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1rme

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{{STRUCTURE_1rme| PDB=1rme | SCENE= }}
{{STRUCTURE_1rme| PDB=1rme | SCENE= }}
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'''DNA (5'-D(5MCP*CP*TP*CP*C)-3') TETRAMER, NMR, 1 STRUCTURE'''
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===DNA (5'-D(5MCP*CP*TP*CP*C)-3') TETRAMER, NMR, 1 STRUCTURE===
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==Overview==
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At slightly acidic pH, protonation of C-rich oligomers results in the formation of a four-stranded structure composed of two parallel duplexes in a head to tail orientation with their hemi-protonated C.C+ pairs intercalated in a so-called i-motif. In all cases reported previously the duplexes are identical. The tetramer formed by the d(5mCCTCC) oligomer is different. The structure is computed on the basis of 55 inter-residue distances derived from NOESY cross-peaks measured at short mixing times. It consists of two intercalated non-equivalent symmetrical duplexes. The base stacking order is C5* C1 C4* C2 (T3*) T3 C2* C4 C1* C5, but the thymidine bases (T3*) of one duplex are looped out and lie in the wide grooves of the tetramer. The thymidine bases T3 stack as a symmetrical T.T pair between the sequentially adjacent C2.C2+ pair and the C2*.C2*+ pair of the other duplex. Numerous exchange cross-peaks provide evidence for duplex interconversion. The interconversion rate is 1.4 s-1 at 0 degree C and the activation energy is 94 kJ/mol. The opening of the T3.T3 pair, the closing of the T3*.T3 pair, and the opening of the C2*.C2*+ pair occur simultaneously with the duplex interconversion. This suggests that the concerted opening and closing of the thymidine bases drive the duplex interconversion. Opening of the C4.C4+ and C4*.C4*+ pairs, and dissociation of the tetramer are not part of the interconversion since they occur at much slower rates. Duplex interconversion within the [d(5mCCTCC)]4 tetramer provides the first structural and kinetics characterization of broken symmetry in a biopolymer. The tetramer formed by d(5mCCUCC) adopts a similar structure, but the rate of duplex interconversion is faster: 40 s-1 at 0 degree C. At 32 degrees C, interconversion is fast on the NMR time scale.
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{{ABSTRACT_PUBMED_8780782}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RME OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RME OCA].
==Reference==
==Reference==
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[[Category: I-motif]]
[[Category: I-motif]]
[[Category: Tetramer]]
[[Category: Tetramer]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 08:44:24 2008''

Revision as of 05:44, 29 July 2008

Image:1rme.png

Template:STRUCTURE 1rme

DNA (5'-D(5MCP*CP*TP*CP*C)-3') TETRAMER, NMR, 1 STRUCTURE

Template:ABSTRACT PUBMED 8780782

About this Structure

Full experimental information is available from OCA.

Reference

Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer., Nonin S, Leroy JL, J Mol Biol. 1996 Aug 23;261(3):399-414. PMID:8780782

Page seeded by OCA on Tue Jul 29 08:44:24 2008

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