The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)2

Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2as an A-DNA duplex

“…Thus, the symmetry in the sequence leads to approximate symmetry in the structure of the duplex as well. This is unlike the situation in the other A-type tetradecanucleotide structure d(CGCGGGTACCCGCG) 2 , in which there is no structural symmetry between the two halves of the duplex (Venkadesh et al, 2011).…”

“…In the d(CCCCGGTACCGGGG) 2 duplex the values of rise and roll were 3.11 and 4.6 Å , respectively, whereas the d(CGCGGGT-ACCCGCG) 2 duplex was characterized by a low rise (2.47 Å ) and a large roll (11.5 Å ) (Venkadesh et al, 2011). The low rise and large roll in the latter duplex may be explained by the effect of alternating sequences with CpG steps (Tippin & Sundaralingam, 1996;Wahl & Sundaralingam, 1997;Venkadesh et al, 2011) and crystal packing (Jain & Sundaralingam, 1989).…”

“…It had r.m.s.d. values of 1.37 and 1.65 Å when subjected to least-squares superposition of the phosphodiester backbones on the A-DNA fibre model (Arnott & Hukins, 1972) and the tetradecanucleotide duplex d(CGCGGGTACCCGCG) 2 (Venkadesh et al, 2011), respectively (see Fig. 2).…”

“…The data were processed in space group P4 1 with almost identical unit-cell parameters to those of the crystal structure of the sequence d(CGCGGGTACCCGCG) 2 , which was solved and refined in space group P4 3 (Venkadesh et al, 2011). Molecular-replacement trials were carried out with the program AMoRe (Navaza, 1994) from the CCP4 suite using fibre models of A-type, B-type and Z-type DNA (the fibre models were generated using INSIGHT II release 98.0; Biosym/MSI, San Diego, USA) for the present tetradecanucleotide in the enantiomeric space groups P4 1 and P4 3 as well as the higher symmetry space groups P4 1 2 1 2 and P4 3 2 1 2.…”

“…The crystal structure of the tetradecanucleotide d(CGCGGGT-ACCCGCG) 2 in the tetragonal space group P4 3 has recently been reported (Venkadesh et al, 2011). Despite the large number of alternating pyrimidine-purine base steps, which favour a Z-type helix, this sequence forms an A-type duplex.…”