Abstract
dApT, a modified deoxyribose dinucleoside phosphate with an uncharged methylphosphonate group, crystallizes as dihydrate in space group P2(1)2(1)2, a = 9.629(3), b = 20.884(6) and c = 14.173(4)A, Z = 4. The structure has been determined using 2176 X-ray diffractometer reflections and refined to a final R of 0.105. Torsion angles about P-O(5') and P-O(3') bonds are -91.8 degrees and 117.8 degrees. The former is in the normal (-)gauche range while the latter is eclipsed. Bases are oriented anti, the sugar of adenosine is puckered 2T3 (C(2')endo) whereas that of thymidine displays puckering disorder with major and minor occupancy sites. Major site is a half-chair 2T (C(2')endo-C(1')exo) and minor site an envelope 3T2 (C(3(1)endo). Adenine and thymine bases of symmetry related molecules form reversed Hoogsteen type base pairs, water molecules are disordered in the crystal lattice.
Full text
PDF
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Altona C., Sundaralingam M. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J Am Chem Soc. 1972 Nov 15;94(23):8205–8212. doi: 10.1021/ja00778a043. [DOI] [PubMed] [Google Scholar]
- Day R. O., Seeman N. C., Rosenberg J. M., Rich A. A crystalline fragment of the double helix: the structure of the dinucleoside phosphate guanylyl-3',5'-cytidine. Proc Natl Acad Sci U S A. 1973 Mar;70(3):849–853. doi: 10.1073/pnas.70.3.849. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dickerson R. E., Drew H. R., Conner B. N., Wing R. M., Fratini A. V., Kopka M. L. The anatomy of A-, B-, and Z-DNA. Science. 1982 Apr 30;216(4545):475–485. doi: 10.1126/science.7071593. [DOI] [PubMed] [Google Scholar]
- HASCHEMEYER A. E., SOBELL H. M. THE CRYSTAL STRUCTURE OF AN INTERMOLECULAR NUCLEOSIDE COMPLEX: ADENOSINE AND 5-BROMOURIDINE. Proc Natl Acad Sci U S A. 1963 Nov;50:872–877. doi: 10.1073/pnas.50.5.872. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kan L. S., Cheng D. M., Miller P. S., Yano J., Ts'o P. O. Proton nuclear magnetic resonance studies on dideoxyribonucleoside methylphosphonates. Biochemistry. 1980 May 13;19(10):2122–2132. doi: 10.1021/bi00551a020. [DOI] [PubMed] [Google Scholar]
- Katz L., Tomita K. I., Rich A. The molecular structure of the crystalline complex ethyladenine: methyl-bromouracil. J Mol Biol. 1965 Sep;13(2):340–350. doi: 10.1016/s0022-2836(65)80101-2. [DOI] [PubMed] [Google Scholar]
- Miller P. S., Yano J., Yano E., Carroll C., Jayaraman K., Ts'o P. O. Nonionic nucleic acid analogues. Synthesis and characterization of dideoxyribonucleoside methylphosphonates. Biochemistry. 1979 Nov 13;18(23):5134–5143. doi: 10.1021/bi00590a017. [DOI] [PubMed] [Google Scholar]
- Rosenberg J. M., Seeman N. C., Day R. O., Rich A. RNA double-helical fragments at atomic resolution. II. The crystal structure of sodium guanylyl-3',5'-cytidine nonahydrate. J Mol Biol. 1976 Jun 14;104(1):145–167. doi: 10.1016/0022-2836(76)90006-1. [DOI] [PubMed] [Google Scholar]
- Seeman N. C., Rosenberg J. M., Suddath F. L., Kim J. J., Rich A. RNA double-helical fragments at atomic resolution. I. The crystal and molecular structure of sodium adenylyl-3',5'-uridine hexahydrate. J Mol Biol. 1976 Jun 14;104(1):109–144. doi: 10.1016/0022-2836(76)90005-x. [DOI] [PubMed] [Google Scholar]
- Voet D., Rich A. The crystal structures of purines, pyrimidines and their intermolecular complexes. Prog Nucleic Acid Res Mol Biol. 1970;10:183–265. doi: 10.1016/s0079-6603(08)60565-6. [DOI] [PubMed] [Google Scholar]
- Wang A. H., Fujii S., van Boom J. H., van der Marel G. A., van Boeckel S. A., Rich A. Molecular structure of r(GCG)d(TATACGC): a DNA--RNA hybrid helix joined to double helical DNA. Nature. 1982 Oct 14;299(5884):601–604. doi: 10.1038/299601a0. [DOI] [PubMed] [Google Scholar]