A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex

Journal of Molecular Biology

Volumn 282, Issue 5, 1998, Pages 1005-1011

  Schuerman, Geertrui S ^a   Van Meervelt, Luc ^a   Loakes, David ^b   Brown, Daniel M ^b   Kong Thoo Lin, Paul ^c   Moore, Madeleine H ^d   Salisbury, Stephen A ^e  

^a UNIVERSITY OF LEUVEN   (Belgium)

^b MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^c ROBERT GORDON UNIVERSITY   (United Kingdom)

^d UNIVERSITY OF YORK   (United Kingdom)

^e CAMBRIDGE CRYSTALLOGRAPHIC DATA CENTRE   (United Kingdom)

Author keywords

Crystallography; Mutagenesis; Pyrimidine analogue; P; P A base pairs

Indexed keywords

ADENINE; DNA Z; DOUBLE STRANDED DNA; NUCLEOSIDE; NUCLEOSIDE ANALOG; THYMINE;

ARTICLE; BASE PAIRING; DNA STRUCTURE; PH; PRIORITY JOURNAL; PROTON TRANSPORT; X RAY CRYSTALLOGRAPHY;

EID: 0032500628     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2080     Document Type: Article

References (34)

1. Anand N., Brown D.M., Salisbury S.A. The stability of oligodeoxyribonucleotide duplexes containing degenerate bases. Nucl. Acids Res. 15:1987;8167-8176
2. Brown D.M., Hewlins M.J.E., Schell P. The tautomeric state of N(4)-hydroxy-and N(4)-amino-cytosine derivatives. J. Chem. Soc. (C). 1968;1925-1929
3. Brown T., Leonard G.A., Booth E.D., Kneale G. Influence of pH on the conformation and stability of mismatch base-pairs in DNA. J. Mol. Biol. 212:1990;437-440
4. Brünger A.T. X-PLOR. A System for X-ray Crystallography and NMR. 1987;Yale University Press, New Haven, CT
5. Clauwaert J., Stockx J. Interactions of polynucleotides and their components I. Dissociation constants of the bases and their derivatives. Z. Naturforsch. (B). 23:1968;25-30
6. Acta Crystallog. sect. D. 50:1994;760-763
7. Driessen H., Haneef M.I.J., Harris G.W., Howlin B., Khan G., Moss D.S. RESTRAIN restrained structure-factor least-squares refinement program for macromolecular structures. J. Appl. Crystallog. 22:1989;510-516
8. Egli M., Gessner P.V. Stereoelectronic effects of deoxyribose O4′ on DNA conformation. Proc. Natl Acad. Sci. USA. 92:1995;180-184
9. 3in methanolic solution. Nucl. Acids Res. 12:1984;1243-1263
10. Hill F., Loakes D., Brown D.M. Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases. Proc. Natl Acad. Sci. USA. 95:1998;4258-4263
11. Ho P.S., Frederick C., Quigley G.J., van der Marel G.A., van Boom J.H., Wang A.H.-J., Rich A. G. T wobble base-pairing in Z-DNA at 1. 0 Åatomic resolution the crystal structure of d(CGCGTG). EMBO J. 4:1985;3617-3623
12. Hunter W.N., Brown T., Anand N.N., Kennard O. of an adenine. cytosine base-pair in DNA and its implications for mismatch repair. Nature. 320:1986;552-555
13. Hunter W.N., Brown T., Kennard O. Structural features and hydration of a dodecamer duplex containing two C·A mispairs. Nucl. Acids Res. 15:1987;6589-6606
14. Katritzky A.R., Waring A.J. Tautomeric azines. II. The tautomerism of 1-methyluracil and 5-bromo-1-methyluracil. J. Chem. Soc. 1962;1540-1544
15. Katritzky A.R., Waring A.J. Tautomeric azines. III. The structure of cytosine and its monocation. J. Chem. Soc. 1963;3040-3051
16. Kong Thoo Lin P., Brown D.M. Synthesis and duplex stability of oligodeoxynucleotides containing cytosine-thymine analogues. Nucl. Acids Res. 17:1989;10373-10383
17. Kong Thoo Lin P., Brown D.M. Synthesis of oligodeoxynucleotides containing degenerate bases and their use as primers in the polymerase chain reaction. Nucl. Acids Res. 20:1992;5149-5152
18. Kwiatkowski J.S., Pullman B. Tautomerism and electronic structure of biological pyrimidines. Advan. Heterocycl. Chem. 18:1975;199-335
19. Langridge R., Marvin D.A., Seeds W.E., Wilson H.R., Hooper C.W., Wilkins M.H.F., Hamilton L.D. The molecular configuration of deoxyribonucleic acid. II. Molecular models and their fourier transforms. J. Mol. Biol. 2:1960;38-64
20. Leonard G.A., Booth E.D., Brown T. Structural and thermodynamic studies on the adenine·guanine mismatch in B-DNA. Nucl. Acids Res. 18:1990;5617-5623
21. Mikol V., Rodeau J.L., Giegé R. Changes of pH during biomolecule crystallization by vapour diffusion using ammonium sulfate as the precipitant. J. Appl. Crystallog. 22:1989;155-161
22. Moore M.H., Van Meervelt L., Salisbury S.A., Kong Thoo Lin P., Brown D.M. Direct observation of two base-pairing modes of a cytosine-thymine analogue with guanine in a DNA Z-form complex significance for base analogue mutagenesis. J. Mol. Biol. 251:1995;665-673
23. 4-methoxycytidine and its methyl derivatives. I. Spectroscopic and quantum chemical investigation of ionic and tantomeric forms: syn-antiisomerisation. J. Photochem. 20:1982;229-252
24. Navaza J. AMoRe an automated package for molecular replacement. Acta Crystallog. sect. A. 50:1994;157-163
25. 1H nuclear magnetic resonance studies of oligonucleotide duplexes containing base-modified cytosine residues. J. Mol. Biol. 230:1993;1068-1076
26. 4oxy-2′-deoxycytidine inEscherichia coli. Nucl. Acids Res. 25:1997;1548-1552
27. Otwinowski Z., Minor W. Processing of X-ray diffraction data in oscillation mode. Methods Enzymol. 276:1997;307-326
28. Saenger W. Principles of Nucleic Acid Structure. 1984;Springer, New York
29. Sheldrick G.M. SHELXL-93. Program for Crystal Structure Refinement. 1993;University of Göttingen, Germany
30. Stone M.J., Nedderman A.N.R., Williams D.H., Kong Thoo Lin P., Brown D.M. Molecular basis for methoxyamine initiated mutagenesis. J. Mol. Biol. 222:1991;711-723
31. Taylor R., Kennard O. Molecular structures of nucleosides and nucleotides. 2. Orthogonal coordinates for standard nucleic and base residues. J. Am. Chem. Soc. 104:1982;3209-3212
32. 4-methoxycytosine·guanine base-pairs inZ-DNA. J. Mol. Biol. 216:1990;773-781
33. Van Meervelt L., Kong Thoo Lin P., Brown D.M. 6-(3,5-Di-O-acetyl-β-D-2-deoxyribofuranosyl)-3,4-dihydro-8-H-pyrimido[4,5- c][1,2]-oxazin-7-one. Acta Crystallog. sect. C. 51:1995;1347-1350
34. Zaccolo M., Williams D.M., Brown D.M., Gherardi E. An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. J. Mol. Biol. 255:1996;589-603