279d
From Proteopedia
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CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCGCGCGCGC) IN THE Z-DNA CONFORMATION-PART I
Overview
Alternating self-complementary oligonucleotides starting with a, 5'-pyrimidine usually form left-handed Z-DNA; however, with a 5'-purine, start sequence they form the right-handed A-DNA. Here we report the, crystal structure of the decamer d(GCGCGCGCGC) with a 5'-purine start in, the Z-DNA form. The decamer crystallizes in the hexagonal space group, P6(5)22, unit cell dimensions a = b = 18.08 and c = 43.10 A, with one of, the following four dinucleotide diphosphates in the asymmetric unit:, d(pGpC)/d(GpCp)/d(pCpG)/d(CpGp). The molecular replacement method, starting with d(pGpC) of the isomorphous Z-DNA hexamer d(araC-dG)3 without, the 2'-OH group of arabinose, was used in the structure analysis. The, method gave the solution only after the sugar-phosphate conformation of, the GpC step was manipulated. The refinement converged to a final R value, of 18.6% for 340 unique reflections in the resolution range 8.0-1.9 A. A, result of the sequence alternation is the alternation in the nucleotide, conformation; guanosine is C3'-endo, syn, and cytidine is C2'-endo, anti., The CpG step phosphodiester conformation is the same as ZI or ZII, whereas, that of the GpC step phosphodiester is "intermediate" in the sense that, zeta (O3'-P bond) is the same as ZII but alpha (P-O5' bond) is the same as, ZI. The duplexes generated from the dinucleotide asymmetric unit are, stacked one on top of the other in the crystal to form an infinite, pseudocontinuous helix. This renders it a quasi-polymerlike structure that, has assumed the Z-DNA conformation further strengthened by the long inner, Z-forming stretch d(CG)4. An interesting feature of the structure is the, presence of water strings in both the major and the minor grooves. In the, minor groove the cytosine carbonyl oxygen atoms of the GpC and CpG steps, are cross-bridged by water molecules that are not themselves hydrogen, bonded but are enclosed by the water rings in the mouth of the minor, groove. In the major groove three independent water molecules form a, zigzagging continuous water string that runs throughout the duplex.
About this Structure
279D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal structure of the self-complementary 5'-purine start decamer d(GCGCGCGCGC) in the Z-DNA conformation. I., Ban C, Ramakrishnan B, Sundaralingam M, Biophys J. 1996 Sep;71(3):1215-21. PMID:8873995
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