DNA Bending by Asymmetric Phosphate Neutralization
10.1126/science.7997878
Crossref journal-article
American Association for the Advancement of Science (AAAS)
Science (221)
Abstract

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.

Bibliography

Strauss, J. K., & Maher, L. J. (1994). DNA Bending by Asymmetric Phosphate Neutralization. Science, 266(5192), 1829–1834.

Authors 2
  1. Juliane K. Strauss (first)
  2. L. James Maher (additional)
References 50 Referenced 206
  1. ADHYA, S, MULTIPARTITE GENETIC-CONTROL ELEMENTS - COMMUNICATION BY DNA LOOP, ANNUAL REVIEW OF GENETICS 23: 227 (1989). (10.1146/annurev.ge.23.120189.001303) / ANNUAL REVIEW OF GENETICS (1989)
  2. BOTFIELD, M.C., BIPARTITE DNA RECOGNITION BY THE HUMAN OCT-2 POU DOMAIN - POU(S)-SPECIFIC PHOSPHATE CONTACTS ARE ANALOGOUS TO THOSE OF BACTERIOPHAGE-LAMBDA REPRESSOR, BIOCHEMISTRY 33: 2349 (1994). (10.1021/bi00175a001) / BIOCHEMISTRY (1994)
  3. BOWER, M, OLIGODEOXYRIBONUCLEOSIDE METHYLPHOSPHONATES - NMR AND UV SPECTROSCOPIC STUDIES OF RP-RP AND SP-SP METHYLPHOSPHONATE (ME) MODIFIED DUPLEXES OF (D[GGAATTCC])2, NUCLEIC ACIDS RESEARCH 15: 4915 (1987). (10.1093/nar/15.12.4915) / NUCLEIC ACIDS RESEARCH (1987)
  4. CALLAHAN, L, B-DNA TO Z-DNA TRANSITION PROBED BY OLIGONUCLEOTIDES CONTAINING METHYLPHOSPHONATES, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 83: 1617 (1986). / PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (1986)
  5. CROTHERS, D.M., ARCHITECTURAL ELEMENTS IN NUCLEOPROTEIN COMPLEXES, CURRENT BIOLOGY 3: 675 (1993). (10.1016/0960-9822(93)90065-V) / CURRENT BIOLOGY (1993)
  6. CROTHERS, D.M., INTRINSICALLY BENT DNA, JOURNAL OF BIOLOGICAL CHEMISTRY 265: 7093 (1990). (10.1016/S0021-9258(19)39080-5) / JOURNAL OF BIOLOGICAL CHEMISTRY (1990)
  7. CROTHERS, D.M., DNA BENDING, FLEXIBILITY, AND HELICAL REPEAT BY CYCLIZATION KINETICS, METHODS IN ENZYMOLOGY 212: 3 (1992). (10.1016/0076-6879(92)12003-9) / METHODS IN ENZYMOLOGY (1992)
  8. CROTHERS, D.M., GLOBAL FEATURES OF DNA-STRUCTURE BY COMPARATIVE GEL-ELECTROPHORESIS, METHODS IN ENZYMOLOGY 212: 46 (1992). (10.1016/0076-6879(92)12005-B) / METHODS IN ENZYMOLOGY (1992)
  9. 10.1080/07391102.1987.10506370
  10. GOODMAN, S.D., FUNCTIONAL REPLACEMENT OF A PROTEIN-INDUCED BEND IN A DNA RECOMBINATION SITE, NATURE 341: 251 (1989). (10.1038/341251a0) / NATURE (1989)
  11. HAGERMAN, P.J., SEQUENCE-DIRECTED CURVATURE OF DNA, ANNUAL REVIEW OF BIOCHEMISTRY 59: 755 (1990). (10.1146/annurev.bi.59.070190.003543) / ANNUAL REVIEW OF BIOCHEMISTRY (1990)
  12. HAGERMAN, P.J., FLEXIBILITY OF DNA, ANNUAL REVIEW OF BIOPHYSICS AND BIOPHYSICAL CHEMISTRY 17: 265 (1988). (10.1146/annurev.bb.17.060188.001405) / ANNUAL REVIEW OF BIOPHYSICS AND BIOPHYSICAL CHEMISTRY (1988)
  13. HAGERMAN, P.J., STRAIGHTENING OUT THE BENDS IN CURVED DNA, BIOCHIMICA ET BIOPHYSICA ACTA 1131: 125 (1992). (10.1016/0167-4781(92)90066-9) / BIOCHIMICA ET BIOPHYSICA ACTA (1992)
  14. HAMY, F, HYDROGEN-BONDING CONTACTS IN THE MAJOR GROOVE ARE REQUIRED FOR HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 TAT PROTEIN RECOGNITION OF TAR RNA, JOURNAL OF MOLECULAR BIOLOGY 230: 111 (1993). (10.1006/jmbi.1993.1129) / JOURNAL OF MOLECULAR BIOLOGY (1993)
  15. HAN, F, MOLECULAR-STRUCTURE OF DEOXYCYTIDYL-3'-METHYLPHOSPHONATE (RP) 5'-DEOXYGUANIDINE, D[CP(CH3)G] - A NEUTRAL DINUCLEOTIDE WITH WATSON-CRICK BASE-PAIRING AND A RIGHT-HANDED HELICAL TWIST, NUCLEIC ACIDS RESEARCH 18: 2759 (1990). (10.1093/nar/18.9.2759) / NUCLEIC ACIDS RESEARCH (1990)
  16. HODGESGARCIA, Y, CYTOSINE METHYLATION CAN INDUCE LOCAL DISTORTIONS IN THE STRUCTURE OF DUPLEX DNA, BIOCHEMISTRY 31: 7595 (1992). (10.1021/bi00148a022) / BIOCHEMISTRY (1992)
  17. HOGREFE, R.I., DEPROTECTION OF METHYLPHOSPHONATE OLIGONUCLEOTIDES USING A NOVEL ONE-POT PROCEDURE, NUCLEIC ACIDS RESEARCH 21: 2031 (1993). (10.1093/nar/21.9.2031) / NUCLEIC ACIDS RESEARCH (1993)
  18. IKEDA, K, POSSIBLE IMPLICATIONS OF SP1-INDUCED BENDING OF DNA ON SYNERGISTIC ACTIVATION OF TRANSCRIPTION, GENE 136: 341 (1993). (10.1016/0378-1119(93)90492-L) / GENE (1993)
  19. KAHN, J.D., DETECTION OF LOCALIZED DNA FLEXIBILITY, NATURE 368: 163 (1994). (10.1038/368163a0) / NATURE (1994)
  20. KAN, L.S., PROTON NUCLEAR MAGNETIC-RESONANCE STUDIES ON DIDEOXYRIBONUCLEOSIDE METHYLPHOSPHONATES, BIOCHEMISTRY 19: 2122 (1980). (10.1021/bi00551a020) / BIOCHEMISTRY (1980)
  21. KERPPOLA, T.K., FOS-JUN HETERODIMERS AND JUN HOMODIMERS BEND DNA IN OPPOSITE ORIENTATIONS - IMPLICATIONS FOR TRANSCRIPTION FACTOR COOPERATIVITY, CELL 66: 317 (1991). (10.1016/0092-8674(91)90621-5) / CELL (1991)
  22. 10.1126/science.1957173
  23. KIM, J.L., CO-CRYSTAL STRUCTURE OF TBP RECOGNIZING THE MINOR-GROOVE OF A TATA ELEMENT, NATURE 365: 520 (1993). (10.1038/365520a0) / NATURE (1993)
  24. KIM, Y.C., CRYSTAL-STRUCTURE OF A YEAST TBP TATA-BOX COMPLEX, NATURE 365: 512 (1993). (10.1038/365512a0) / NATURE (1993)
  25. KOO, H.S., DETERMINATION OF THE EXTENT OF DNA BENDING BY AN ADENINE THYMINE TRACT, BIOCHEMISTRY 29: 4227 (1990). (10.1021/bi00469a027) / BIOCHEMISTRY (1990)
  26. KOO, H.S., DNA BENDING AT ADENINE . THYMINE TRACTS, NATURE 320: 501 (1986). (10.1038/320501a0) / NATURE (1986)
  27. KOO, H.S., CALIBRATION OF DNA CURVATURE AND A UNIFIED DESCRIPTION OF SEQUENCE-DIRECTED BENDING, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 85: 1763 (1988). / PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (1988)
  28. 10.1126/science.2237403
  29. MAHER, L.J., COMPARATIVE HYBRID ARREST BY TANDEM ANTISENSE OLIGODEOXYRIBONUCLEOTIDES OR OLIGODEOXYRIBONUCLEOSIDE METHYLPHOSPHONATES IN A CELL-FREE SYSTEM, NUCLEIC ACIDS RESEARCH 16: 3341 (1988). (10.1093/nar/16.8.3341) / NUCLEIC ACIDS RESEARCH (1988)
  30. MANNING, G.S., AN ESTIMATE OF THE EXTENT OF FOLDING OF NUCLEOSOMAL DNA BY LATERALLY ASYMMETRIC NEUTRALIZATION OF PHOSPHATE GROUPS, JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 6: 877 (1989). (10.1080/07391102.1989.10506519) / JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (1989)
  31. MANNING, G.S., MOLECULAR THEORY OF POLYELECTROLYTE SOLUTIONS WITH APPLICATIONS TO ELECTROSTATIC PROPERTIES OF POLYNUCLEOTIDES, QUARTERLY REVIEWS OF BIOPHYSICS 11: 179 (1978). (10.1017/S0033583500002031) / QUARTERLY REVIEWS OF BIOPHYSICS (1978)
  32. MATTHEWS, K.S., DNA LOOPING, MICROBIOLOGICAL REVIEWS 56: 123 (1992). (10.1128/mr.56.1.123-136.1992) / MICROBIOLOGICAL REVIEWS (1992)
  33. MCGHEE, J.D., THE NUMBER OF CHARGE-CHARGE INTERACTIONS STABILIZING THE ENDS OF NUCLEOSOME DNA, NUCLEIC ACIDS RESEARCH 8: 2751 (1980). (10.1093/nar/8.12.2751) / NUCLEIC ACIDS RESEARCH (1980)
  34. MILLER, P.S., OLIGONUCLEOTIDE INHIBITORS OF GENE-EXPRESSION IN LIVING CELLS - NEW OPPORTUNITIES IN DRUG DESIGN, ANNUAL REPORTS IN MEDICINAL CHEMISTRY 23: 295 (1988). (10.1016/S0065-7743(08)60858-1) / ANNUAL REPORTS IN MEDICINAL CHEMISTRY (1988)
  35. MILLER, P.S., A NEW APPROACH TO CHEMOTHERAPY BASED ON MOLECULAR-BIOLOGY AND NUCLEIC-ACID CHEMISTRY - MATAGEN (MASKING TAPE FOR GENE-EXPRESSION), ANTI-CANCER DRUG DESIGN 2: 117 (1987). / ANTI-CANCER DRUG DESIGN (1987)
  36. Miller, P. S., Herpesviruses, the Immune System and AIDS: 343 (1990). / Herpesviruses, the Immune System and AIDS (1990)
  37. NOBLE, S.A., STUDIES ON GENE-CONTROL REGIONS .15. METHYLPHOSPHONATES AS PROBES OF PROTEIN-NUCLEIC ACID INTERACTIONS, NUCLEIC ACIDS RESEARCH 12: 3387 (1984). (10.1093/nar/12.7.3387) / NUCLEIC ACIDS RESEARCH (1984)
  38. OLSON, W.K., INFLUENCE OF FLUCTUATIONS ON DNA CURVATURE - A COMPARISON OF FLEXIBLE AND STATIC WEDGE MODELS OF INTRINSICALLY BENT DNA, JOURNAL OF MOLECULAR BIOLOGY 232: 530 (1993). (10.1006/jmbi.1993.1409) / JOURNAL OF MOLECULAR BIOLOGY (1993)
  39. PIELES, U, MATRIX-ASSISTED LASER-DESORPTION IONIZATION TIME-OF-FLIGHT MASS-SPECTROMETRY - A POWERFUL TOOL FOR THE MASS AND SEQUENCE-ANALYSIS OF NATURAL AND MODIFIED OLIGONUCLEOTIDES, NUCLEIC ACIDS RESEARCH 21: 3191 (1993). (10.1093/nar/21.14.3191) / NUCLEIC ACIDS RESEARCH (1993)
  40. RICE, J.A., DNA BENDING BY THE BULGE DEFECT, BIOCHEMISTRY 28: 4512 (1989). (10.1021/bi00436a058) / BIOCHEMISTRY (1989)
  41. ROJO, F, A DNA CURVATURE CAN SUBSTITUTE PHAGE-PHI-29 REGULATORY PROTEIN-P4 WHEN ACTING AS A TRANSCRIPTIONAL REPRESSOR, EMBO JOURNAL 10: 3429 (1991). (10.1002/j.1460-2075.1991.tb04907.x) / EMBO JOURNAL (1991)
  42. SCHULTZ, S.C., CRYSTAL-STRUCTURE OF A CAP-DNA COMPLEX - THE DNA IS BENT BY 90-DEGREES, SCIENCE 253: 1001 (1991). (10.1126/science.1653449) / SCIENCE (1991)
  43. SNYDER, U.K., PHASING OF PROTEIN-INDUCED DNA BENDS IN A RECOMBINATION COMPLEX, NATURE 341: 255 (1989). (10.1038/341255a0) / NATURE (1989)
  44. 10.1093/nar/16.20.9687
  45. TRAVERS, A.A., DNA CHAPERONES - A SOLUTION TO A PERSISTENCE PROBLEM, CELL 77: 167 (1994). (10.1016/0092-8674(94)90306-9) / CELL (1994)
  46. Uhlmann, E., Chemical Reviews 90: 543 (1990). (10.1021/cr00102a001) / Chemical Reviews (1990)
  47. 10.1002/prot.340020404
  48. 10.1126/science.8178167
  49. 10.1038/308509a0
  50. ZINKEL, S.S., DNA BEND DIRECTION BY PHASE SENSITIVE DETECTION, NATURE 328: 178 (1987). (10.1038/328178a0) / NATURE (1987)
Dates
Type When
Created 18 years, 10 months ago (Oct. 5, 2006, 8:01 p.m.)
Deposited 1 year, 7 months ago (Jan. 14, 2024, 11:29 p.m.)
Indexed 2 days ago (Aug. 27, 2025, 11:35 a.m.)
Issued 30 years, 8 months ago (Dec. 16, 1994)
Published 30 years, 8 months ago (Dec. 16, 1994)
Published Print 30 years, 8 months ago (Dec. 16, 1994)
Funders 0

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@article{Strauss_1994, title={DNA Bending by Asymmetric Phosphate Neutralization}, volume={266}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.7997878}, DOI={10.1126/science.7997878}, number={5192}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Strauss, Juliane K. and Maher, L. James}, year={1994}, month=dec, pages={1829–1834} }