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. 1992 Dec;56(4):509–528. doi: 10.1128/mr.56.4.509-528.1992

Use of gel retardation to analyze protein-nucleic acid interactions.

D Lane 1, P Prentki 1, M Chandler 1
PMCID: PMC372885  PMID: 1480106

Abstract

Protein-nucleic acid interactions are crucial in the regulation of many fundamental cellular processes. The nature of these interactions is susceptible to analysis by a variety of methods, but the combination of high analytical power and technical simplicity offered by the gel retardation (band shift) technique has made this perhaps the most widely used such method over the last decade. This procedure is based on the observation that the formation of protein-nucleic complexes generally reduces the electrophoretic mobility of the nucleic acid component in the gel matrix. This review attempts to give a simplified account of the physical basis of the behavior of protein-nucleic acid complexes in gels and an overview of many of the applications in which the technique has proved especially useful. The factors which contribute most to the resolution of the complex from the naked nucleic acid are the gel pore size, the relative mass of protein compared with nucleic acid, and changes in nucleic acid conformation (bending) induced by binding. The consequences of induced bending on the mobility of double-strand DNA fragments are similar to those arising from sequence-directed bends, and the latter can be used to help characterize the angle and direction of protein-induced bends. Whether a complex formed in solution is actually detected as a retarded band on a gel depends not only on resolution but also on complex stability within the gel. This is strongly influenced by the composition and, particularly, the ionic strength of the gel buffer. We discuss the applications of the technique to analyzing complex formation and stability, including characterizing cooperative binding, defining binding sites on nucleic acids, analyzing DNA conformation in complexes, assessing binding to supercoiled DNA, defining protein complexes by using cell extracts, and analyzing biological processes such as transcription and splicing.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abrahams J. P., Kraal B., Bosch L. Zone-interference gel electrophoresis: a new method for studying weak protein-nucleic acid complexes under native equilibrium conditions. Nucleic Acids Res. 1988 Nov 11;16(21):10099–10108. doi: 10.1093/nar/16.21.10099. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Alazard R., Bétermier M., Chandler M. Escherichia coli integration host factor stabilizes bacteriophage Mu repressor interactions with operator DNA in vitro. Mol Microbiol. 1992 Jun;6(12):1707–1714. doi: 10.1111/j.1365-2958.1992.tb00895.x. [DOI] [PubMed] [Google Scholar]
  3. Aragay A. M., Diaz P., Daban J. R. Association of nucleosome core particle DNA with different histone oligomers. Transfer of histones between DNA-(H2A,H2B) and DNA-(H3,H4) complexes. J Mol Biol. 1988 Nov 5;204(1):141–154. doi: 10.1016/0022-2836(88)90605-5. [DOI] [PubMed] [Google Scholar]
  4. Arcangioli B., Lescure B. Identification of proteins involved in the regulation of yeast iso- 1-cytochrome C expression by oxygen. EMBO J. 1985 Oct;4(10):2627–2633. doi: 10.1002/j.1460-2075.1985.tb03980.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bading H. Determination of the molecular weight of DNA-bound protein(s) responsible for gel electrophoretic mobility shift of linear DNA fragments examplified with purified viral myb protein. Nucleic Acids Res. 1988 Jun 24;16(12):5241–5248. doi: 10.1093/nar/16.12.5241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Barat C., Lullien V., Schatz O., Keith G., Nugeyre M. T., Grüninger-Leitch F., Barré-Sinoussi F., LeGrice S. F., Darlix J. L. HIV-1 reverse transcriptase specifically interacts with the anticodon domain of its cognate primer tRNA. EMBO J. 1989 Nov;8(11):3279–3285. doi: 10.1002/j.1460-2075.1989.tb08488.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Barcelo F., Muzard G., Mendoza R., Révet B., Roques B. P., Le Pecq J. B. Removal of DNA curving by DNA ligands: gel electrophoresis study. Biochemistry. 1991 May 21;30(20):4863–4873. doi: 10.1021/bi00234a005. [DOI] [PubMed] [Google Scholar]
  8. Barton H. A., Eisenstein R. S., Bomford A., Munro H. N. Determinants of the interaction between the iron-responsive element-binding protein and its binding site in rat L-ferritin mRNA. J Biol Chem. 1990 Apr 25;265(12):7000–7008. [PubMed] [Google Scholar]
  9. Berg O. G., Winter R. B., von Hippel P. H. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry. 1981 Nov 24;20(24):6929–6948. doi: 10.1021/bi00527a028. [DOI] [PubMed] [Google Scholar]
  10. Berman J., Eisenberg S., Tye B. K. An agarose gel electrophoresis assay for the detection of DNA-binding activities in yeast cell extracts. Methods Enzymol. 1987;155:528–537. doi: 10.1016/0076-6879(87)55034-0. [DOI] [PubMed] [Google Scholar]
  11. Bhattacharyya A., Lilley D. M. The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles). Nucleic Acids Res. 1989 Sep 12;17(17):6821–6840. doi: 10.1093/nar/17.17.6821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Blackwell T. K., Weintraub H. Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection. Science. 1990 Nov 23;250(4984):1104–1110. doi: 10.1126/science.2174572. [DOI] [PubMed] [Google Scholar]
  13. Boffini A., Prentki P. Identification of protein binding sites in genomic DNA by two-dimensional gel electrophoresis. Nucleic Acids Res. 1991 Apr 11;19(7):1369–1374. doi: 10.1093/nar/19.7.1369. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Bonnefoy E., Rouvière-Yaniv J. HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments. EMBO J. 1991 Mar;10(3):687–696. doi: 10.1002/j.1460-2075.1991.tb07998.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Brown B. M., Bowie J. U., Sauer R. T. Arc repressor is tetrameric when bound to operator DNA. Biochemistry. 1990 Dec 25;29(51):11189–11195. doi: 10.1021/bi00503a006. [DOI] [PubMed] [Google Scholar]
  16. Bruist M. F., Glasgow A. C., Johnson R. C., Simon M. I. Fis binding to the recombinational enhancer of the Hin DNA inversion system. Genes Dev. 1987 Oct;1(8):762–772. doi: 10.1101/gad.1.8.762. [DOI] [PubMed] [Google Scholar]
  17. Brunelle A., Schleif R. F. Missing contact probing of DNA-protein interactions. Proc Natl Acad Sci U S A. 1987 Oct;84(19):6673–6676. doi: 10.1073/pnas.84.19.6673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Buckle M., Geiselmann J., Kolb A., Buc H. Protein-DNA cross-linking at the lac promoter. Nucleic Acids Res. 1991 Feb 25;19(4):833–840. doi: 10.1093/nar/19.4.833. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Bustamante C. Direct observation and manipulation of single DNA molecules using fluorescence microscopy. Annu Rev Biophys Biophys Chem. 1991;20:415–446. doi: 10.1146/annurev.bb.20.060191.002215. [DOI] [PubMed] [Google Scholar]
  20. Bétermier M., Alazard R., Lefrère V., Chandler M. Functional domains of bacteriophage Mu transposase: properties of C-terminal deletions. Mol Microbiol. 1989 Sep;3(9):1159–1171. doi: 10.1111/j.1365-2958.1989.tb00266.x. [DOI] [PubMed] [Google Scholar]
  21. Bétermier M., Lefrère V., Koch C., Alazard R., Chandler M. The Escherichia coli protein, Fis: specific binding to the ends of phage Mu DNA and modulation of phage growth. Mol Microbiol. 1989 Apr;3(4):459–468. doi: 10.1111/j.1365-2958.1989.tb00192.x. [DOI] [PubMed] [Google Scholar]
  22. Calladine C. R., Collis C. M., Drew H. R., Mott M. R. A study of electrophoretic mobility of DNA in agarose and polyacrylamide gels. J Mol Biol. 1991 Oct 5;221(3):981–1005. doi: 10.1016/0022-2836(91)80187-y. [DOI] [PubMed] [Google Scholar]
  23. Cann J. R. Phenomenological theory of gel electrophoresis of protein-nucleic acid complexes. J Biol Chem. 1989 Oct 15;264(29):17032–17040. [PubMed] [Google Scholar]
  24. Carey J. Gel retardation at low pH resolves trp repressor-DNA complexes for quantitative study. Proc Natl Acad Sci U S A. 1988 Feb;85(4):975–979. doi: 10.1073/pnas.85.4.975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Chelm B. K., Geiduschek E. P. Gel electrophoretic separation of transcription complexes: an assay for RNA polymerase selectivity and a method for promoter mapping. Nucleic Acids Res. 1979 Dec 11;7(7):1851–1867. doi: 10.1093/nar/7.7.1851. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Chen J. W., Evans B. R., Yang S. H., Teplow D. B., Jayaram M. Domain of a yeast site-specific recombinase (Flp) that recognizes its target site. Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):5944–5948. doi: 10.1073/pnas.88.14.5944. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Collado-Vides J., Magasanik B., Gralla J. D. Control site location and transcriptional regulation in Escherichia coli. Microbiol Rev. 1991 Sep;55(3):371–394. doi: 10.1128/mr.55.3.371-394.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Dahlberg A. E., Dingman C. W., Peacock A. C. Electrophoretic characterization of bacterial polyribosomes in agarose-acrylamide composite gels. J Mol Biol. 1969 Apr 14;41(1):139–147. doi: 10.1016/0022-2836(69)90131-4. [DOI] [PubMed] [Google Scholar]
  29. Deutsch J. M. Theoretical studies of DNA during gel electrophoresis. Science. 1988 May 13;240(4854):922–924. doi: 10.1126/science.3363374. [DOI] [PubMed] [Google Scholar]
  30. Diekmann S. Temperature and salt dependence of the gel migration anomaly of curved DNA fragments. Nucleic Acids Res. 1987 Jan 12;15(1):247–265. doi: 10.1093/nar/15.1.247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Diekmann S., Wang J. C. On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities. J Mol Biol. 1985 Nov 5;186(1):1–11. doi: 10.1016/0022-2836(85)90251-7. [DOI] [PubMed] [Google Scholar]
  32. Dingwall C., Ernberg I., Gait M. J., Green S. M., Heaphy S., Karn J., Lowe A. D., Singh M., Skinner M. A. HIV-1 tat protein stimulates transcription by binding to a U-rich bulge in the stem of the TAR RNA structure. EMBO J. 1990 Dec;9(12):4145–4153. doi: 10.1002/j.1460-2075.1990.tb07637.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Drak J., Crothers D. M. Helical repeat and chirality effects on DNA gel electrophoretic mobility. Proc Natl Acad Sci U S A. 1991 Apr 15;88(8):3074–3078. doi: 10.1073/pnas.88.8.3074. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Dunderdale H. J., Benson F. E., Parsons C. A., Sharples G. J., Lloyd R. G., West S. C. Formation and resolution of recombination intermediates by E. coli RecA and RuvC proteins. Nature. 1991 Dec 19;354(6354):506–510. doi: 10.1038/354506a0. [DOI] [PubMed] [Google Scholar]
  35. Eismann E. R., Müller-Hill B. lac repressor forms stable loops in vitro with supercoiled wild-type lac DNA containing all three natural lac operators. J Mol Biol. 1990 Jun 20;213(4):763–775. doi: 10.1016/S0022-2836(05)80262-1. [DOI] [PubMed] [Google Scholar]
  36. Filutowicz M., Uhlenhopp E., Helinski D. R. Binding of purified wild-type and mutant pi initiation proteins to a replication origin region of plasmid R6K. J Mol Biol. 1986 Jan 20;187(2):225–239. doi: 10.1016/0022-2836(86)90230-5. [DOI] [PubMed] [Google Scholar]
  37. Fried M. G., Crothers D. M. CAP and RNA polymerase interactions with the lac promoter: binding stoichiometry and long range effects. Nucleic Acids Res. 1983 Jan 11;11(1):141–158. doi: 10.1093/nar/11.1.141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Fried M. G., Crothers D. M. Equilibrium studies of the cyclic AMP receptor protein-DNA interaction. J Mol Biol. 1984 Jan 25;172(3):241–262. doi: 10.1016/s0022-2836(84)80025-x. [DOI] [PubMed] [Google Scholar]
  39. Fried M. G., Crothers D. M. Kinetics and mechanism in the reaction of gene regulatory proteins with DNA. J Mol Biol. 1984 Jan 25;172(3):263–282. doi: 10.1016/s0022-2836(84)80026-1. [DOI] [PubMed] [Google Scholar]
  40. Fried M. G. Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay. Electrophoresis. 1989 May-Jun;10(5-6):366–376. doi: 10.1002/elps.1150100515. [DOI] [PubMed] [Google Scholar]
  41. Fried M., Crothers D. M. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 1981 Dec 11;9(23):6505–6525. doi: 10.1093/nar/9.23.6505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Gaillard C., Strauss F. Sequence-specific single-strand-binding protein for the simian virus 40 early promoter stimulates transcription in vitro. J Mol Biol. 1990 Sep 20;215(2):245–255. doi: 10.1016/S0022-2836(05)80343-2. [DOI] [PubMed] [Google Scholar]
  43. Gaillard C., Weber M., Strauss F. A sequence-specific single-strand-binding protein for the late-coding strand of the simian virus 40 control region. J Virol. 1988 Jul;62(7):2380–2385. doi: 10.1128/jvi.62.7.2380-2385.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Gama M. J., Toussaint A., Higgins N. P. Stabilization of bacteriophage Mu repressor-operator complexes by the Escherichia coli integration host factor protein. Mol Microbiol. 1992 Jun;6(12):1715–1722. doi: 10.1111/j.1365-2958.1992.tb00896.x. [DOI] [PubMed] [Google Scholar]
  45. Garner M. M., Revzin A. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res. 1981 Jul 10;9(13):3047–3060. doi: 10.1093/nar/9.13.3047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Garner M. M., Revzin A. Stoichiometry of catabolite activator protein/adenosine cyclic 3',5'-monophosphate interactions at the lac promoter of Escherichia coli. Biochemistry. 1982 Nov 23;21(24):6032–6036. doi: 10.1021/bi00267a001. [DOI] [PubMed] [Google Scholar]
  47. Gartenberg M. R., Crothers D. M. DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature. 1988 Jun 30;333(6176):824–829. doi: 10.1038/333824a0. [DOI] [PubMed] [Google Scholar]
  48. Gogos J. A., Tzertzinis G., Kafatos F. C. Binding site selection analysis of protein-DNA interactions via solid phase sequencing of oligonucleotide mixtures. Nucleic Acids Res. 1991 Apr 11;19(7):1449–1453. doi: 10.1093/nar/19.7.1449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Granger-Schnarr M., Lloubes R., de Murcia G., Schnarr M. Specific protein-DNA complexes: immunodetection of the protein component after gel electrophoresis and Western blotting. Anal Biochem. 1988 Oct;174(1):235–238. doi: 10.1016/0003-2697(88)90540-4. [DOI] [PubMed] [Google Scholar]
  50. Green R., Ellington A. D., Szostak J. W. In vitro genetic analysis of the Tetrahymena self-splicing intron. Nature. 1990 Sep 27;347(6291):406–408. doi: 10.1038/347406a0. [DOI] [PubMed] [Google Scholar]
  51. Griffith J., Bleyman M., Rauch C. A., Kitchin P. A., Englund P. T. Visualization of the bent helix in kinetoplast DNA by electron microscopy. Cell. 1986 Aug 29;46(5):717–724. doi: 10.1016/0092-8674(86)90347-8. [DOI] [PubMed] [Google Scholar]
  52. Hagerman P. J. Evidence for the existence of stable curvature of DNA in solution. Proc Natl Acad Sci U S A. 1984 Aug;81(15):4632–4636. doi: 10.1073/pnas.81.15.4632. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Hagerman P. J. Flexibility of DNA. Annu Rev Biophys Biophys Chem. 1988;17:265–286. doi: 10.1146/annurev.bb.17.060188.001405. [DOI] [PubMed] [Google Scholar]
  54. Hagerman P. J. Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. Biochemistry. 1985 Dec 3;24(25):7033–7037. doi: 10.1021/bi00346a001. [DOI] [PubMed] [Google Scholar]
  55. Hendrickson W., Schleif R. A dimer of AraC protein contacts three adjacent major groove regions of the araI DNA site. Proc Natl Acad Sci U S A. 1985 May;82(10):3129–3133. doi: 10.1073/pnas.82.10.3129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Higgins N. P., Collier D. A., Kilpatrick M. W., Krause H. M. Supercoiling and integration host factor change the DNA conformation and alter the flow of convergent transcription in phage Mu. J Biol Chem. 1989 Feb 15;264(5):3035–3042. [PubMed] [Google Scholar]
  57. Hochschild A., Ptashne M. Cooperative binding of lambda repressors to sites separated by integral turns of the DNA helix. Cell. 1986 Mar 14;44(5):681–687. doi: 10.1016/0092-8674(86)90833-0. [DOI] [PubMed] [Google Scholar]
  58. Hockensmith J. W., Kubasek W. L., Vorachek W. R., von Hippel P. H. Laser cross-linking of nucleic acids to proteins. Methodology and first applications to the phage T4 DNA replication system. J Biol Chem. 1986 Mar 15;261(8):3512–3518. [PubMed] [Google Scholar]
  59. Hope I. A., Struhl K. Functional dissection of a eukaryotic transcriptional activator protein, GCN4 of yeast. Cell. 1986 Sep 12;46(6):885–894. doi: 10.1016/0092-8674(86)90070-x. [DOI] [PubMed] [Google Scholar]
  60. Hope I. A., Struhl K. GCN4 protein, synthesized in vitro, binds HIS3 regulatory sequences: implications for general control of amino acid biosynthetic genes in yeast. Cell. 1985 Nov;43(1):177–188. doi: 10.1016/0092-8674(85)90022-4. [DOI] [PubMed] [Google Scholar]
  61. Hope I. A., Struhl K. GCN4, a eukaryotic transcriptional activator protein, binds as a dimer to target DNA. EMBO J. 1987 Sep;6(9):2781–2784. doi: 10.1002/j.1460-2075.1987.tb02573.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Horowitz D. S., Wang J. C. Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J Mol Biol. 1984 Feb 15;173(1):75–91. doi: 10.1016/0022-2836(84)90404-2. [DOI] [PubMed] [Google Scholar]
  63. Hudson J. M., Crowe L. G., Fried M. G. A new DNA binding mode for CAP. J Biol Chem. 1990 Feb 25;265(6):3219–3225. [PubMed] [Google Scholar]
  64. Hughes R. E., Hatfull G. F., Rice P., Steitz T. A., Grindley N. D. Cooperativity mutants of the gamma delta resolvase identify an essential interdimer interaction. Cell. 1990 Dec 21;63(6):1331–1338. doi: 10.1016/0092-8674(90)90428-h. [DOI] [PubMed] [Google Scholar]
  65. Jiricny J., Su S. S., Wood S. G., Modrich P. Mismatch-containing oligonucleotide duplexes bound by the E. coli mutS-encoded protein. Nucleic Acids Res. 1988 Aug 25;16(16):7843–7853. doi: 10.1093/nar/16.16.7843. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Johnson R. C., Glasgow A. C., Simon M. I. Spatial relationship of the Fis binding sites for Hin recombinational enhancer activity. Nature. 1987 Oct 1;329(6138):462–465. doi: 10.1038/329462a0. [DOI] [PubMed] [Google Scholar]
  67. Kim J., Zwieb C., Wu C., Adhya S. Bending of DNA by gene-regulatory proteins: construction and use of a DNA bending vector. Gene. 1989 Dec 21;85(1):15–23. doi: 10.1016/0378-1119(89)90459-9. [DOI] [PubMed] [Google Scholar]
  68. Kleinschmidt C., Tovar K., Hillen W. Computer simulations and experimental studies of gel mobility patterns for weak and strong non-cooperative protein binding to two targets on the same DNA: application to binding of tet repressor variants to multiple and single tet operator sites. Nucleic Acids Res. 1991 Mar 11;19(5):1021–1028. doi: 10.1093/nar/19.5.1021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Kolb A., Spassky A., Chapon C., Blazy B., Buc H. On the different binding affinities of CRP at the lac, gal and malT promoter regions. Nucleic Acids Res. 1983 Nov 25;11(22):7833–7852. doi: 10.1093/nar/11.22.7833. [DOI] [PMC free article] [PubMed] [Google Scholar]
  70. Konarska M. M., Sharp P. A. Electrophoretic separation of complexes involved in the splicing of precursors to mRNAs. Cell. 1986 Sep 12;46(6):845–855. doi: 10.1016/0092-8674(86)90066-8. [DOI] [PubMed] [Google Scholar]
  71. Koo H. S., Crothers D. M. Calibration of DNA curvature and a unified description of sequence-directed bending. Proc Natl Acad Sci U S A. 1988 Mar;85(6):1763–1767. doi: 10.1073/pnas.85.6.1763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  72. Koo H. S., Wu H. M., Crothers D. M. DNA bending at adenine . thymine tracts. Nature. 1986 Apr 10;320(6062):501–506. doi: 10.1038/320501a0. [DOI] [PubMed] [Google Scholar]
  73. Kotlarz D., Fritsch A., Buc H. Variations of intramolecular ligation rates allow the detection of protein-induced bends in DNA. EMBO J. 1986 Apr;5(4):799–803. doi: 10.1002/j.1460-2075.1986.tb04284.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  74. Kristie T. M., Roizman B. Alpha 4, the major regulatory protein of herpes simplex virus type 1, is stably and specifically associated with promoter-regulatory domains of alpha genes and of selected other viral genes. Proc Natl Acad Sci U S A. 1986 May;83(10):3218–3222. doi: 10.1073/pnas.83.10.3218. [DOI] [PMC free article] [PubMed] [Google Scholar]
  75. Krämer H., Amouyal M., Nordheim A., Müller-Hill B. DNA supercoiling changes the spacing requirement of two lac operators for DNA loop formation with lac repressor. EMBO J. 1988 Feb;7(2):547–556. doi: 10.1002/j.1460-2075.1988.tb02844.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  76. Krämer H., Niemöller M., Amouyal M., Revet B., von Wilcken-Bergmann B., Müller-Hill B. lac repressor forms loops with linear DNA carrying two suitably spaced lac operators. EMBO J. 1987 May;6(5):1481–1491. doi: 10.1002/j.1460-2075.1987.tb02390.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  77. Kunkel T. A., Eckstein F., Mildvan A. S., Koplitz R. M., Loeb L. A. Deoxynucleoside [1-thio]triphosphates prevent proofreading during in vitro DNA synthesis. Proc Natl Acad Sci U S A. 1981 Nov;78(11):6734–6738. doi: 10.1073/pnas.78.11.6734. [DOI] [PMC free article] [PubMed] [Google Scholar]
  78. Kuwabara M. D., Sigman D. S. Footprinting DNA-protein complexes in situ following gel retardation assays using 1,10-phenanthroline-copper ion: Escherichia coli RNA polymerase-lac promoter complexes. Biochemistry. 1987 Nov 17;26(23):7234–7238. doi: 10.1021/bi00397a006. [DOI] [PubMed] [Google Scholar]
  79. Laundon C. H., Griffith J. D. Cationic metals promote sequence-directed DNA bending. Biochemistry. 1987 Jun 30;26(13):3759–3762. doi: 10.1021/bi00387a003. [DOI] [PubMed] [Google Scholar]
  80. Liu-Johnson H. N., Gartenberg M. R., Crothers D. M. The DNA binding domain and bending angle of E. coli CAP protein. Cell. 1986 Dec 26;47(6):995–1005. doi: 10.1016/0092-8674(86)90814-7. [DOI] [PubMed] [Google Scholar]
  81. Lloubès R., Granger-Schnarr M., Lazdunski C., Schnarr M. LexA repressor induces operator-dependent DNA bending. J Mol Biol. 1988 Dec 20;204(4):1049–1054. doi: 10.1016/0022-2836(88)90062-9. [DOI] [PubMed] [Google Scholar]
  82. Lobell R. B., Schleif R. F. DNA looping and unlooping by AraC protein. Science. 1990 Oct 26;250(4980):528–532. doi: 10.1126/science.2237403. [DOI] [PubMed] [Google Scholar]
  83. Lu C., Echols H. RecA protein and SOS. Correlation of mutagenesis phenotype with binding of mutant RecA proteins to duplex DNA and LexA cleavage. J Mol Biol. 1987 Aug 5;196(3):497–504. doi: 10.1016/0022-2836(87)90027-1. [DOI] [PubMed] [Google Scholar]
  84. Lumpkin O. J., Déjardin P., Zimm B. H. Theory of gel electrophoresis of DNA. Biopolymers. 1985 Aug;24(8):1573–1593. doi: 10.1002/bip.360240812. [DOI] [PubMed] [Google Scholar]
  85. Lumpkin O. J. Mobility of DNA in gel electrophoresis. Biopolymers. 1982 Nov;21(11):2315–2316. doi: 10.1002/bip.360211116. [DOI] [PubMed] [Google Scholar]
  86. Mardian J. K., Paton A. E., Bunick G. J., Olins D. E. Nucleosome cores have two specific binding sites for nonhistone chromosomal proteins HMG 14 and HMG 17. Science. 1980 Sep 26;209(4464):1534–1536. doi: 10.1126/science.7433974. [DOI] [PubMed] [Google Scholar]
  87. Marini J. C., Levene S. D., Crothers D. M., Englund P. T. Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7664–7668. doi: 10.1073/pnas.79.24.7664. [DOI] [PMC free article] [PubMed] [Google Scholar]
  88. Matthews K. S. DNA looping. Microbiol Rev. 1992 Mar;56(1):123–136. doi: 10.1128/mr.56.1.123-136.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  89. Mavrothalassitis G., Beal G., Papas T. S. Defining target sequences of DNA-binding proteins by random selection and PCR: determination of the GCN4 binding sequence repertoire. DNA Cell Biol. 1990 Dec;9(10):783–788. doi: 10.1089/dna.1990.9.783. [DOI] [PubMed] [Google Scholar]
  90. McClarin J. A., Frederick C. A., Wang B. C., Greene P., Boyer H. W., Grable J., Rosenberg J. M. Structure of the DNA-Eco RI endonuclease recognition complex at 3 A resolution. Science. 1986 Dec 19;234(4783):1526–1541. doi: 10.1126/science.3024321. [DOI] [PubMed] [Google Scholar]
  91. McKay D. B., Pickover C. A., Steitz T. A. Escherichia coli lac repressor is elongated with its operator DNA binding domains located at both ends. J Mol Biol. 1982 Mar 25;156(1):175–183. doi: 10.1016/0022-2836(82)90465-x. [DOI] [PubMed] [Google Scholar]
  92. McKown R. L., Waddell C. S., Arciszewska L. K., Craig N. L. Identification of a transposon Tn7-dependent DNA-binding activity that recognizes the ends of Tn7. Proc Natl Acad Sci U S A. 1987 Nov;84(22):7807–7811. doi: 10.1073/pnas.84.22.7807. [DOI] [PMC free article] [PubMed] [Google Scholar]
  93. Nash H. A. Bending and supercoiling of DNA at the attachment site of bacteriophage lambda. Trends Biochem Sci. 1990 Jun;15(6):222–227. doi: 10.1016/0968-0004(90)90034-9. [DOI] [PubMed] [Google Scholar]
  94. Nordheim A., Meese K. Topoisomer gel retardation: detection of anti-Z-DNA antibodies bound to Z-DNA within supercoiled DNA minicircles. Nucleic Acids Res. 1988 Jan 11;16(1):21–37. doi: 10.1093/nar/16.1.21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  95. Oehler S., Eismann E. R., Krämer H., Müller-Hill B. The three operators of the lac operon cooperate in repression. EMBO J. 1990 Apr;9(4):973–979. doi: 10.1002/j.1460-2075.1990.tb08199.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  96. Orita M., Iwahana H., Kanazawa H., Hayashi K., Sekiya T. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2766–2770. doi: 10.1073/pnas.86.8.2766. [DOI] [PMC free article] [PubMed] [Google Scholar]
  97. Paillard S., Strauss F. Analysis of the mechanism of interaction of simian Ku protein with DNA. Nucleic Acids Res. 1991 Oct 25;19(20):5619–5624. doi: 10.1093/nar/19.20.5619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  98. Parsons C. A., Kemper B., West S. C. Interaction of a four-way junction in DNA with T4 endonuclease VII. J Biol Chem. 1990 Jun 5;265(16):9285–9289. [PubMed] [Google Scholar]
  99. Parsons C. A., West S. C. Specificity of binding to four-way junctions in DNA by bacteriophage T7 endonuclease I. Nucleic Acids Res. 1990 Aug 11;18(15):4377–4384. doi: 10.1093/nar/18.15.4377. [DOI] [PMC free article] [PubMed] [Google Scholar]
  100. Perri S., Helinski D. R., Toukdarian A. Interactions of plasmid-encoded replication initiation proteins with the origin of DNA replication in the broad host range plasmid RK2. J Biol Chem. 1991 Jul 5;266(19):12536–12543. [PubMed] [Google Scholar]
  101. Pikielny C. W., Rymond B. C., Rosbash M. Electrophoresis of ribonucleoproteins reveals an ordered assembly pathway of yeast splicing complexes. 1986 Nov 27-Dec 3Nature. 324(6095):341–345. doi: 10.1038/324341a0. [DOI] [PubMed] [Google Scholar]
  102. Pollock R., Treisman R. A sensitive method for the determination of protein-DNA binding specificities. Nucleic Acids Res. 1990 Nov 11;18(21):6197–6204. doi: 10.1093/nar/18.21.6197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  103. Porschke D., Hillen W., Takahashi M. The change of DNA structure by specific binding of the cAMP receptor protein from rotation diffusion and dichroism measurements. EMBO J. 1984 Dec 1;3(12):2873–2878. doi: 10.1002/j.1460-2075.1984.tb02223.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  104. Prentki P., Chandler M., Galas D. J. Escherichia coli integration host factor bends the DNA at the ends of IS1 and in an insertion hotspot with multiple IHF binding sites. EMBO J. 1987 Aug;6(8):2479–2487. doi: 10.1002/j.1460-2075.1987.tb02529.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  105. Prentki P., Pham M. H., Galas D. J. Plasmid permutation vectors to monitor DNA bending. Nucleic Acids Res. 1987 Dec 10;15(23):10060–10060. doi: 10.1093/nar/15.23.10060. [DOI] [PMC free article] [PubMed] [Google Scholar]
  106. Putney S. D., Benkovic S. J., Schimmel P. R. A DNA fragment with an alpha-phosphorothioate nucleotide at one end is asymmetrically blocked from digestion by exonuclease III and can be replicated in vivo. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7350–7354. doi: 10.1073/pnas.78.12.7350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  107. Record M. T., Jr, Mazur S. J., Melançon P., Roe J. H., Shaner S. L., Unger L. Double helical DNA: conformations, physical properties, and interactions with ligands. Annu Rev Biochem. 1981;50:997–1024. doi: 10.1146/annurev.bi.50.070181.005025. [DOI] [PubMed] [Google Scholar]
  108. Revzin A., Ceglarek J. A., Garner M. M. Comparison of nucleic acid-protein interactions in solution and in polyacrylamide gels. Anal Biochem. 1986 Feb 15;153(1):172–177. doi: 10.1016/0003-2697(86)90077-1. [DOI] [PubMed] [Google Scholar]
  109. Revzin A. Gel electrophoresis assays for DNA-protein interactions. Biotechniques. 1989 Apr;7(4):346–355. [PubMed] [Google Scholar]
  110. Rice J. A., Crothers D. M. DNA bending by the bulge defect. Biochemistry. 1989 May 16;28(10):4512–4516. doi: 10.1021/bi00436a058. [DOI] [PubMed] [Google Scholar]
  111. Rimphanitchayakit V., Hatfull G. F., Grindley N. D. The 43 residue DNA binding domain of gamma delta resolvase binds adjacent major and minor grooves of DNA. Nucleic Acids Res. 1989 Feb 11;17(3):1035–1050. doi: 10.1093/nar/17.3.1035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  112. Rosenbaum V., Riesner D. Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. Biophys Chem. 1987 May 9;26(2-3):235–246. doi: 10.1016/0301-4622(87)80026-1. [DOI] [PubMed] [Google Scholar]
  113. Rupp R. A., Sippel A. E. Chicken liver TGGCA protein purified by preparative mobility shift electrophoresis (PMSE) shows a 36.8 to 29.8 kd microheterogeneity. Nucleic Acids Res. 1987 Dec 10;15(23):9707–9726. doi: 10.1093/nar/15.23.9707. [DOI] [PMC free article] [PubMed] [Google Scholar]
  114. Salvo J. J., Grindley N. D. Helical phasing between DNA bends and the determination of bend direction. Nucleic Acids Res. 1987 Dec 10;15(23):9771–9779. doi: 10.1093/nar/15.23.9771. [DOI] [PMC free article] [PubMed] [Google Scholar]
  115. Sandeen G., Wood W. I., Felsenfeld G. The interaction of high mobility proteins HMG14 and 17 with nucleosomes. Nucleic Acids Res. 1980 Sep 11;8(17):3757–3778. doi: 10.1093/nar/8.17.3757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  116. Sandman K., Krzycki J. A., Dobrinski B., Lurz R., Reeve J. N. HMf, a DNA-binding protein isolated from the hyperthermophilic archaeon Methanothermus fervidus, is most closely related to histones. Proc Natl Acad Sci U S A. 1990 Aug;87(15):5788–5791. doi: 10.1073/pnas.87.15.5788. [DOI] [PMC free article] [PubMed] [Google Scholar]
  117. Sauer B., Henderson N. The cyclization of linear DNA in Escherichia coli by site-specific recombination. Gene. 1988 Oct 30;70(2):331–341. doi: 10.1016/0378-1119(88)90205-3. [DOI] [PubMed] [Google Scholar]
  118. Schneider G. J., Sayre M. H., Geiduschek E. P. DNA-bending properties of TF1. J Mol Biol. 1991 Oct 5;221(3):777–794. doi: 10.1016/0022-2836(91)80175-t. [DOI] [PubMed] [Google Scholar]
  119. Schreiber E., Matthias P., Müller M. M., Schaffner W. Identification of a novel lymphoid specific octamer binding protein (OTF-2B) by proteolytic clipping bandshift assay (PCBA). EMBO J. 1988 Dec 20;7(13):4221–4229. doi: 10.1002/j.1460-2075.1988.tb03319.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  120. Schroth G. P., Gottesfeld J. M., Bradbury E. M. TFIIIA induced DNA bending: effect of low ionic strength electrophoresis buffer conditions. Nucleic Acids Res. 1991 Feb 11;19(3):511–516. doi: 10.1093/nar/19.3.511. [DOI] [PMC free article] [PubMed] [Google Scholar]
  121. Schultz S. C., Shields G. C., Steitz T. A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science. 1991 Aug 30;253(5023):1001–1007. doi: 10.1126/science.1653449. [DOI] [PubMed] [Google Scholar]
  122. Schöler H. R., Hatzopoulos A. K., Balling R., Suzuki N., Gruss P. A family of octamer-specific proteins present during mouse embryogenesis: evidence for germline-specific expression of an Oct factor. EMBO J. 1989 Sep;8(9):2543–2550. doi: 10.1002/j.1460-2075.1989.tb08392.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  123. Senear D. F., Brenowitz M. Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay. J Biol Chem. 1991 Jul 25;266(21):13661–13671. [PubMed] [Google Scholar]
  124. Serwer P., Hayes S. J. Exclusion of spheres by agarose gels during agarose gel electrophoresis: dependence on the sphere's radius and the gel's concentration. Anal Biochem. 1986 Oct;158(1):72–78. doi: 10.1016/0003-2697(86)90591-9. [DOI] [PubMed] [Google Scholar]
  125. Shore D., Baldwin R. L. Energetics of DNA twisting. II. Topoisomer analysis. J Mol Biol. 1983 Nov 15;170(4):983–1007. doi: 10.1016/s0022-2836(83)80199-5. [DOI] [PubMed] [Google Scholar]
  126. Smith D. R., Jackson I. J., Brown D. D. Domains of the positive transcription factor specific for the Xenopus 5S RNA gene. Cell. 1984 Jun;37(2):645–652. doi: 10.1016/0092-8674(84)90396-9. [DOI] [PubMed] [Google Scholar]
  127. Snyder U. K., Thompson J. F., Landy A. Phasing of protein-induced DNA bends in a recombination complex. Nature. 1989 Sep 21;341(6239):255–257. doi: 10.1038/341255a0. [DOI] [PubMed] [Google Scholar]
  128. Stasiak A., Stasiak A. Z., Koller T. Visualization of RecA-DNA complexes involved in consecutive stages of an in vitro strand exchange reaction. Cold Spring Harb Symp Quant Biol. 1984;49:561–570. doi: 10.1101/sqb.1984.049.01.063. [DOI] [PubMed] [Google Scholar]
  129. Stenzel T. T., Patel P., Bastia D. The integration host factor of Escherichia coli binds to bent DNA at the origin of replication of the plasmid pSC101. Cell. 1987 Jun 5;49(5):709–717. doi: 10.1016/0092-8674(87)90547-2. [DOI] [PubMed] [Google Scholar]
  130. Stirling C. J., Szatmari G., Stewart G., Smith M. C., Sherratt D. J. The arginine repressor is essential for plasmid-stabilizing site-specific recombination at the ColE1 cer locus. EMBO J. 1988 Dec 20;7(13):4389–4395. doi: 10.1002/j.1460-2075.1988.tb03338.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  131. Straney D. C., Crothers D. M. Intermediates in transcription initiation from the E. coli lac UV5 promoter. Cell. 1985 Dec;43(2 Pt 1):449–459. doi: 10.1016/0092-8674(85)90175-8. [DOI] [PubMed] [Google Scholar]
  132. Straney D. C., Straney S. B., Crothers D. M. Synergy between Escherichia coli CAP protein and RNA polymerase in the lac promoter open complex. J Mol Biol. 1989 Mar 5;206(1):41–57. doi: 10.1016/0022-2836(89)90522-6. [DOI] [PubMed] [Google Scholar]
  133. Straney S. B., Crothers D. M. Lac repressor is a transient gene-activating protein. Cell. 1987 Dec 4;51(5):699–707. doi: 10.1016/0092-8674(87)90093-6. [DOI] [PubMed] [Google Scholar]
  134. Strauss F., Varshavsky A. A protein binds to a satellite DNA repeat at three specific sites that would be brought into mutual proximity by DNA folding in the nucleosome. Cell. 1984 Jul;37(3):889–901. doi: 10.1016/0092-8674(84)90424-0. [DOI] [PubMed] [Google Scholar]
  135. Studier F. W., Rosenberg A. H., Dunn J. J., Dubendorff J. W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 1990;185:60–89. doi: 10.1016/0076-6879(90)85008-c. [DOI] [PubMed] [Google Scholar]
  136. Thiesen H. J., Bach C. Target Detection Assay (TDA): a versatile procedure to determine DNA binding sites as demonstrated on SP1 protein. Nucleic Acids Res. 1990 Jun 11;18(11):3203–3209. doi: 10.1093/nar/18.11.3203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  137. Travers A. A. DNA conformation and protein binding. Annu Rev Biochem. 1989;58:427–452. doi: 10.1146/annurev.bi.58.070189.002235. [DOI] [PubMed] [Google Scholar]
  138. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 1990 Aug 3;249(4968):505–510. doi: 10.1126/science.2200121. [DOI] [PubMed] [Google Scholar]
  139. Wagenhöfer M., Hansen D., Hillen W. Thermal denaturation of engineered tet repressor proteins and their complexes with tet operator and tetracycline studied by temperature gradient gel electrophoresis. Anal Biochem. 1988 Dec;175(2):422–432. doi: 10.1016/0003-2697(88)90566-0. [DOI] [PubMed] [Google Scholar]
  140. Weber I. T., Steitz T. A. Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 A resolution. J Mol Biol. 1987 Nov 20;198(2):311–326. doi: 10.1016/0022-2836(87)90315-9. [DOI] [PubMed] [Google Scholar]
  141. Weeks K. M., Crothers D. M. RNA recognition by Tat-derived peptides: interaction in the major groove? Cell. 1991 Aug 9;66(3):577–588. doi: 10.1016/0092-8674(81)90020-9. [DOI] [PubMed] [Google Scholar]
  142. White S. W., Appelt K., Wilson K. S., Tanaka I. A protein structural motif that bends DNA. Proteins. 1989;5(4):281–288. doi: 10.1002/prot.340050405. [DOI] [PubMed] [Google Scholar]
  143. Wu H. M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 1984 Apr 5;308(5959):509–513. doi: 10.1038/308509a0. [DOI] [PubMed] [Google Scholar]
  144. Yamada H., Muramatsu S., Mizuno T. An Escherichia coli protein that preferentially binds to sharply curved DNA. J Biochem. 1990 Sep;108(3):420–425. doi: 10.1093/oxfordjournals.jbchem.a123216. [DOI] [PubMed] [Google Scholar]
  145. Zahn K., Blattner F. R. Binding and bending of the lambda replication origin by the phage O protein. EMBO J. 1985 Dec 16;4(13A):3605–3616. doi: 10.1002/j.1460-2075.1985.tb04124.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  146. Zahn K., Blattner F. R. Direct evidence for DNA bending at the lambda replication origin. Science. 1987 Apr 24;236(4800):416–422. doi: 10.1126/science.2951850. [DOI] [PubMed] [Google Scholar]
  147. Zerbib D., Jakowec M., Prentki P., Galas D. J., Chandler M. Expression of proteins essential for IS1 transposition: specific binding of InsA to the ends of IS1. EMBO J. 1987 Oct;6(10):3163–3169. doi: 10.1002/j.1460-2075.1987.tb02627.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  148. Zerbib D., Prentki P., Gamas P., Freund E., Galas D. J., Chandler M. Functional organization of the ends of IS1: specific binding site for an IS 1-encoded protein. Mol Microbiol. 1990 Sep;4(9):1477–1486. [PubMed] [Google Scholar]
  149. Zinkel S. S., Crothers D. M. Comparative gel electrophoresis measurement of the DNA bend angle induced by the catabolite activator protein. Biopolymers. 1990 Jan;29(1):29–38. doi: 10.1002/bip.360290106. [DOI] [PubMed] [Google Scholar]
  150. Zinkel S. S., Crothers D. M. DNA bend direction by phase sensitive detection. Nature. 1987 Jul 9;328(6126):178–181. doi: 10.1038/328178a0. [DOI] [PubMed] [Google Scholar]
  151. Zivanovic Y., Duband-Goulet I., Schultz P., Stofer E., Oudet P., Prunell A. Chromatin reconstitution on small DNA rings. III. Histone H5 dependence of DNA supercoiling in the nucleosome. J Mol Biol. 1990 Jul 20;214(2):479–495. doi: 10.1016/0022-2836(90)90195-R. [DOI] [PubMed] [Google Scholar]
  152. Zwieb C., Kim J., Adhya S. DNA bending by negative regulatory proteins: Gal and Lac repressors. Genes Dev. 1989 May;3(5):606–611. doi: 10.1101/gad.3.5.606. [DOI] [PubMed] [Google Scholar]

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