Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1987 Jan 12;15(1):105–118. doi: 10.1093/nar/15.1.105

Sequence dependent electrophoretic mobilities and melting temperatures for A-T containing oligodeoxyribonucleotides.

W D Wilson, E T Zuo, R L Jones, G L Zon, B R Baumstark
PMCID: PMC340400  PMID: 3822802

Abstract

The electrophoretic mobilities and thermal melting properties of self complementary A-T containing dodecamer oligodeoxyribonucleotides have been investigated as a function of solution conditions. The oligomers contained tracts of nonalternating A-T base pairs of 2 (d(A2T2)3), 3 (d(A3T3)2), and 6 (d(A6T6] as well as the fully alternating (d(A-T)6) sequence. The melting temperature increased with the length of the nonalternating sequence and was approximately 12 degrees C higher in the d(A6T6) sequence than in the alternating oligomer. Under denaturing conditions all oligomers had the same electrophoretic mobility on acrylamide gels. Under conditions which favor duplex formation, the oligomers exhibited significant sequence dependent mobility differences. The mobilities of two oligomers, d(A-T)6 and d(A6-T6), were approximately equal and were less than those of the other oligonucleotides. The greatest mobility was observed for d(A2T2)3. These results are best explained by a model which requires bending at a junction of two or more continuous A or T bases with another sequence.

Full text

PDF
105

Images in this article

111Image
on p.111
113Image
on p.113

Selected References

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

  1. Arnott S., Chandrasekaran R., Hall I. H., Puigjaner L. C., Walker J. K., Wang M. DNA secondary structures: helices, wrinkles, and junctions. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):53–65. doi: 10.1101/sqb.1983.047.01.008. [DOI] [PubMed] [Google Scholar]
  2. Behling R. W., Kearns D. R. 1H two-dimensional nuclear Overhauser effect and relaxation studies of poly(dA).poly(dT) Biochemistry. 1986 Jun 3;25(11):3335–3346. doi: 10.1021/bi00359a037. [DOI] [PubMed] [Google Scholar]
  3. Bresloff J. L., Crothers D. M. Equilibrium studies of ethidium--polynucleotide interactions. Biochemistry. 1981 Jun 9;20(12):3547–3553. doi: 10.1021/bi00515a038. [DOI] [PubMed] [Google Scholar]
  4. Calladine C. R. Mechanics of sequence-dependent stacking of bases in B-DNA. J Mol Biol. 1982 Oct 25;161(2):343–352. doi: 10.1016/0022-2836(82)90157-7. [DOI] [PubMed] [Google Scholar]
  5. Chaires J. B. Equilibrium studies on the interaction of daunomycin with deoxypolynucleotides. Biochemistry. 1983 Aug 30;22(18):4204–4211. doi: 10.1021/bi00287a007. [DOI] [PubMed] [Google Scholar]
  6. Dickerson R. E. Base sequence and helix structure variation in B and A DNA. J Mol Biol. 1983 May 25;166(3):419–441. doi: 10.1016/s0022-2836(83)80093-x. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Drew H. R., Weeks J. R., Travers A. A. Negative supercoiling induces spontaneous unwinding of a bacterial promoter. EMBO J. 1985 Apr;4(4):1025–1032. doi: 10.1002/j.1460-2075.1985.tb03734.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Frank R., Köster H. DNA chain length markers and the influence of base composition on electrophoretic mobility of oligodeoxyribonucleotides in polyacrylamide-gels. Nucleic Acids Res. 1979;6(6):2069–2087. doi: 10.1093/nar/6.6.2069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. 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]
  11. 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]
  12. Kunkel G. R., Martinson H. G. Nucleosomes will not form on double-stranded RNa or over poly(dA).poly(dT) tracts in recombinant DNA. Nucleic Acids Res. 1981 Dec 21;9(24):6869–6888. doi: 10.1093/nar/9.24.6869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Levene S. D., Wu H. M., Crothers D. M. Bending and flexibility of kinetoplast DNA. Biochemistry. 1986 Jul 15;25(14):3988–3995. doi: 10.1021/bi00362a003. [DOI] [PubMed] [Google Scholar]
  14. Marky L. A., Curry J., Breslauer K. J. Netropsin binding to polyd(AT) X polyd(AT) and to polydA X polydT: a comparative thermodynamic study. Prog Clin Biol Res. 1985;172B:155–173. [PubMed] [Google Scholar]
  15. Petersheim M., Turner D. H. Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry. 1983 Jan 18;22(2):256–263. doi: 10.1021/bi00271a004. [DOI] [PubMed] [Google Scholar]
  16. Sarma M. H., Gupta G., Sarma R. H. Untenability of the heteronomous DNA model for poly(dA).poly(dT) in solution. This DNA adopts a right-handed B-DNA duplex in which the two strands are conformationally equivalent. A 500 MHz NMR study using one dimensional NOE. J Biomol Struct Dyn. 1985 Jun;2(6):1057–1084. doi: 10.1080/07391102.1985.10507624. [DOI] [PubMed] [Google Scholar]
  17. Scheffler I. E., Elson E. L., Baldwin R. L. Helix formation by dAT oligomers. I. Hairpin and straight-chain helices. J Mol Biol. 1968 Sep 28;36(3):291–304. doi: 10.1016/0022-2836(68)90156-3. [DOI] [PubMed] [Google Scholar]
  18. Sturm J. Binding of ligands to a one-dimensional heterogeneous lattice. III. Kinetic model and relaxation study of the interaction of tilorone with DNA and polynucleotides. Biopolymers. 1982 Jun;21(6):1189–1206. doi: 10.1002/bip.360210613. [DOI] [PubMed] [Google Scholar]
  19. Trifonov E. N. Curved DNA. CRC Crit Rev Biochem. 1985;19(2):89–106. doi: 10.3109/10409238509082540. [DOI] [PubMed] [Google Scholar]
  20. Tung C. S., Harvey S. C. Base sequence, local helix structure, and macroscopic curvature of A-DNA and B-DNA. J Biol Chem. 1986 Mar 15;261(8):3700–3709. [PubMed] [Google Scholar]
  21. Tung C. S., Harvey S. C. Computer graphics program to reveal the dependence of the gross three-dimensional structure of the B-DNA double helix on primary structure. Nucleic Acids Res. 1986 Jan 10;14(1):381–387. doi: 10.1093/nar/14.1.381. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Ulanovsky L., Bodner M., Trifonov E. N., Choder M. Curved DNA: design, synthesis, and circularization. Proc Natl Acad Sci U S A. 1986 Feb;83(4):862–866. doi: 10.1073/pnas.83.4.862. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Wartell R. M., Harrell J. T. Characteristics and variations of B-type DNA conformations in solution: a quantitative analysis of Raman band intensities of eight DNAs. Biochemistry. 1986 May 6;25(9):2664–2671. doi: 10.1021/bi00357a056. [DOI] [PubMed] [Google Scholar]
  24. Wilson W. D., Wang Y. H., Krishnamoorthy C. R., Smith J. C. Intercalators as probes of DNA conformation: propidium binding to alternating and non-alternating polymers containing guanine. Chem Biol Interact. 1986 Apr;58(1):41–56. doi: 10.1016/s0009-2797(86)80085-0. [DOI] [PubMed] [Google Scholar]
  25. Wilson W. D., Wang Y. H., Krishnamoorthy C. R., Smith J. C. Poly(dA).poly(dT) exists in an unusual conformation under physiological conditions: propidium binding to poly(dA).poly(dT) and poly[d(A-T)].poly[d(A-T)]. Biochemistry. 1985 Jul 16;24(15):3991–3999. doi: 10.1021/bi00336a029. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES