Related Content
Search Google Scholar for:
|
|
Science 16 December 1994:
Vol. 266. no. 5192, pp. 1829 - 1834
DOI: 10.1126/science.7997878
|
|
Articles
Science, Vol 266, Issue 5192, 1829-1834
Copyright © 1994 by American Association for the Advancement of Science
DNA bending by asymmetric phosphate neutralization
JK Strauss
and
LJ Maher 3rd
Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha 68198-6805.
DNA is often bent when complexed with proteins. Understanding the forces responsible for DNA bending would be of fundamental value in exploring the interplay of these macromolecules. A series of experiments was devised to test the hypothesis that proteins with cationic surfaces can induce substantial DNA bending by neutralizing phosphates on one DNA face. Repulsions between phosphates in the remaining anionic helix are predicted to result in an unbalanced compression force acting to deform the DNA toward the protein. This hypothesis is supported by the results of electrophoretic experiments in which DNA spontaneously bends when one helical face is partially modified by incorporation of neutral phosphate analogs. Phasing with respect to a site of intrinsic DNA curvature (hexadeoxyadenylate tract) permits estimation of the electrostatic bend angle, and demonstrates that such modified DNAs are deformed toward the neutralized surface, as predicted. Similar model systems may be useful in exploring the extent to which phosphate neutralization can account for DNA bending by particular proteins.
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
- Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation.
- N. A. Becker, J. D. Kahn, and L. J. Maher III (2008)
Nucleic Acids Res.
36, 4009-4021
| Abstract »
| Full Text »
| PDF »
- Electrostatic Free Energy Landscapes for DNA Helix Bending.
- Z.-J. Tan and S.-J. Chen (2008)
Biophys. J.
94, 3137-3149
| Abstract »
| Full Text »
| PDF »
- Monovalent Cation Binding by Curved DNA Molecules Containing Variable Numbers of A-Tracts.
- Y. Lu and N. C. Stellwagen (2008)
Biophys. J.
94, 1719-1725
| Abstract »
| Full Text »
| PDF »
- Ability of Polymerase {eta} and T7 DNA Polymerase to Bypass Bulge Structures.
- V. J. Cannistraro and J.-S. Taylor (2007)
J. Biol. Chem.
282, 11188-11196
| Abstract »
| Full Text »
| PDF »
- DNA bending by bHLH charge variants.
- R. J. McDonald, J. D. Kahn, and L. J. Maher III (2006)
Nucleic Acids Res.
34, 4846-4856
| Abstract »
| Full Text »
| PDF »
- Crystal Structure of the Human FOXK1a-DNA Complex and Its Implications on the Diverse Binding Specificity of Winged Helix/Forkhead Proteins.
- K.-L. Tsai, C.-Y. Huang, C.-H. Chang, Y.-J. Sun, W.-J. Chuang, and C.-D. Hsiao (2006)
J. Biol. Chem.
281, 17400-17409
| Abstract »
| Full Text »
| PDF »
- The Contribution of Transient Counterion Imbalances to DNA Bending Fluctuations.
- G. S. Manning (2006)
Biophys. J.
90, 3208-3215
| Abstract »
| Full Text »
| PDF »
- Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer.
- S. L. Williams, L. K. Parkhurst, and L. J. Parkhurst (2006)
Nucleic Acids Res.
34, 1028-1035
| Abstract »
| Full Text »
| PDF »
- Positively Charged Surfaces Increase the Flexibility of DNA.
- A. Podesta, M. Indrieri, D. Brogioli, G. S. Manning, P. Milani, R. Guerra, L. Finzi, and D. Dunlap (2005)
Biophys. J.
89, 2558-2563
| Abstract »
| Full Text »
| PDF »
- The contribution of phosphate-phosphate repulsions to the free energy of DNA bending.
- K. Range, E. Mayaan, L. J. Maher III, and D. M. York (2005)
Nucleic Acids Res.
33, 1257-1268
| Abstract »
| Full Text »
| PDF »
- Ion motions in molecular dynamics simulations on DNA.
- S. Y. Ponomarev, K. M. Thayer, and D. L. Beveridge (2004)
PNAS
101, 14771-14775
| Abstract »
| Full Text »
| PDF »
- Origin of the intrinsic rigidity of DNA.
- J. B. Mills and P. J. Hagerman (2004)
Nucleic Acids Res.
32, 4055-4059
| Abstract »
| Full Text »
| PDF »
- Identification of Cre Residues Involved in Synapsis, Isomerization, and Catalysis.
- L. Lee and P. D. Sadowski (2003)
J. Biol. Chem.
278, 36905-36915
| Abstract »
| Full Text »
| PDF »
- Structural Determinants for Substrate Binding and Catalysis by the Structure-specific Endonuclease XPG.
- M. Hohl, F. Thorel, S. G. Clarkson, and O. D. Scharer (2003)
J. Biol. Chem.
278, 19500-19508
| Abstract »
| Full Text »
| PDF »
- DNA curvature at A tracts containing a non-polar thymine mimic.
- A. Maki, F. E. Brownewell, D. Liu, and E. T. Kool (2003)
Nucleic Acids Res.
31, 1059-1066
| Abstract »
| Full Text »
| PDF »
- Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies.
- D. Hamelberg, L. D. Williams, and W. D. Wilson (2002)
Nucleic Acids Res.
30, 3615-3623
| Abstract »
| Full Text »
| PDF »
- Thermodynamic and hydration effects for the incorporation of a cationic 3-aminopropyl chain into DNA.
- A. M. Soto, B. I. Kankia, P. Dande, B. Gold, and L. A. Marky (2002)
Nucleic Acids Res.
30, 3171-3180
| Abstract »
| Full Text »
| PDF »
- Charge neutralization and DNA bending by the Escherichia coli catabolite activator protein.
- P. R. Hardwidge, J. M. Zimmerman, and L. J. Maher III (2002)
Nucleic Acids Res.
30, 1879-1885
| Abstract »
| Full Text »
| PDF »
- Phosphate backbone neutralization increases duplex DNA flexibility: A model for protein binding.
- T. M. Okonogi, S. C. Alley, E. A. Harwood, P. B. Hopkins, and B. H. Robinson (2002)
PNAS
99, 4156-4160
| Abstract »
| Full Text »
| PDF »
- Solution structure of a DNA duplex with a chiral alkyl phosphonate moiety.
- R. Soliva, V. Monaco, I. Gomez-Pinto, N. J. Meeuwenoord, G. A. V. d. Marel, J. H. V. Boom, C. Gonzalez, and M. Orozco (2001)
Nucleic Acids Res.
29, 2973-2985
| Abstract »
| Full Text »
| PDF »
- Design and calibration of a semi-synthetic DNA phasing assay.
- P. R. Hardwidge, J. M. Zimmerman, and L. J. Maher, III (2000)
Nucleic Acids Res.
28, e102
| Abstract »
| Full Text »
| PDF »
- In Vitro Selection of Integration Host Factor Binding Sites.
- S. D. Goodman, N. J. Velten, Q. Gao, S. Robinson, and A. M. Segall (1999)
J. Bacteriol.
181, 3246-3255
| Abstract »
| Full Text »
- Characterization of CorR, a Transcriptional Activator Which Is Required for Biosynthesis of the Phytotoxin Coronatine.
- A. Peñaloza-Vázquez and C. L. Bender (1998)
J. Bacteriol.
180, 6252-6259
| Abstract »
| Full Text »
- Role of Asymmetric Phosphate Neutralization in DNA Bending by PU.1.
- J. K. Strauss-Soukup and L. J. Maher III (1997)
J. Biol. Chem.
272, 31570-31575
| Abstract »
| Full Text »
| PDF »
- Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun.
- D. A. Leonard, N. Rajaram, and T. K. Kerppola (1997)
PNAS
94, 4913-4918
| Abstract »
| Full Text »
| PDF »
- Local DNA stretching mimics the distortion caused by the TATA box-binding protein.
- A. Lebrun, Z. Shakked, and R. Lavery (1997)
PNAS
94, 2993-2998
| Abstract »
| Full Text »
| PDF »
- Microscopic DNA Flexibility Analysis. PROBING THE BASE COMPOSITION AND ION DEPENDENCE OF MINOR GROOVE COMPRESSION WITH AN ARTIFICIAL DNA BENDING AGENT.
- T. Akiyama and M. E. Hogan (1996)
J. Biol. Chem.
271, 29126-29135
| Abstract »
| Full Text »
| PDF »
- Histone H1 Enhances the DNA Binding Activity of the Transcription Factor EmBP-1.
- T. F. Schultz, S. Spiker, and R. S. Quatrano (1996)
J. Biol. Chem.
271, 25742-25745
| Abstract »
| Full Text »
| PDF »
- New Insights on DNA Recognition by ets Proteins from the Crystal Structure of the PU.1 ETS Domain-DNA Complex.
- F. Pio, R. Kodandapani, C.-Z. Ni, W. Shepard, M. Klemsz, S. R. McKercher, R. A. Maki, and K. R. Ely (1996)
J. Biol. Chem.
271, 23329-23337
| Abstract »
| Full Text »
| PDF »
- A Conserved Domain of the viviparous-1 Gene Product Enhances the DNA Binding Activity of the bZIP Protein EmBP-1 and Other Transcription Factors.
- A. Hill, A. Nantel, C. D. Rock, and R. S. Quatrano (1996)
J. Biol. Chem.
271, 3366-3374
| Abstract »
| Full Text »
| PDF »
- Mapping the intrinsic curvature and flexibility along the DNA chain.
- G. Zuccheri, A. Scipioni, V. Cavaliere, G. Gargiulo, P. De Santis, and B. Samori (2001)
PNAS
98, 3074-3079
| Abstract »
| Full Text »
| PDF »
- Crystallographic snapshots along a protein-induced DNA-bending pathway.
- N. C. Horton and J. J. Perona (2000)
PNAS
97, 5729-5734
| Abstract »
| Full Text »
| PDF »
|
|
