From Proteopedia
(Difference between revisions)
proteopedia linkproteopedia link
|
|
| Line 1: |
Line 1: |
| - | [[Image:1rme.gif|left|200px]] | + | {{Seed}} |
| | + | [[Image:1rme.png|left|200px]] |
| | | | |
| | <!-- | | <!-- |
| Line 9: |
Line 10: |
| | {{STRUCTURE_1rme| PDB=1rme | SCENE= }} | | {{STRUCTURE_1rme| PDB=1rme | SCENE= }} |
| | | | |
| - | '''DNA (5'-D(5MCP*CP*TP*CP*C)-3') TETRAMER, NMR, 1 STRUCTURE'''
| + | ===DNA (5'-D(5MCP*CP*TP*CP*C)-3') TETRAMER, NMR, 1 STRUCTURE=== |
| | | | |
| | | | |
| - | ==Overview==
| + | <!-- |
| - | 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.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_8780782}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 8780782 is the PubMed ID number. |
| | + | --> |
| | + | {{ABSTRACT_PUBMED_8780782}} |
| | | | |
| | ==About this Structure== | | ==About this Structure== |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RME OCA]. | + | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RME OCA]. |
| | | | |
| | ==Reference== | | ==Reference== |
| Line 25: |
Line 29: |
| | [[Category: I-motif]] | | [[Category: I-motif]] |
| | [[Category: Tetramer]] | | [[Category: Tetramer]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 07:40:09 2008'' | + | |
| | + | ''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
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
