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. 1996 Oct 29;93(22):12122–12127. doi: 10.1073/pnas.93.22.12122

The design of an agent to bend DNA.

T Akiyama 1, M E Hogan 1
PMCID: PMC37953  PMID: 8901543

Abstract

An artificial DNA bending agent has been designed to assess helix flexibility over regions as small as a protein binding site. Bending was obtained by linking a pair of 15-base-long triple helix forming oligonucleotides (TFOs) by an adjustable polymeric linker. By design, DNA bending was introduced into the double helix within a 10-bp spacer region positioned between the two sites of 15-base triple helix formation. The existence of this bend has been confirmed by circular permutation and phase-sensitive electrophoresis, and the directionality of the bend has been determined as a compression of the minor helix groove. The magnitude of the resulting duplex bend was found to be dependent on the length of the polymeric linker in a fashion consistent with a simple geometric model. Data suggested that a 50-70 degrees bend was achieved by binding of the TFO chimera with the shortest linker span (18 rotatable bonds). Equilibrium analysis showed that, relative to a chimera which did not bend the duplex, the stability of the triple helix possessing a 50-70 degrees bend was reduced by less than 1 kcal/mol of that of the unbent complex. Based upon this similarity, it is proposed that duplex DNA may be much more flexible with respect to minor groove compression than previously assumed. It is shown that this unusual flexibility is consistent with recent quantitation of protein-induced minor groove bending.

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Selected References

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

  1. Beal P. A., Dervan P. B. Second structural motif for recognition of DNA by oligonucleotide-directed triple-helix formation. Science. 1991 Mar 15;251(4999):1360–1363. doi: 10.1126/science.2003222. [DOI] [PubMed] [Google Scholar]
  2. Beechem J. M. Global analysis of biochemical and biophysical data. Methods Enzymol. 1992;210:37–54. doi: 10.1016/0076-6879(92)10004-w. [DOI] [PubMed] [Google Scholar]
  3. Chow K. L., Hogan M. E., Schwartz R. J. Phased cis-acting promoter elements interact at short distances to direct avian skeletal alpha-actin gene transcription. Proc Natl Acad Sci U S A. 1991 Feb 15;88(4):1301–1305. doi: 10.1073/pnas.88.4.1301. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Durland R. H., Kessler D. J., Gunnell S., Duvic M., Pettitt B. M., Hogan M. E. Binding of triple helix forming oligonucleotides to sites in gene promoters. Biochemistry. 1991 Sep 24;30(38):9246–9255. doi: 10.1021/bi00102a017. [DOI] [PubMed] [Google Scholar]
  6. Gartenberg M. R., Crothers D. M. Synthetic DNA bending sequences increase the rate of in vitro transcription initiation at the Escherichia coli lac promoter. J Mol Biol. 1991 May 20;219(2):217–230. doi: 10.1016/0022-2836(91)90563-l. [DOI] [PubMed] [Google Scholar]
  7. Goodman S. D., Nash H. A. Functional replacement of a protein-induced bend in a DNA recombination site. Nature. 1989 Sep 21;341(6239):251–254. doi: 10.1038/341251a0. [DOI] [PubMed] [Google Scholar]
  8. Hagerman P. J. Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers. 1981 Jul;20(7):1503–1535. doi: 10.1002/bip.1981.360200710. [DOI] [PubMed] [Google Scholar]
  9. Hogan M. E., Austin R. H. Importance of DNA stiffness in protein-DNA binding specificity. Nature. 1987 Sep 17;329(6136):263–266. doi: 10.1038/329263a0. [DOI] [PubMed] [Google Scholar]
  10. Jin Y., Mead J., Li T., Wolberger C., Vershon A. K. Altered DNA recognition and bending by insertions in the alpha 2 tail of the yeast a1/alpha 2 homeodomain heterodimer. Science. 1995 Oct 13;270(5234):290–293. doi: 10.1126/science.270.5234.290. [DOI] [PubMed] [Google Scholar]
  11. Kahn J. D., Crothers D. M. Protein-induced bending and DNA cyclization. Proc Natl Acad Sci U S A. 1992 Jul 15;89(14):6343–6347. doi: 10.1073/pnas.89.14.6343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kerppola T. K., Curran T. DNA bending by Fos and Jun: the flexible hinge model. Science. 1991 Nov 22;254(5035):1210–1214. doi: 10.1126/science.1957173. [DOI] [PubMed] [Google Scholar]
  13. Kerppola T. K., Curran T. Fos-Jun heterodimers and Jun homodimers bend DNA in opposite orientations: implications for transcription factor cooperativity. Cell. 1991 Jul 26;66(2):317–326. doi: 10.1016/0092-8674(91)90621-5. [DOI] [PubMed] [Google Scholar]
  14. Kessler D. J., Pettitt B. M., Cheng Y. K., Smith S. R., Jayaraman K., Vu H. M., Hogan M. E. Triple helix formation at distant sites: hybrid oligonucleotides containing a polymeric linker. Nucleic Acids Res. 1993 Oct 11;21(20):4810–4815. doi: 10.1093/nar/21.20.4810. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. 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]
  16. Kovacic R. T., van Holde K. E. Sedimentation of homogeneous double-strand DNA molecules. Biochemistry. 1977 Apr 5;16(7):1490–1498. doi: 10.1021/bi00626a038. [DOI] [PubMed] [Google Scholar]
  17. Levene S. D., Zimm B. H. Understanding the anomalous electrophoresis of bent DNA molecules: a reptation model. Science. 1989 Jul 28;245(4916):396–399. doi: 10.1126/science.2756426. [DOI] [PubMed] [Google Scholar]
  18. Li T., Stark M. R., Johnson A. D., Wolberger C. Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA. Science. 1995 Oct 13;270(5234):262–269. doi: 10.1126/science.270.5234.262. [DOI] [PubMed] [Google Scholar]
  19. 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]
  20. McGhee J. D., Felsenfeld G. Nucleosome structure. Annu Rev Biochem. 1980;49:1115–1156. doi: 10.1146/annurev.bi.49.070180.005343. [DOI] [PubMed] [Google Scholar]
  21. Moitoso de Vargas L., Kim S., Landy A. DNA looping generated by DNA bending protein IHF and the two domains of lambda integrase. Science. 1989 Jun 23;244(4911):1457–1461. doi: 10.1126/science.2544029. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Olson W. K., Marky N. L., Jernigan R. L., Zhurkin V. B. Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. J Mol Biol. 1993 Jul 20;232(2):530–554. doi: 10.1006/jmbi.1993.1409. [DOI] [PubMed] [Google Scholar]
  23. Parvin J. D., McCormick R. J., Sharp P. A., Fisher D. E. Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor. Nature. 1995 Feb 23;373(6516):724–727. doi: 10.1038/373724a0. [DOI] [PubMed] [Google Scholar]
  24. Pérez-Martín J., Espinosa M. Protein-induced bending as a transcriptional switch. Science. 1993 May 7;260(5109):805–807. doi: 10.1126/science.8387228. [DOI] [PubMed] [Google Scholar]
  25. 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]
  26. Shin C., Koo H. S. Helical periodicity of GA-alternating triple-stranded DNA. Biochemistry. 1996 Jan 23;35(3):968–972. doi: 10.1021/bi952163j. [DOI] [PubMed] [Google Scholar]
  27. Shore D., Langowski J., Baldwin R. L. DNA flexibility studied by covalent closure of short fragments into circles. Proc Natl Acad Sci U S A. 1981 Aug;78(8):4833–4837. doi: 10.1073/pnas.78.8.4833. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Strauss J. K., Maher L. J., 3rd DNA bending by asymmetric phosphate neutralization. Science. 1994 Dec 16;266(5192):1829–1834. doi: 10.1126/science.7997878. [DOI] [PubMed] [Google Scholar]
  29. Taylor W. H., Hagerman P. J. Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA flexibility and helical repeat. J Mol Biol. 1990 Mar 20;212(2):363–376. doi: 10.1016/0022-2836(90)90131-5. [DOI] [PubMed] [Google Scholar]
  30. Thompson J. F., Landy A. Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. Nucleic Acids Res. 1988 Oct 25;16(20):9687–9705. doi: 10.1093/nar/16.20.9687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. 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]
  32. Zhurkin V. B., Ulyanov N. B., Gorin A. A., Jernigan R. L. Static and statistical bending of DNA evaluated by Monte Carlo simulations. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7046–7050. doi: 10.1073/pnas.88.16.7046. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. 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]

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