Crystal and Molecular Structure of the Sodium Salt of the Dinucleotide Duplex d(CpG) |
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Authors: | M. Coll X. Solans M. Font-Altaba J. A. Subirana |
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Affiliation: | 1. Unidad de Quimica Macromolecular, C.S.I.C Escuela T.S. de Ingenieros Industriales , Diagonal, 647, 08028 , Barcelona , Spain;2. Departamento de Cristalografia y Mineralogia , Universidad de Barcelona , Barcelona , Spain |
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Abstract: | Abstract The crystal and molecular structure of the sodium salt of deoxycytidylyl-{3′ ?5′)-deoxyguanosine has been determined from X-ray diffraction data. The crystals, obtained from an aqueous y- butyrolactone solution at pH = 5.3, are orthorhombic, P212121, a= 10.640(2), b= 11.184(2) and c=44.618(4) A. The structure was refined to an R = 0.041. The d(CpG) structure is similar to the ammonium salt solved by Cruse et al.(1). Both structures form a parallel self base paired mini-double helix. In d(CpG).Na+, one of the two paired cytosines is protonated on N(3). The cytosines form 3 hydrogen bonds while the guanines form only 2. The Na+ ion is coordinated with five groups: two water molecules, 0(6) of guanine A, N(7) of guanine B and 0(5′) of cytosine B, forming a square pyramid. The hydration shell around the mini-helix is analysed and compared with that of the ammonium salt. d(CpG).Na+ is the second d(CpG) oligonucleotide found with a self base pairing arrangement despite of the fact that the crystallization conditions and counterion were different in both cases. The hypothesis that self base pairing is not only a crystallization artifact but may play a role under physiological conditions as a source of transversion mutations is discussed. |
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Keywords: | Sumoylation site Minimum Redundancy Maximum Relevance Feature Selection Nearest Neighbor Algorithm K-fold cross-validation |
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