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. 2001 Jul;81(1):371–381. doi: 10.1016/S0006-3495(01)75706-2

Sedimentation analysis of novel DNA structures formed by homo-oligonucleotides.

D M Hatters 1, L Wilson 1, B W Atcliffe 1, T D Mulhern 1, N Guzzo-Pernell 1, G J Howlett 1
PMCID: PMC1301518  PMID: 11423421

Abstract

Sedimentation velocity analysis has been used to examine the base-specific structural conformations and unusual hydrogen bonding patterns of model oligonucleotides. Homo-oligonucleotides composed of 8-28 residues of dA, dT, or dC nucleotides in 100 mM sodium phosphate, pH 7.4, at 20 degrees C behave as extended monomers. Comparison of experimentally determined sedimentation coefficients with theoretical values calculated for assumed helical structures show that dT and dC oligonucleotides are more compact than dA oligonucleotides. For dA oligonucleotides, the average width (1.7 nm), assuming a cylindrical model, is smaller than for control duplex DNA whereas the average rise per base (0.34 nm) is similar to that of B-DNA. For dC and dT oligonucleotides, there is an increase in the average widths (1.8 nm and 2.1 nm, respectively) whereas the average rise per base is smaller (0.28 nm and 0.23 nm, respectively). A significant shape change is observed for oligo dC(28) at lower temperatures (10 degrees C), corresponding to a fourfold decrease in axial ratio. Optical density, circular dichroism, and differential scanning calorimetry data confirm this shape change, attributable from nuclear magnetic resonance analysis to i-motif formation. Sedimentation equilibrium studies of oligo dG(8) and dG(16) reveal extensive self-association and the formation of G-quadruplexes. Continuous distribution analysis of sedimentation velocity data for oligo dG(16) identifies the presence of discrete dimers, tetramers, and dodecamers. These studies distinguish the conformational and colligative properties of the individual bases in DNA and their inherent capacity to promote specific folding pathways.

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Selected References

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

  1. Ahmed S., Henderson E. Formation of novel hairpin structures by telomeric C-strand oligonucleotides. Nucleic Acids Res. 1992 Feb 11;20(3):507–511. doi: 10.1093/nar/20.3.507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arnott S., Bond P. J., Selsing E., Smith P. J. Models of triple-stranded polynucleotides with optimised stereochemistry. Nucleic Acids Res. 1976 Oct;3(10):2459–2470. doi: 10.1093/nar/3.10.2459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Blackburn E. H. The molecular structure of centromeres and telomeres. Annu Rev Biochem. 1984;53:163–194. doi: 10.1146/annurev.bi.53.070184.001115. [DOI] [PubMed] [Google Scholar]
  4. Bonifacio G. F., Brown T., Conn G. L., Lane A. N. Comparison of the electrophoretic and hydrodynamic properties of DNA and RNA oligonucleotide duplexes. Biophys J. 1997 Sep;73(3):1532–1538. doi: 10.1016/S0006-3495(97)78185-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cantor C. R., Warshaw M. M., Shapiro H. Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers. 1970;9(9):1059–1077. doi: 10.1002/bip.1970.360090909. [DOI] [PubMed] [Google Scholar]
  6. Cassani G. R., Bollum F. J. Oligodeoxythymidylate: polydeoxyadenylate and oligodeoxyadenylate: polydeoxythymidylate interactions. Biochemistry. 1969 Oct;8(10):3928–3936. doi: 10.1021/bi00838a008. [DOI] [PubMed] [Google Scholar]
  7. Catasti P., Chen X., Moyzis R. K., Bradbury E. M., Gupta G. Structure-function correlations of the insulin-linked polymorphic region. J Mol Biol. 1996 Dec 6;264(3):534–545. doi: 10.1006/jmbi.1996.0659. [DOI] [PubMed] [Google Scholar]
  8. Chakrabarti M. C., Schwarz F. P. Thermal stability of PNA/DNA and DNA/DNA duplexes by differential scanning calorimetry. Nucleic Acids Res. 1999 Dec 15;27(24):4801–4806. doi: 10.1093/nar/27.24.4801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chen X., Mariappan S. V., Catasti P., Ratliff R., Moyzis R. K., Laayoun A., Smith S. S., Bradbury E. M., Gupta G. Hairpins are formed by the single DNA strands of the fragile X triplet repeats: structure and biological implications. Proc Natl Acad Sci U S A. 1995 May 23;92(11):5199–5203. doi: 10.1073/pnas.92.11.5199. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fahlman R. P., Sen D. Cation-regulated self-association of "synapsable" DNA duplexes. J Mol Biol. 1998 Jul 10;280(2):237–244. doi: 10.1006/jmbi.1998.1875. [DOI] [PubMed] [Google Scholar]
  11. Ferrer N., Azorín F., Villasante A., Gutiérrez C., Abad J. P. Centromeric dodeca-satellite DNA sequences form fold-back structures. J Mol Biol. 1995 Jan 6;245(1):8–21. doi: 10.1016/s0022-2836(95)80034-4. [DOI] [PubMed] [Google Scholar]
  12. García De La Torre J., Huertas M. L., Carrasco B. Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys J. 2000 Feb;78(2):719–730. doi: 10.1016/S0006-3495(00)76630-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gehring K., Leroy J. L., Guéron M. A tetrameric DNA structure with protonated cytosine.cytosine base pairs. Nature. 1993 Jun 10;363(6429):561–565. doi: 10.1038/363561a0. [DOI] [PubMed] [Google Scholar]
  14. Guo Q., Lu M., Kallenbach N. R. Effect of thymine tract length on the structure and stability of model telomeric sequences. Biochemistry. 1993 Apr 13;32(14):3596–3603. doi: 10.1021/bi00065a010. [DOI] [PubMed] [Google Scholar]
  15. Guzzo-Pernell N., Lawlor J. M., Haralambidis J. Triple helical DNA. Biomed Pept Proteins Nucleic Acids. 1996;2(4):107–122. [PubMed] [Google Scholar]
  16. Han X., Leroy J. L., Guéron M. An intramolecular i-motif: the solution structure and base-pair opening kinetics of d(5mCCT3CCT3ACCT3CC). J Mol Biol. 1998 May 22;278(5):949–965. doi: 10.1006/jmbi.1998.1740. [DOI] [PubMed] [Google Scholar]
  17. Holbrook J. A., Capp M. W., Saecker R. M., Record M. T., Jr Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices. Biochemistry. 1999 Jun 29;38(26):8409–8422. doi: 10.1021/bi990043w. [DOI] [PubMed] [Google Scholar]
  18. Howell R. M., Woodford K. J., Weitzmann M. N., Usdin K. The chicken beta-globin gene promoter forms a novel "cinched" tetrahelical structure. J Biol Chem. 1996 Mar 1;271(9):5208–5214. doi: 10.1074/jbc.271.9.5208. [DOI] [PubMed] [Google Scholar]
  19. Kang C., Zhang X., Ratliff R., Moyzis R., Rich A. Crystal structure of four-stranded Oxytricha telomeric DNA. Nature. 1992 Mar 12;356(6365):126–131. doi: 10.1038/356126a0. [DOI] [PubMed] [Google Scholar]
  20. Kettani A., Kumar R. A., Patel D. J. Solution structure of a DNA quadruplex containing the fragile X syndrome triplet repeat. J Mol Biol. 1995 Dec 8;254(4):638–656. doi: 10.1006/jmbi.1995.0644. [DOI] [PubMed] [Google Scholar]
  21. LANGRIDGE R., RICH A. Molecular structure of helical polycytidylic acid. Nature. 1963 May 25;198:725–728. doi: 10.1038/198725a0. [DOI] [PubMed] [Google Scholar]
  22. Laughlan G., Murchie A. I., Norman D. G., Moore M. H., Moody P. C., Lilley D. M., Luisi B. The high-resolution crystal structure of a parallel-stranded guanine tetraplex. Science. 1994 Jul 22;265(5171):520–524. doi: 10.1126/science.8036494. [DOI] [PubMed] [Google Scholar]
  23. Leroy J. L., Gehring K., Kettani A., Guéron M. Acid multimers of oligodeoxycytidine strands: stoichiometry, base-pair characterization, and proton exchange properties. Biochemistry. 1993 Jun 15;32(23):6019–6031. doi: 10.1021/bi00074a013. [DOI] [PubMed] [Google Scholar]
  24. Leroy J. L., Guéron M., Mergny J. L., Hélène C. Intramolecular folding of a fragment of the cytosine-rich strand of telomeric DNA into an i-motif. Nucleic Acids Res. 1994 May 11;22(9):1600–1606. doi: 10.1093/nar/22.9.1600. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Manzini G., Yathindra N., Xodo L. E. Evidence for intramolecularly folded i-DNA structures in biologically relevant CCC-repeat sequences. Nucleic Acids Res. 1994 Nov 11;22(22):4634–4640. doi: 10.1093/nar/22.22.4634. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Nadeau J. G., Crothers D. M. Structural basis for DNA bending. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2622–2626. doi: 10.1073/pnas.86.8.2622. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Nonin S., Leroy J. L. Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer. J Mol Biol. 1996 Aug 23;261(3):399–414. doi: 10.1006/jmbi.1996.0472. [DOI] [PubMed] [Google Scholar]
  28. Olsthoorn C. S., Bostelaar L. J., De Rooij J. F., Van Boom J. H., Altona C. Circular dichroism study of stacking properties of oligodeoxyadenylates and polydeoxyadenylate. A three-state conformational model. Eur J Biochem. 1981 Apr;115(2):309–321. doi: 10.1111/j.1432-1033.1981.tb05240.x. [DOI] [PubMed] [Google Scholar]
  29. Phan A. T., Guéron M., Leroy J. L. The solution structure and internal motions of a fragment of the cytidine-rich strand of the human telomere. J Mol Biol. 2000 May 26;299(1):123–144. doi: 10.1006/jmbi.2000.3613. [DOI] [PubMed] [Google Scholar]
  30. Schuck P., MacPhee C. E., Howlett G. J. Determination of sedimentation coefficients for small peptides. Biophys J. 1998 Jan;74(1):466–474. doi: 10.1016/S0006-3495(98)77804-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Schuck P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys J. 2000 Mar;78(3):1606–1619. doi: 10.1016/S0006-3495(00)76713-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Uliel L., Weisman-Shomer P., Oren-Jazan H., Newcomb T., Loeb L. A., Fry M. Human Ku antigen tightly binds and stabilizes a tetrahelical form of the Fragile X syndrome d(CGG)n expanded sequence. J Biol Chem. 2000 Oct 20;275(42):33134–33141. doi: 10.1074/jbc.M005542200. [DOI] [PubMed] [Google Scholar]
  33. Venczel E. A., Sen D. Synapsable DNA. J Mol Biol. 1996 Mar 29;257(2):219–224. doi: 10.1006/jmbi.1996.0157. [DOI] [PubMed] [Google Scholar]
  34. Weitzmann M. N., Woodford K. J., Usdin K. The mouse Ms6-hm hypervariable microsatellite forms a hairpin and two unusual tetraplexes. J Biol Chem. 1998 Nov 13;273(46):30742–30749. doi: 10.1074/jbc.273.46.30742. [DOI] [PubMed] [Google Scholar]
  35. Wing R., Drew H., Takano T., Broka C., Tanaka S., Itakura K., Dickerson R. E. Crystal structure analysis of a complete turn of B-DNA. Nature. 1980 Oct 23;287(5784):755–758. doi: 10.1038/287755a0. [DOI] [PubMed] [Google Scholar]
  36. Zimmerman S. B., Cohen G. H., Davies D. R. X-ray fiber diffraction and model-building study of polyguanylic acid and polyinosinic acid. J Mol Biol. 1975 Feb 25;92(2):181–192. doi: 10.1016/0022-2836(75)90222-3. [DOI] [PubMed] [Google Scholar]

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