The folding of centromeric DNA strands into intercalated structures: A physicochemical and computational study

Journal of Molecular Biology

Volumn 285, Issue 3, 1999, Pages 1039-1052

  Gallego, José ^a   Golden, Elisabeth B ^a   Stanley, David E ^a   Reid, Brian R ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Centromere; DNA; i Motif; Protonated cytosine; Stacking

Indexed keywords

CYTOSINE; DNA;

ARTICLE; CENTROMERE; COMPUTER ANALYSIS; DNA CONFORMATION; DNA STRAND; MOLECULAR MODEL; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTON TRANSPORT; THERMODYNAMICS;

EID: 0033593467     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2334     Document Type: Article

References (39)

1. Ahmed S., Kintanar A., Henderson E. Human telomeric C-strand tetraplexes. Nature Struct. Biol. 1:1994;83-88.
2. Berger I., Kan C., Fredian A., Ratliff R., Moyzis R., Rich A. Extension of the four-stranded intercalated cytosine motif by adenine·adenine base pairing in the crystal structure of d(CCCAAT). Nature Struct. Biol. 2:1995;416-425.
3. Berger I., Egli M., Rich A. Inter-strand C-H···O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4′ in cytosine-rich DNA. Proc. Natl Acad. Sci. USA. 93:1996;12116-12121.
4. Berstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F. Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
5. +·cytosine pairs. J. Mol. Biol. 272:1997;369-382.
6. 4). Biochemistry. 33:1994;13540-13546.
7. Cruse W. B. T., Egert E., Kennard O., Sala G. B., Salisbury S. A., Viswamitra M. A. Self base pairing in a complementary deoxydinucleoside monophosphate duplex: crystal and molecular structure of deoxycytidylyl-(3′-5′)-deoxyguanosine. Biochemistry. 22:1983;1833-1839.
8. Drew H. R., Wing R. M., Takano T., Broka C., Tanaka S., Itakura K., Dickerson R. E. Sructure of a B-DNA dodecamer: conformation and dynamics. Proc. Natl Acad. Sci. USA. 78:1981;2179-2183.
9. Fasman G. D. ed. Handbook of Biochemistry and Molecular Biology. 1975;CRC Press, Cleveland. p. 589.
10. Friedman R. A., Honig B. A free energy analysis of nucleic acid base stacking in aqueous solution. Biophys. J. 69:1995;1528-1535.
11. 2: distinct stacking interactions dictate the sequence-dependent formation of Hoogsteen base pairs. J. Biomol. Struct. Dynam. 12:1994;111-129.
12. Gallego J., Chou S.-H., Reid B. Centromeric pyrimidine sequences fold into an intercalated motif by forming a double hairpin with a novel T:G:G:T tetrad: solution structure of the d(TCCCGTTTCCA) dimer. J. Mol. Biol. 273:1997a;840-856.
13. Gallego J., Ortiz A. R., de Pascual-Teresa B., Gago F. Structure-affinity relationships for the binding of actinomycin D to DNA. J. Comp. Aided Mol. Des. 11:1997b;114-128.
14. Gehring K., Leroy J.-L., Guéron M. A tetrameric DNA structure with protonated cytosine·cytosine base pairs. Nature. 363:1993;561-565.
15. Gilson M. K., Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies and conformational analysis. Proteins: Struct. Funct. Genet. 4:1988;7-18.
16. Honig B., Sharp K., Yang A.-S. Macroscopic models of aqueous solutions: biological and chemical applications. J. Phys. Chem. 97:1993;1101-1109.
17. 3T) at 1.4 Å resolution. Proc. Natl Acad. Sci. USA. 91:1994;11636-11640.
18. Kang C., Berger I., Lockshin C., Ratliff R., Moyzis R., Rich A. Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere. Proc. Natl Acad. Sci. USA. 92:1995;3874-3878.
19. Kappler I., Hagstrom R., Fine R., Sharp K., Honig B. Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins: Struct. Funct. Genet. 1:1986;47-59.
20. Kipling D., Warburton P. E. Centromeres, CENP-B and Tigger too. Trends Genet. 13:1997;141-145.
21. 6]; evidence for a proton switch. Nucl. Acids Res. 23:1995;2692-2705.
22. Leroy J.-L., Guéron M. Solution structures of the i-motif tetramers of d(TCC), d(5methylCCT) and (T5methylCC): novel NOE connections between amino protons and sugar protons. Structure. 3:1995;101-120.
23. Leroy J.-L., Guéron M., Mergny J.-L., Hélene C. Intramolecular folding of a fragment of the cytosine-rich strand of telomeric DNA into an i-motif. Nucl. Acids Res. 22:1994;1600-1606.
24. a calculations with continuum dielectric models. J. Phys. Chem. 95:1991;5610-5620.
25. Manning G. S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Quart. Rev. Biophys. 11:1978;179-246.
26. Manzini G., Yathindra N., Xodo L. E. Evidence for intramolecularly folded i-DNA structures in biologically relevant CCC-repeat sequences. Nucl. Acids Res. 22:1994;4634-4640.
27. Marky L. A., Breslauer K. J. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers. 21:1987;2185-2194.
28. Masumoto H., Masukata H., Muro Y., Nozaki N., Okazaki T. A human centromere antigen (CENP-B) interacts with a short specific sequence in alphoid DNA, a human centromeric satellite. J. Cell. Biol. 109:1989;1963-1973.
29. Mergny J.-L., Lacroix L., Han X., Leroy J.-L., Hélene C. Intramolecular folding of pyrimidine oligodeoxynucleotides into an i-DNA motif. J. Am. Chem. Soc. 117:1995;8887-8898.
30. Nonin S., Phan A. T., Leroy J.-L. Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTACC): a noncanonical structure with possible roles in chromosome stability. Structure. 5:1997;1231-1246.
31. Pearlman D. A., Case D. A., Caldwell J. C., Seibel G. L., Singh U. C., Weiner P., Kollman P. A. AMBER 4.0. 1991;University of California, San Francisco.
32. Plateau P., Guéron M. Exchangeable proton NMR without base-line distortion, using new strong-pulse sequences. J. Am. Chem. Soc. 104:1982;7310-7311.
33. Robinson H., van der Marel G. A., van Boom J. H., Wang A. H.-J. Unusual DNA conformation at low pH revealed by NMR: parallel-stranded DNA duplex with homo base-pairs. Biochemistry. 31:1992;10510-10517.
34. Spacková N., Berger I., Egli M., Sponer J. Molecular dynamics of hemiprotonated intercalated four-stranded i-DNA: stable trajectories on a nanosecond scale. J. Am. Chem. Soc. 120:1998;6147-6151.
35. Sponer J., Leszczynski J., Vetterl V., Hobza P. Base stacking and hydrogen bonding in protonated cytosine dimer: the role of molecular ion-dipole and induction interactions. J. Biomol. Struct. Dynam. 13:1996;695-706.
36. Tyler-Smith C., Willard H. F. Mammalian chromosome structure. Curr. Opin. Gen. Dev. 3:1993;390-397.
37. +, G:G and A:A pairs. J. Mol. Biol. 242:1994;508-526.
38. Weiner S. J., Kollman P. A., Nguyen D. T., Case D. A. An all-atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7:1986;230-252.
39. 2 terminus, which is separable from dimerizing activity. J. Cell. Biol. 119:1992;1413-1427.