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. 1992 Jan;61(1):58–62. doi: 10.1016/S0006-3495(92)81815-5

Calculated enhancement of open base pair probability downstream of a (TATA)2 box.

R Beger 1, E W Prohofsky 1
PMCID: PMC1260222  PMID: 1540699

Abstract

The modified self-consistent phonon approximation is generalized to calculate the open base pair probability of a (TATA)2 insert between two semi-infinite poly(dA-dC) . poly(dG-dT) helices. An iterative method based entirely on the Green's function method is developed to compute the open interbase hydrogen bond probability of the insert and near bases versus temperature. The open interbase hydrogen bond probability is calculated for two temperatures and compared with perfect homopolymer open base pair probabilities at room temperature. The probability of opening is enhanced by a factor of two for the major groove bond of the AT pair at the transcriptional downstream end of the (TATA)2 insert. The total base pair opening probability of that pair is enhanced by 54%. The probability of the next inline GC base pair to be open is increased by a factor of ten.

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Selected References

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

  1. Burd J. F., Wartell R. M., Dodgson J. B., Wells R. D. Transmission of stability (telestability) in deoxyribonucleic acid. Physical and enzymatic studies on the duplex block polymer d(C15A15) - d(T15G15). J Biol Chem. 1975 Jul 10;250(13):5109–5113. [PubMed] [Google Scholar]
  2. Chen Y. Z., Feng Y., Prohofsky E. W. Premelting thermal fluctuational base pair opening probability of poly(dA).poly(dT) as predicted by the modified self-consistent phonon theory. Biopolymers. 1991 Feb 5;31(2):139–148. doi: 10.1002/bip.360310202. [DOI] [PubMed] [Google Scholar]
  3. Chen YZ, Feng Y, Prohofsky EW. Criterion of thermal denaturation for modified-self-consistent-phonon-theory mean-field calculations in DNA polymers. Phys Rev B Condens Matter. 1990 Dec 15;42(17):11335–11338. doi: 10.1103/physrevb.42.11335. [DOI] [PubMed] [Google Scholar]
  4. Cho K. O., Yanofsky C. Development of a trpE promoter-strength measuring system and its use in comparison of the trpEDCBA, trpR and aroH promoters. J Mol Biol. 1988 Nov 5;204(1):41–50. doi: 10.1016/0022-2836(88)90597-9. [DOI] [PubMed] [Google Scholar]
  5. Devi Prasad K. V., Prohofsky E. W. Low-frequency lattice mode predictions in A-DNA compared to experimental observations and significance for A-to-B conformation change. Biopolymers. 1984 Sep;23(9):1795–1798. doi: 10.1002/bip.360230912. [DOI] [PubMed] [Google Scholar]
  6. Eyster J. M., Prohofsky E. W. Lattice vibrational modes of poly(rU)-poly(rA). A coupled single-helical approach. Biopolymers. 1974 Dec;13(12):2527–2543. doi: 10.1002/bip.1974.360131210. [DOI] [PubMed] [Google Scholar]
  7. Feng Y, Beger RD, Hua X, Prohofsky EW. Breathing modes near a junction of DNA double helices. Phys Rev A Gen Phys. 1989 Oct 15;40(8):4612–4619. doi: 10.1103/physreva.40.4612. [DOI] [PubMed] [Google Scholar]
  8. Feng Y, Zhuang W, Prohofsky EW. Calculation of temperature dependence of interbase breathing motion of a guanine-cytosine DNA double helix with adenine-thymine insert. Phys Rev A. 1991 Jan 15;43(2):1049–1053. doi: 10.1103/physreva.43.1049. [DOI] [PubMed] [Google Scholar]
  9. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kim Y, Prohofsky EW. Defect-mediated hydrogen-bond instability of poly(dG)-poly(dC). Phys Rev B Condens Matter. 1986 Apr 15;33(8):5676–5681. doi: 10.1103/physrevb.33.5676. [DOI] [PubMed] [Google Scholar]
  11. Kim Y, Prohofsky EW. Vibrational modes of a DNA polymer at low temperature. Phys Rev B Condens Matter. 1987 Aug 15;36(6):3449–3451. doi: 10.1103/physrevb.36.3449. [DOI] [PubMed] [Google Scholar]
  12. Lamba O. P., Wang A. H., Thomas G. J., Jr Low-frequency dynamics and Raman scattering of crystals, of B-, A-, and Z-DNA, and fibers of C-DNA. Biopolymers. 1989 Feb;28(2):667–678. doi: 10.1002/bip.360280210. [DOI] [PubMed] [Google Scholar]
  13. Powell JW, Edwards GS, Genzel L, Kremer F, Wittlin A, Kubasek W, Peticolas W. Investigation of far-infrared vibrational modes in polynucleotides. Phys Rev A Gen Phys. 1987 May 1;35(9):3929–3939. doi: 10.1103/physreva.35.3929. [DOI] [PubMed] [Google Scholar]
  14. Putnam B. F., Prohofsky E. W. Localized vibrational modes at a double-helix-single-strand junction. Biopolymers. 1983 Jul;22(7):1759–1767. doi: 10.1002/bip.360220711. [DOI] [PubMed] [Google Scholar]
  15. Putnam B. F., Van Zandt L. L., Prohofsky E. W., Mei W. N. Resonant and localized breathing modes in terminal regions of the DNA double helix. Biophys J. 1981 Aug;35(2):271–287. doi: 10.1016/S0006-3495(81)84789-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Weidlich T, Lindsay SM, Rupprecht A. Counterion effects on the structure and dynamics of solid DNA. Phys Rev Lett. 1988 Oct 3;61(14):1674–1677. doi: 10.1103/PhysRevLett.61.1674. [DOI] [PubMed] [Google Scholar]
  17. Wells R. D., Blakesley R. W., Hardies S. C., Horn G. T., Larson J. E., Selsing E., Burd J. F., Chan H. W., Dodgson J. B., Jensen K. F. The role of DNA structure in genetic regulation. CRC Crit Rev Biochem. 1977;4(3):305–340. doi: 10.3109/10409237709102561. [DOI] [PubMed] [Google Scholar]

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