'''SOLUTION DNA STRUCTURE CONTAINING (A-A)-T TRIADS INTERDIGITATED BETWEEN A-T BASE PAIRS AND GGGG TETRADS; NMR, 8 STRUCT.'''
===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.
The line below this paragraph, {{ABSTRACT_PUBMED_10623538}}, adds the Publication Abstract to the page
(as it appears on PubMed at http://www.pubmed.gov), where 10623538 is the PubMed ID number.
-->
{{ABSTRACT_PUBMED_10623538}}
==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D6D OCA].
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D6D OCA].
==Reference==
==Reference==
Line 29:
Line 33:
[[Category: Multi-stranded dna architecture]]
[[Category: Multi-stranded dna architecture]]
[[Category: Zipper motif]]
[[Category: Zipper motif]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:29:57 2008''
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:31:52 2008''
Revision as of 19:31, 30 June 2008
This article has been automatically seeded. Changes to this page should pertain to the PDB entry only and not to the protein or biomolecule in general.
Full experimental 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
