Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers.

The crystal and molecular structure of d(CGUA'CG)2 (where A' is 2-aminoadenine) has been determined and refined to an R factor of 13.8% for data 8.0-1.3 A. The structure is very similar to the original Z-DNA structures with the sequence d(CGCGCG)2 [Gessner, R. V., Frederick, C. A., Quigley, G. J., Rich, A., & Wang, A. H.-J. (1989) J. Biol. Chem. 264, 7921] and shows that the substitution of 2-aminoadenine-uracil base pairs in the two central steps is consistent with Z-DNA formation. In addition, we show how waters mediating intermolecular interactions may help to explain the ZI-ZII conformational pattern found in many Z-DNA structures.

[1]  P. S. Ho,et al.  Stabilization of Z-DNA by demethylation of thymine bases: 1.3-A single-crystal structure of d(m5CGUAm5CG). , 1990, Biochemistry.

[2]  G. Schroth,et al.  Prediction of a crystallization pathway for Z-DNA hexanucleotides. , 1991, Science.

[3]  A. Rich,et al.  The molecular structure of the left-handed Z-DNA double helix at 1.0-A atomic resolution. Geometry, conformation, and ionic interactions of d(CGCGCG). , 1989, The Journal of biological chemistry.

[4]  A. Rich,et al.  Crystal structure of a Z-DNA fragment containing thymine/2-aminoadenine base pairs. , 1986, Journal of biomolecular structure & dynamics.

[5]  Laser raman studies on the conformation and interactions of DNA in crystals an in solution , 1989 .

[6]  A. Rich,et al.  AT base pairs are less stable than GC base pairs in Z-DNA: The crystal structure of d(m5CGTAm5CG) , 1984, Cell.

[7]  T. A. Jones,et al.  A graphics model building and refinement system for macromolecules , 1978 .

[8]  H M Berman,et al.  Hydration of DNA bases: Analysis of crystallographic data , 1992, Biopolymers.

[9]  S. Diekmann,et al.  Definitions and nomenclature of nucleic acid structure parameters. , 1989, The EMBO journal.

[10]  A. Rich,et al.  Left-handed double helical DNA: variations in the backbone conformation. , 1981, Science.

[11]  P. Fitzgerald.  MERLOT, an integrated package of computer programs for the determination of crystal structures by molecular replacement , 1988 .

[12]  A. Rich,et al.  Effects of 5-fluorouracil/guanine wobble base pairs in Z-DNA: molecular and crystal structure of d(CGCGFG). , 1989, Nucleic Acids Research.

[13]  Jacques H. van Boom,et al.  Molecular structure of a left-handed double helical DNA fragment at atomic resolution , 1979, Nature.

[14]  A. Rich,et al.  Molecular structure of (m5 dC-dG)3: the role of the methyl group on 5-methyl cytosine in stabilizing Z-DNA. , 1982, Nucleic acids research.

[15]  R. Dickerson,et al.  Conformation and dynamics in a Z-DNA tetramer. , 1981, Journal of molecular biology.

[16]  G. Quigley,et al.  Base-specific binding of copper(II) to Z-DNA. The 1.3-A single crystal structure of d(m5CGUAm5CG) in the presence of CuCl2. , 1991, The Journal of biological chemistry.

[17]  George M. Church,et al.  A structure-factor least-squares refinement procedure for macromolecular structures using constrained and restrained parameters , 1977 .

[18]  H. Berman,et al.  Crystal and molecular structure of a DNA duplex containing the carcinogenic lesion O6-methylguanine. , 1990, Biochemistry.

[19]  E. Westhof,et al.  Solvation of the left-handed hexamer d(5BrC-G-5BrC-G-5 BrC-G) in crystals grown at two temperatures. , 1986, Journal of molecular biology.

[20]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[21]  A. Wang,et al.  Covalent modification of guanine bases in double-stranded DNA. The 1.2-A Z-DNA structure of d(CGCGCG) in the presence of CuCl2. , 1992, The Journal of biological chemistry.

[22]  Roger A. Jones,et al.  The influence of the purine 2-amino group on DNA conformation and stability. II: Synthesis and physical characterization of d[CGT(2-NH2)ACG], d[CGU(2-NH2)ACG], and d[CGT(2-NH2)AT(2-NH2)ACG] , 1984 .

[23]  A. Rich,et al.  Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-A resolution. , 1991, Biochemistry.

[24]  E Westhof,et al.  Crystallographic refinement of yeast aspartic acid transfer RNA. , 1985, Journal of molecular biology.

[25]  A. Rich,et al.  Crystal structure of Z-DNA without an alternating purine-pyrimidine sequence. , 1985, Proceedings of the National Academy of Sciences of the United States of America.