1d6d
From Proteopedia
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SOLUTION DNA STRUCTURE CONTAINING (A-A)-T TRIADS INTERDIGITATED BETWEEN A-T BASE PAIRS AND GGGG TETRADS; NMR, 8 STRUCT.
Overview
The present study reports on the solution structure of the guanine plus, adenine rich d(A(2)G(2)T(4)A(2)G(2)) 12-mer sequence which forms a unique, fold in moderate NaCl solution. Proton resonance assignments for this, sequence, which contains a pair of AAGG repeats separated by a T(4) linker, segment, were aided by site-specific (15)N-labeling of guanine and adenine, bases, as well as site-specific incorporation of 2,6-diaminopurine and, 8-bromoadenine for adenine, 8-bromoguanine, 7-deazaguanine and inosine for, guanine, and uracil and 5-bromouracil for thymine. The solution structure, which was solved by a combined NMR and intensity-refined computational, approach, consists of a diamond-shaped architecture formed through, dimerization of a pair of d(A(2)G(2)T(4)A(2)G(2)) hairpins. This 2-fold, symmetric structure contains a quadruplex core consisting of a pair of, symmetry-related G(syn).G(syn).G(anti). G(anti) tetrads, where adjacent, strands have both parallel and anti-parallel neighbors and connecting T(4), segments which form diagonal loops. Each of the, G(syn).G(syn).G(anti).G(anti) tetrads forms a platform on which stacks a, T(anti).[A(syn)-A(anti)] triad containing a novel A(syn)-A(anti) platform, step and a reversed Hoogsteen A(syn).T(anti) pair. We observe both, base-base and base-sugar stacking interactions, with the latter occuring, at a sheared A-G step where the sugar of the A stacks on the purine plane, of the G. Unexpectedly, the topology of this sheared A(anti)-G(syn) step, has many similarities with the C(anti)-G(syn) step in left-handed Z-DNA., The T.(A-A) triad is sandwiched between the G-tetrad on one side and a, reversed Hoogsteen A(anti).T(anti) pair on the other. This intercalative, topology is facilitated by a zipper-like motif where the A(anti) residue, of the triad is interdigitated within a stretched A(anti)-G(syn) step. Our, structural study reports on new aspects of A-A platforms, base triads, zipper-like interdigitation and sheared base steps, together with, base-base and base-sugar stacking defining a diamond-like architecture for, the d(A(2)G(2)T(4)A(2)G(2)) sequence. One can anticipate that mixed, guanine-adenine sequences will exhibit a rich diversity of polymorphic, architectures that will provide unique topologies for recognition by both, nucleic acids and proteins.
About this Structure
1D6D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
A diamond-shaped zipper-like DNA architecture containing triads sandwiched between mismatches and tetrads., Kuryavyi V, Kettani A, Wang W, Jones R, Patel DJ, J Mol Biol. 2000 Jan 21;295(3):455-69. PMID:10623538
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