+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Structure and thermodynamics of nonalternating C.G base pairs in Z-DNA: the 1.3-A crystal structure of the asymmetric hexanucleotide d(m5CGGGm5CG).d(m5CGCCm5CG)



Structure and thermodynamics of nonalternating C.G base pairs in Z-DNA: the 1.3-A crystal structure of the asymmetric hexanucleotide d(m5CGGGm5CG).d(m5CGCCm5CG)



Biochemistry 32(49): 13381-13392



We have solved the single-crystal X-ray structure of the complementary hexanucleotides d(m5CGGGm5CG) and d(m5CGCCm5CG). The hexamer duplex was crystallized as Z-DNA, but contains a single CG base pair that does not follow the alternating pyrimidine/purine rule for Z-DNA formation. This is the first crystal structure which serves to illustrate the structural consequences of placing a cytosine in the sterically disfavored syn conformation. In addition, since these sequences are not self-complementary, the individual strands of this asymmetric hexamer are unique in sequence and therefore distinguishable in the crystal lattice. Nevertheless, the crystal of this duplex is isomorphous with other Z-DNA hexamer structures. The asymmetry of this hexamer sequence required that the structure be solved using two unique models, which are distinguished by the orientation of hexanucleotides in the crystal lattice. In one model (the GG model) the cytosine in the syn conformation is packed against the terminal guanine base of a symmetry-related hexamer, while in the alternative model (the CC model) this cytosine sits exposed in a solvent channel of the lattice. We find that neither model alone can completely account for the observed electron densities. The two models ultimately were refined together. A composite structure consisting of 65% GG model and 35% CC model refined to an R-factor of 19.3%, which was significantly lower than refinements using either model alone. A detailed analysis of these two structures shows that, in spite of the out-of-alternation CG base pair, the features characteristic of Z-DNA have been maintained. Both models, however, show significant local structural adjustments to accommodate the single cytosine base which is forced to adopt the syn conformation in each hexamer. In general, it appears that in order to relieve the energetically unfavorable steric contacts between the cytosine base in the syn conformation and the deoxyribose sugar, the base is forced into a highly buckled conformation, and that this large buckle in turn alters the conformation of neighboring residues. This unusual conformation also significantly weakens base-stacking interactions between the cytosine in syn and the adjacent residues in the helix and affects the exposure of the bases to solvent. We conclude that this crystal structure provides a molecular rationale for why nonalternating bases are energetically disfavored in Z-DNA. Copyright 1993, American Chemical Society. .

Please choose payment method:






(PDF emailed within 1 workday: $29.90)

Accession: 009986723

Download citation: RISBibTeXText

PMID: 8257675


Related references

Structure and thermodynamics of nonalternating C.cntdot.G base pairs in Z-Dna: The 1.3-.Ang. crystal structure of the asymmetric hexanucleotide d(m5Cgggm5Cg).cntdot.d(m5Cgccm5Cg). Biochemistry 32(49): 13381-13392, 1993

The crystal structure of N4-methylcytosine.guanosine base-pairs in the synthetic hexanucleotide d(CGCGm4CG). Nucleic Acids Research 21(24): 5623-5629, 1993

AT base pairs are less stable than GC base pairs in Z-DNA: the crystal structure of d(m5CGTAm5CG). Cell 37(1): 321-331, 1984

Adenine thymine base pairs are less stable than guanine cytosine base pairs in z dna the crystal structure of deoxy 5 methyldeoxycytidylyl 3' 5' deoxyguanylyl 3' 5' thymidylyl 3' 5' deoxyadenylyl 3 5' 5 methyldeoxycytidylyl 3 5' guanosine. Cell 37(1): 321-332, 1984

Structure and thermodynamics of adjacent mismatched ga base pairs. Abstracts of Papers American Chemical Society 201(1-2): BIOT 33, 1991

Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs. Nucleic Acids Research 30(23): 5253-5260, 2002

Crystal structure of d(GCGAAAGCT) containing parallel-stranded duplex with homo base pairs and anti-parallel duplex with Watson-Crick base pairs. Nucleic Acids Research. Supplement 2002(2): 51-52, 2002

G . T base-pairs in a DNA helix: the crystal structure of d(G-G-G-G-T-C-C-C). Journal of Molecular Biology 186(4): 805-814, 1985

Synthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G.G/U.U tandem wobble base pairs: comparison with other tandem G.U pairs. Nucleic Acids Research 28(21): 4376-4381, 2000

Synthesis and crystal structure of an octamer RNA r /r with GcntdotG/UcntdotU tandem wobble base pairs Comparison with other tandem GcntdotU pairs. Nucleic Acids Research 28(21): 4376-4381, 2000

Crystal structure studies of RNA duplexes containing s(2)U:A and s(2)U:U base pairs. Journal of the American Chemical Society 136(39): 13916-13924, 2014

Crystal structure of a DNA duplex containing 8-hydroxydeoxyguanine-adenine base pairs. Biochemistry. 33(34): 10266-10270, 1994

Crystal and molecular structure of r An RNA duplex containing two G cntdot A base pairs. Structure 2(6): 483-494, 1994

Crystal structure of a Z-DNA fragment containing thymine/2-aminoadenine base pairs. Journal of Biomolecular Structure and Dynamics 4(2): 157-172, 1986

Crystal structure and stability of a DNA duplex containing A(anti).G(syn) base-pairs. Journal of Molecular Biology 207(2): 455-457, 1989