1d6d
From Proteopedia
(New page: 200px<br /><applet load="1d6d" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d6d" /> '''SOLUTION DNA STRUCTURE CONTAINING (A-A)-T TR...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1d6d.gif|left|200px]]<br /><applet load="1d6d" size=" | + | [[Image:1d6d.gif|left|200px]]<br /><applet load="1d6d" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1d6d" /> | caption="1d6d" /> | ||
'''SOLUTION DNA STRUCTURE CONTAINING (A-A)-T TRIADS INTERDIGITATED BETWEEN A-T BASE PAIRS AND GGGG TETRADS; NMR, 8 STRUCT.'''<br /> | '''SOLUTION DNA STRUCTURE CONTAINING (A-A)-T TRIADS INTERDIGITATED BETWEEN A-T BASE PAIRS AND GGGG TETRADS; NMR, 8 STRUCT.'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The present study reports on the solution structure of the guanine plus | + | 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== | ==About this Structure== | ||
| - | 1D6D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1D6D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D6D OCA]. |
==Reference== | ==Reference== | ||
| Line 14: | Line 14: | ||
[[Category: Jones, R.]] | [[Category: Jones, R.]] | ||
[[Category: Kettani, A.]] | [[Category: Kettani, A.]] | ||
| - | [[Category: Kuryavyi, V | + | [[Category: Kuryavyi, V V.]] |
| - | [[Category: Patel, D | + | [[Category: Patel, D J.]] |
[[Category: Wang, W.]] | [[Category: Wang, W.]] | ||
[[Category: a(syn)-a(anti) platform]] | [[Category: a(syn)-a(anti) platform]] | ||
| Line 24: | Line 24: | ||
[[Category: zipper motif]] | [[Category: zipper motif]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:13:29 2008'' |
Revision as of 10:13, 21 February 2008
|
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
Page seeded by OCA on Thu Feb 21 12:13:29 2008
