Pulsed dipolar spectroscopy distance measurements in biomacromolecules labeled with Gd(III) markers

Y. Song; T. J. Meade; A. V. Astashkin; E. L. Klein; J. H. Enemark; A. Raitsimring

doi:10.1016/j.jmr.2011.02.010

Pulsed dipolar spectroscopy distance measurements in biomacromolecules labeled with Gd(III) markers

Y. Song, T. J. Meade, A. V. Astashkin, E. L. Klein, J. H. Enemark, A. Raitsimring^*

^*Corresponding author for this work

Chemistry

Research output: Contribution to journal › Article › peer-review

71 Scopus citations

Abstract

This work demonstrates the feasibility of using Gd(III) tags for long-range Double Electron Electron Resonance (DEER) distance measurements in biomacromolecules. Double-stranded 14- base pair Gd(III)-DNA conjugates were synthesized and investigated at K_a band. For the longest Gd(III) tag the average distance and average deviation between Gd(III) ions determined from the DEER time domains was about 59 ± 12 . This result demonstrates that DEER measurements with Gd(III) tags can be routinely carried out for distances of at least 60 , and analysis indicates that distance measurements up to 100 are possible. Compared with commonly used nitroxide labels, Gd(III)-based labels will be most beneficial for the detection of distance variations in large biomacromolecules, with an emphasis on large scale changes in shape or distance. Tracking the folding/unfolding and domain interactions of proteins and the conformational changes in DNA are examples of such applications.

Original language	English (US)
Pages (from-to)	59-68
Number of pages	10
Journal	Journal of Magnetic Resonance
Volume	210
Issue number	1
DOIs	https://doi.org/10.1016/j.jmr.2011.02.010
State	Published - May 2011

Keywords

DEER
Distance measurements
Gd(III) tags
Oligonucleotides
Pulse Dipolar Spectroscopy (PDS)

ASJC Scopus subject areas

Biophysics
Biochemistry
Nuclear and High Energy Physics
Condensed Matter Physics

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10.1016/j.jmr.2011.02.010

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title = "Pulsed dipolar spectroscopy distance measurements in biomacromolecules labeled with Gd(III) markers",

abstract = "This work demonstrates the feasibility of using Gd(III) tags for long-range Double Electron Electron Resonance (DEER) distance measurements in biomacromolecules. Double-stranded 14- base pair Gd(III)-DNA conjugates were synthesized and investigated at Ka band. For the longest Gd(III) tag the average distance and average deviation between Gd(III) ions determined from the DEER time domains was about 59 ± 12 . This result demonstrates that DEER measurements with Gd(III) tags can be routinely carried out for distances of at least 60 , and analysis indicates that distance measurements up to 100 are possible. Compared with commonly used nitroxide labels, Gd(III)-based labels will be most beneficial for the detection of distance variations in large biomacromolecules, with an emphasis on large scale changes in shape or distance. Tracking the folding/unfolding and domain interactions of proteins and the conformational changes in DNA are examples of such applications.",

keywords = "DEER, Distance measurements, Gd(III) tags, Oligonucleotides, Pulse Dipolar Spectroscopy (PDS)",

author = "Y. Song and Meade, {T. J.} and Astashkin, {A. V.} and Klein, {E. L.} and Enemark, {J. H.} and A. Raitsimring",

note = "Funding Information: This research was supported by the Binational Science Foundation (USA-Israel, BSF#2006179) NIH 1R01 EB005866-01, NSF DBI-0139459, DBI-9604939, BIR-922443 and NIH S10RR020959. A.R. is very thankful to Prof. D. Goldfarb for stimulating discussions. ",

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language = "English (US)",

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AU - Meade, T. J.

AU - Astashkin, A. V.

AU - Klein, E. L.

AU - Enemark, J. H.

AU - Raitsimring, A.

N1 - Funding Information: This research was supported by the Binational Science Foundation (USA-Israel, BSF#2006179) NIH 1R01 EB005866-01, NSF DBI-0139459, DBI-9604939, BIR-922443 and NIH S10RR020959. A.R. is very thankful to Prof. D. Goldfarb for stimulating discussions.

PY - 2011/5

Y1 - 2011/5

N2 - This work demonstrates the feasibility of using Gd(III) tags for long-range Double Electron Electron Resonance (DEER) distance measurements in biomacromolecules. Double-stranded 14- base pair Gd(III)-DNA conjugates were synthesized and investigated at Ka band. For the longest Gd(III) tag the average distance and average deviation between Gd(III) ions determined from the DEER time domains was about 59 ± 12 . This result demonstrates that DEER measurements with Gd(III) tags can be routinely carried out for distances of at least 60 , and analysis indicates that distance measurements up to 100 are possible. Compared with commonly used nitroxide labels, Gd(III)-based labels will be most beneficial for the detection of distance variations in large biomacromolecules, with an emphasis on large scale changes in shape or distance. Tracking the folding/unfolding and domain interactions of proteins and the conformational changes in DNA are examples of such applications.

AB - This work demonstrates the feasibility of using Gd(III) tags for long-range Double Electron Electron Resonance (DEER) distance measurements in biomacromolecules. Double-stranded 14- base pair Gd(III)-DNA conjugates were synthesized and investigated at Ka band. For the longest Gd(III) tag the average distance and average deviation between Gd(III) ions determined from the DEER time domains was about 59 ± 12 . This result demonstrates that DEER measurements with Gd(III) tags can be routinely carried out for distances of at least 60 , and analysis indicates that distance measurements up to 100 are possible. Compared with commonly used nitroxide labels, Gd(III)-based labels will be most beneficial for the detection of distance variations in large biomacromolecules, with an emphasis on large scale changes in shape or distance. Tracking the folding/unfolding and domain interactions of proteins and the conformational changes in DNA are examples of such applications.

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Pulsed dipolar spectroscopy distance measurements in biomacromolecules labeled with Gd(III) markers

Abstract

Keywords

ASJC Scopus subject areas

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