Open Access
Proceedings of the National Academy of Sciences of the United States of America, volume 109, issue 49, pages 19971-19976
Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets
Douglas R. Davies
1
,
Amy D Gelinas
2
,
Chi Zhang
2
,
John C. Rohloff
2
,
Jeffrey D. Carter
2
,
Daniel O'Connell
2, 3
,
Sheela M. Waugh
2
,
Steven K. Wolk
2
,
Wesley S. Mayfield
2
,
Alex B. Burgin
1
,
Thomas E. Edwards
1
,
Lance J. Stewart
1
,
Larry Gold
2
,
Nebojsa Janjic
2
,
Thale C. Jarvis
2
1
Emerald BioStructures, Inc., Bainbridge Island, WA 98110;
|
2
SomaLogic, Inc., Boulder, CO 80301; and
|
3
St. Andrew’s School, Middletown, DE 19709
|
Publication type: Journal Article
Publication date: 2012-11-08
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 11.1
ISSN: 00278424, 10916490
Multidisciplinary
Abstract
Selection of aptamers from nucleic acid libraries by in vitro evolution represents a powerful method of identifying high-affinity ligands for a broad range of molecular targets. Nevertheless, a sizeable fraction of proteins remain difficult targets due to inherently limited chemical diversity of nucleic acids. We have exploited synthetic nucleotide modifications that confer protein-like diversity on a nucleic acid scaffold, resulting in a new generation of binding reagents called SOMAmers (Slow Off-rate Modified Aptamers). Here we report a unique crystal structure of a SOMAmer bound to its target, platelet-derived growth factor B (PDGF-BB). The SOMAmer folds into a compact structure and exhibits a hydrophobic binding surface that mimics the interface between PDGF-BB and its receptor, contrasting sharply with mainly polar interactions seen in traditional protein-binding aptamers. The modified nucleotides circumvent the intrinsic diversity constraints of natural nucleic acids, thereby greatly expanding the structural vocabulary of nucleic acid ligands and considerably broadening the range of accessible protein targets.
Top-30
Citations by journals
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1
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3
4
5
6
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8
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PLoS ONE
5 publications, 2.44%
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Angewandte Chemie
5 publications, 2.44%
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Angewandte Chemie - International Edition
5 publications, 2.44%
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Molecular Therapy - Nucleic Acids
4 publications, 1.95%
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Journal of the American Chemical Society
4 publications, 1.95%
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Organic and Biomolecular Chemistry
4 publications, 1.95%
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Proceedings of the National Academy of Sciences of the United States of America
4 publications, 1.95%
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Nucleic Acid Therapeutics
3 publications, 1.46%
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Nature Communications
3 publications, 1.46%
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3 publications, 1.46%
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Analytical Chemistry
3 publications, 1.46%
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Chemical Reviews
3 publications, 1.46%
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Pharmaceutics
2 publications, 0.98%
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Journal of Hepatology
2 publications, 0.98%
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Biotechnology Advances
2 publications, 0.98%
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Journal of Molecular Graphics and Modelling
2 publications, 0.98%
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Methods
2 publications, 0.98%
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Cell Reports Medicine
2 publications, 0.98%
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Journal of Biological Chemistry
2 publications, 0.98%
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ChemBioChem
2 publications, 0.98%
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2 publications, 0.98%
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ACS Nano
2 publications, 0.98%
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ACS Combinatorial Science
2 publications, 0.98%
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ACS Chemical Biology
2 publications, 0.98%
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ACS Central Science
2 publications, 0.98%
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1
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7
8
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Citations by publishers
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5
10
15
20
25
30
35
40
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Elsevier
36 publications, 17.56%
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Wiley
27 publications, 13.17%
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American Chemical Society (ACS)
26 publications, 12.68%
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Multidisciplinary Digital Publishing Institute (MDPI)
22 publications, 10.73%
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Springer Nature
20 publications, 9.76%
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Royal Society of Chemistry (RSC)
12 publications, 5.85%
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Oxford University Press
8 publications, 3.9%
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Public Library of Science (PLoS)
6 publications, 2.93%
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Proceedings of the National Academy of Sciences (PNAS)
4 publications, 1.95%
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Mary Ann Liebert
3 publications, 1.46%
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Frontiers Media S.A.
3 publications, 1.46%
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Wolters Kluwer Health
3 publications, 1.46%
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American Society for Biochemistry and Molecular Biology
3 publications, 1.46%
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Taylor & Francis
3 publications, 1.46%
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Cold Spring Harbor Laboratory
3 publications, 1.46%
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Pleiades Publishing
2 publications, 0.98%
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American Institute of Physics (AIP)
1 publication, 0.49%
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The American Association of Immunologists
1 publication, 0.49%
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Future Medicine
1 publication, 0.49%
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Future Science
1 publication, 0.49%
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Japan Society for Analytical Chemistry
1 publication, 0.49%
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Social Science Electronic Publishing
1 publication, 0.49%
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EMBO press
1 publication, 0.49%
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American Association for the Advancement of Science (AAAS)
1 publication, 0.49%
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American Society for Microbiology
1 publication, 0.49%
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The Electrochemical Society
1 publication, 0.49%
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American Diabetes Association
1 publication, 0.49%
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IOS Press
1 publication, 0.49%
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Nippon Yakuri Gakkai
1 publication, 0.49%
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5
10
15
20
25
30
35
40
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- We do not take into account publications without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Davies D. R. et al. Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets // Proceedings of the National Academy of Sciences of the United States of America. 2012. Vol. 109. No. 49. pp. 19971-19976.
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Davies D. R., Gelinas A. D., Zhang C., Rohloff J. C., Carter J. D., O'Connell D., Waugh S. M., Wolk S. K., Mayfield W. S., Burgin A. B., Edwards T. E., Stewart L. J., Gold L., Janjic N., Jarvis T. C. Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets // Proceedings of the National Academy of Sciences of the United States of America. 2012. Vol. 109. No. 49. pp. 19971-19976.
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TY - JOUR
DO - 10.1073/pnas.1213933109
UR - https://doi.org/10.1073/pnas.1213933109
TI - Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets
T2 - Proceedings of the National Academy of Sciences of the United States of America
AU - Davies, Douglas R.
AU - Gelinas, Amy D
AU - Zhang, Chi
AU - Rohloff, John C.
AU - Carter, Jeffrey D.
AU - O'Connell, Daniel
AU - Waugh, Sheela M.
AU - Wolk, Steven K.
AU - Mayfield, Wesley S.
AU - Burgin, Alex B.
AU - Edwards, Thomas E.
AU - Stewart, Lance J.
AU - Gold, Larry
AU - Janjic, Nebojsa
AU - Jarvis, Thale C.
PY - 2012
DA - 2012/11/08 00:00:00
PB - Proceedings of the National Academy of Sciences (PNAS)
SP - 19971-19976
IS - 49
VL - 109
SN - 0027-8424
SN - 1091-6490
ER -
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@article{2012_Davies,
author = {Douglas R. Davies and Amy D Gelinas and Chi Zhang and John C. Rohloff and Jeffrey D. Carter and Daniel O'Connell and Sheela M. Waugh and Steven K. Wolk and Wesley S. Mayfield and Alex B. Burgin and Thomas E. Edwards and Lance J. Stewart and Larry Gold and Nebojsa Janjic and Thale C. Jarvis},
title = {Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2012},
volume = {109},
publisher = {Proceedings of the National Academy of Sciences (PNAS)},
month = {nov},
url = {https://doi.org/10.1073/pnas.1213933109},
number = {49},
pages = {19971--19976},
doi = {10.1073/pnas.1213933109}
}
Cite this
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Davies, Douglas R., et al. “Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets.” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 49, Nov. 2012, pp. 19971-19976. https://doi.org/10.1073/pnas.1213933109.