the procedures for measuring nanometer distances in nucleic acids using a nitroxide probe that can be attached to any nucleotide within a given sequence. Two nitroxides are attached to phosphorothioates that are chemically substituted at specific sites of DNA or RNA. Inter-nitroxide distances are measured using a four-pulse double electron-electron resonance technique, and the measured distances are correlated to the parent structures using a Web-accessible computer program. Four to five days are needed for sample labeling, purification and distance measurement. The procedures described herein provide a method for probing global structures and studying conformational changes of nucleic acids and protein/nucleic acid complexes.

SUBMITTER: Qin PZ

PROVIDER: S-EPMC2430106 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature

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Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe.

Qin Peter Z PZ Haworth Ian S IS Cai Qi Q Kusnetzow Ana K AK Grant Gian Paola G GP Price Eric A EA Sowa Glenna Z GZ Popova Anna A Herreros Bruno B He Honghang H

Nature protocols 20070101 10

This protocol describes the procedures for measuring nanometer distances in nucleic acids using a nitroxide probe that can be attached to any nucleotide within a given sequence. Two nitroxides are attached to phosphorothioates that are chemically substituted at specific sites of DNA or RNA. Inter-nitroxide distances are measured using a four-pulse double electron-electron resonance technique, and the measured distances are correlated to the parent structures using a Web-accessible computer progr ...[more]

PMID: 17947978

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