Unknown

Dataset Information

0

Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe.


ABSTRACT: In site-directed spin labeling (SDSL), local structural and dynamic information is obtained via electron paramagnetic resonance (EPR) spectroscopy of a stable nitroxide radical attached site-specifically to a macromolecule. Analysis of electron spin dipolar interactions between pairs of nitroxides yields the inter-nitroxide distance, which provides quantitative structural information. The development of pulse EPR methods has enabled such distance measurements up to 70 A in bio-molecules, thus opening up the possibility of SDSL global structural mapping. This study evaluates SDSL distance measurement using a nitroxide (designated as R5) that can be attached, in an efficient and cost-effective manner, to a phosphorothioate backbone position at arbitrary DNA or RNA sequences. R5 pairs were attached to selected positions of a dodecamer DNA duplex with a known NMR structure, and eight distances, ranging from 20 to 40 A, were measured using double electron-electron resonance (DEER). The measured distances correlated strongly (R2 = 0.98) with the predicted values calculated based on a search of sterically allowable R5 conformations in the NMR structure, thus demonstrating accurate distance measurements using R5. Furthermore, distance measurement in a 42 kD DNA was demonstrated. The results establish R5 as a sequence-independent probe for global structural mapping of DNA and DNA-protein complexes.

SUBMITTER: Cai Q 

PROVIDER: S-EPMC1635252 | BioStudies | 2006-01-01

REPOSITORIES: biostudies

Similar Datasets

2015-01-01 | S-EPMC4641853 | BioStudies
2009-01-01 | S-EPMC2766618 | BioStudies
2007-01-01 | S-EPMC1959523 | BioStudies
1000-01-01 | S-EPMC1904292 | BioStudies
2020-01-01 | S-EPMC7187341 | BioStudies
2019-01-01 | S-EPMC6790680 | BioStudies
2012-01-01 | S-EPMC3382087 | BioStudies
2016-01-01 | S-EPMC5027493 | BioStudies
2009-01-01 | S-EPMC2799802 | BioStudies
2020-01-01 | S-EPMC7667596 | BioStudies