Structural ensemble and microscopic elasticity of freely diffusing DNA by direct measurement of fluctuations
Open accessAbstract
Significance: Deformation of the double helix is a ubiquitous feature of the protein–DNA interactions that regulate, replicate, repair, and pack DNA in cells. Understanding the energetics of DNA deformation is therefore of central importance. DNA is generally modeled as a linear elastic rod, but it has not been possible to test this directly by observing the nanometer-scale bending and twisting of the helix. Using an X-ray interferometry technique, we measured the structural fluctuations of a short B-form duplex. The results expose a potential nonlinearity of DNA elasticity and illustrate how to measure the structural ensemble of a freely diffusing macromolecule.
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RNA and DNA exist as conformational ensembles in freely diffusing states, crystals, nucleosomes, ribosomes, and spliceosomes.
“RNA and DNA also exist as conformational ensembles, no matter whether in freely diffusing state,540 in crystal,541 or in large nucleosomes,542 ribosomes, or spliceosomes.”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [540]
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Cites
Genetic Algorithms in Search, Optimization and Machine Learning
Goldberg, D. E., & Robson, D. (1988) · Cited by 18,391 · see citing works
Goldberg, D. E., & Shakespeare, W. (2002) · Cited by 16,077 · see citing works
Structure of a Thiol Monolayer-Protected Gold Nanoparticle at 1.1 A Resolution
Jadzinsky, P. D., Calero, G. A., Ackerson, C. J., et al. (2007) · Science · doi:10.1126/science.1148624 · Cited by 2,655 · see citing works
The DNA-encoded nucleosome organization of a eukaryotic genome
Kaplan, N., Moore, I. K., Fondufe-Mittendorf, Y., Gossett, A., Tillo, D., Field, Y., Leproust, E., Hughes, T., Lieb, J., Widom, J., et al. (2008) · Nature · doi:10.1038/nature07667 · Cited by 1,296 · see citing works
Ten years of tension: single-molecule DNA mechanics
Bustamante, C., Bryant, Z. D., & Smith, S. B. (2003) · Nature · doi:10.1038/nature01405 · Cited by 1,291 · see citing works
The structure of DNA in the nucleosome core
Richmond, T. J., & Davey, C. A. (2003) · Nature · doi:10.1038/nature01595 · Cited by 1,287 · see citing works
The role of DNA shape in protein–DNA recognition
Rohs, R., West, S. M., Sosinsky, A., Liu, P., Mann, R. S., & Honig, B. (2009) · Nature · doi:10.1038/nature08473 · Cited by 1,096 · see citing works
Hagerman, P. J. (1988) · Annual Review of Biophysics and Biophysical Chemistry · doi:10.1146/annurev.bb.17.060188.001405 · Cited by 1,061 · see citing works
Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution
Lange, O. F., Lakomek, N., Farès, C., Schroeder, G. F., Walter, K. F. A., Becker, S., Meiler, J., Grubmüller, H., Griesinger, C., & de Groot, B. L. (2008) · Science · doi:10.1126/science.1157092 · Cited by 1,044 · see citing works
DNA sequence-dependent deformability deduced from protein–DNA crystal complexes
Olson, W. K., Gorin, A. A., Lu, X., Hock, L. M., & Zhurkin, V. B. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.19.11163 · Cited by 1,039 · see citing works
DEER Distance Measurements on Proteins
Jeschke, G. (2012) · Annual Review of Physical Chemistry · doi:10.1146/annurev-physchem-032511-143716 · Cited by 980 · see citing works
Crystal structure of trp represser/operator complex at atomic resolution
Otwinowski, Z., Schevitz, R. W., Zhang, R.-G., Lawson, C. L., Joachimiak, A., Marmorstein, R. Q., Luisi, B. F., & Sigler, P. B. (1988) · Nature · doi:10.1038/335321a0 · Cited by 908 · see citing works
Origins of Specificity in Protein-DNA Recognition
Rohs, R., Jin, X., West, S. M., Joshi, R., Honig, B. H., & Mann, R. S. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060408-091030 · Cited by 902 · see citing works
DNA bending and its relation to nucleosome positioning
Drew, H. R., & TRAVERS, A. A. (1985) · Journal of Molecular Biology · doi:10.1016/0022-2836(85)90396-1 · Cited by 706 · see citing works
Structural transitions and elasticity from torque measurements on DNA
Bryant, Z. D., Stone, M. D., Gore, J., et al. (2003) · Nature · doi:10.1038/nature01810 · Cited by 587 · see citing works
Shore, D., & Baldwin, R. L. (1983) · Journal of Molecular Biology · doi:10.1016/s0022-2836(83)80198-3 · Cited by 418 · see citing works
Gore, J., Bryant, Z. D., Nöllmann, M., et al. (2006) · Nature · doi:10.1038/nature04974 · Cited by 407 · see citing works
Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling
Horowitz, D. S., & Wang, J. C. (1984) · Journal of Molecular Biology · doi:10.1016/0022-2836(84)90404-2 · Cited by 399 · see citing works
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
Zhang, Y., Moqtaderi, Z., Rattner, B. P., Euskirchen, G. M., Snyder, M. P., Kadonaga, J. T., Liu, X. S., & Struhl, K. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1636 · Cited by 365 · see citing works
Helical periodicity of DNA determined by enzyme digestion
Rhodes, D., & Klug, A. (1980) · Nature · doi:10.1038/286573a0 · Cited by 350 · see citing works
Structure and Function of DNA Methyltransferases
Cheng, X. (1995) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.bb.24.060195.001453 · Cited by 319 · see citing works
Extreme Bendability of DNA Less than 100 Base Pairs Long Revealed by Single-Molecule Cyclization
Vafabakhsh, R., & Ha, T. (2012) · Science · doi:10.1126/science.1224139 · Cited by 301 · see citing works
Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments
Lipfert, J., Kerssemakers, J. W. J., Jager, T., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1520 · Cited by 293 · see citing works
Torsional directed walks, entropic elasticity, and DNA twist stiffness
Moroz, J. D., & Nelson, P. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.26.14418 · Cited by 286 · see citing works
Action at a distance: DNA-looping and initiation of transcription
Rippe, K., von Hippel, P. H., & Langowski, J. (1995) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)89117-3 · Cited by 282 · see citing works
Visualizing spatially correlated dynamics that directs RNA conformational transitions
Zhang, Q., Stelzer, A. C., Fisher, C. K., et al. (2007) · Nature · doi:10.1038/nature06389 · Cited by 250 · see citing works
Sequence dependence of DNA bending rigidity
Geggier, S., & Vologodskii, A. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1004809107 · Cited by 230 · see citing works
Taylor, W. H., & Hagerman, P. J. (1990) · Journal of Molecular Biology · doi:10.1016/0022-2836(90)90131-5 · Cited by 225 · see citing works
Mathew, R. S., Das, R., & Harbury, P. B. (2008) · Science · doi:10.1126/science.1158881 · Cited by 218 · see citing works
Self-citationThe unique structure of A-tracts and intrinsic DNA bending
Haran, T. E., & Mohanty, U. (2009) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583509004752 · Cited by 210 · see citing works
Bending of the bacteriophage lambda attachment site by Escherichia coli integration host factor.
Robertson, C. A., & Nash, H. A. (1988) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)68960-4 · Cited by 196 · see citing works
Dass, A. (2009) · Journal of the American Chemical Society · doi:10.1021/ja904713f · Cited by 183 · see citing works
Using DNA mechanics to predict in vitro nucleosome positions and formation energies
Morozov, A. V., Fortney, K., Gaykalova, D. A., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp475 · Cited by 180 · see citing works
DNA bending by an adenine–thymine tract and its role in gene regulation
Hizver, J., Rozenberg, H., Frolow, F., Rabinovich, D., & Shakked, Z. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.151247298 · Cited by 138 · see citing works
Kalinin, S., Sisamakis, E., Magennis, S. W., Felekyan, S., & Seidel, C. A. M. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp100025v · Cited by 113 · see citing works
Generalized theory of semiflexible polymers
Wiggins, P. A., & Nelson, P. (2006) · Physical Review E · doi:10.1103/physreve.73.031906 · Cited by 110 · see citing works
The conformation of the DNA double helix in the crystal is dependent on its environment
Shakked, Z., Guerstein-Guzikevich, G., Eisenstein, M., Frolow, F., & Rabinovich, D. (1989) · Nature · doi:10.1038/342456a0 · Cited by 110 · see citing works
Corrections and Clarifications
(2010) · Science · doi:10.1126/science.328.5985.1480-b · Cited by 107 · see citing works
Hagerman, P. J., & Ramadevi, V. A. (1990) · Journal of Molecular Biology · doi:10.1016/0022-2836(90)90130-e · Cited by 106 · see citing works
Schwieters, C. D., & Clore, G. M. (2007) · Biochemistry · doi:10.1021/bi061943x · Cited by 96 · see citing works
Effect of Bending Strain on the Torsion Elastic Constant of DNA
Heath, P. J., Clendenning, J. B., Fujimoto, B. S., et al. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0432 · Cited by 93 · see citing works
Sequence-Dependent Effects in the Cyclization of Short DNA
Czapla, L., Swigon, D., & Olson, W. K. (2006) · Journal of Chemical Theory and Computation · doi:10.1021/ct060025+ · Cited by 88 · see citing works
Sequence-Dependent Motions of DNA: A Normal Mode Analysis at the Base-Pair Level
Matsumoto, A., & Olson, W. K. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)75147-3 · Cited by 87 · see citing works
A Molecular Ruler for Measuring Quantitative Distance Distributions
Mathew-Fenn, R. S., Das, R., Silverman, J., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003229 · Cited by 61 · see citing works
Zhang, Y., Moqtaderi, Z., Rattner, B. P., Euskirchen, G. M., Snyder, M. P., Kadonaga, J. T., Liu, X. S., & Struhl, K. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb0810-920 · Cited by 52 · see citing works
Conformational averaging in structural biology: issues, challenges and computational solutions
Kruschel, D., & Žagrović, B. (2009) · Molecular BioSystems · doi:10.1039/b917186j · Cited by 43 · see citing works
Zheng, G., Czapla, L., Srinivasan, A. R., et al. (2009) · Physical Chemistry Chemical Physics · doi:10.1039/b916183j · Cited by 30 · see citing works
Comment on “Remeasuring the Double Helix”
Becker, N. B., & Everaers, R. (2009) · Science · doi:10.1126/science.1168786 · Cited by 26 · see citing works
Torsional Rigidities of Weakly Strained DNAs
Fujimoto, B. S., Brewood, G. P., & Schurr, J. M. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.087593 · Cited by 25 · see citing works
Influence of packing interactions on the average conformation of B-DNA in crystalline structures
Tereshko, V., & Subirana, J. A. (1999) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444999000591 · Cited by 22 · see citing works
Analysis of accordion DNA stretching revealed by the gold cluster ruler
Mazur, A. K. (2009) · Physical Review E · doi:10.1103/physreve.80.010901 · Cited by 17 · see citing works
Nikolova, E. N., & Al‐Hashimi, H. M. (2009) · Journal of Biomolecular NMR · doi:10.1007/s10858-009-9350-y · Cited by 16 · see citing works
Insights into the Sequence-Dependent Macromolecular Properties of DNA from Base-Pair Level Modeling
Colasanti, A. V., Czapla, L., Zheng, G., et al. (2008) · CRC Press eBooks · doi:10.1201/9781420059564.ch14 · Cited by 15 · see citing works
Can reliable torsion elastic constants be determined from FPA data on 24 and 27 base-pair DNAs?
Fujimoto, B. S., & Schurr, J. M. (2005) · Biophysical Chemistry · doi:10.1016/j.bpc.2005.02.001 · Cited by 2 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- Zhang Y, et al. (2010) Evidence against a genomic code for nucleosome positioning. Nat Struct Mol Biol 17(8):920-923.
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Sorted by citations
Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436 · see citing works
From a structural average to the conformational ensemble of a DNA bulge
Shi, X., Beauchamp, K. A., Harbury, P. B., & Herschlag, D. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317032111 · Cited by 38 · see citing works
Self-citation
- Authors
- Shi, X., Herschlag, D., & Harbury, P. A. B.
- Affiliations
- Stanford University (US)
- Department of Biochemistry, Stanford University, Stanford, CA 94305
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2013-04
- Volume
- 110
- Issue
- 16
- Pages
- E1444-51
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3631670
- OpenAlex
- W2126505866
- Cited by
- 41
- References
- 54
- Citations by year
- 2024: 3 · 2023: 3 · 2022: 2 · 2021: 3 · 2020: 3 · 2019: 4 · 2018: 2 · 2017: 2 · 2016: 5 · 2015: 7 · 2014: 4 · 2013: 3
- FWCI
- 2.84
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (DP1OD000429, GM49243)
- National Institute of General Medical Sciences (P01GM066275, R37GM049243, GM49243, R01GM068126, R01GM049243)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Force Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- B-DNA, DNA elasticity, torsional stiffness, X-ray interferometry, protein-DNA interactions, polymer mechanics, DNA stretching
- MeSH terms
- Diffusion, DNA, DNA-Binding Proteins, Interferometry, Models, Molecular, Nucleic Acid Conformation
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