106d: Difference between revisions
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|PDB= 106d |SIZE=350|CAPTION= <scene name='initialview01'>106d</scene> | |PDB= 106d |SIZE=350|CAPTION= <scene name='initialview01'>106d</scene> | ||
|SITE= | |SITE= | ||
|LIGAND= | |LIGAND= <scene name='pdbligand=5CM:5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=106d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=106d OCA], [http://www.ebi.ac.uk/pdbsum/106d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=106d RCSB]</span> | |||
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[[Category: dna]] | [[Category: dna]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:26:33 2008'' | ||
Revision as of 18:26, 30 March 2008
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SOLUTION STRUCTURES OF THE I-MOTIF TETRAMERS OF D(TCC), D(5MCCT) AND D(T5MCC). NOVEL NOE CONNECTIONS BETWEEN AMINO PROTONS AND SUGAR PROTONS
OverviewOverview
BACKGROUND: At slightly acid or even neutral pH, oligodeoxynucleotides that include a stretch of cytidines form a tetramer structure in which two parallel-stranded duplexes have their hemi-protonated C.C+ base pairs face-to-face and fully intercalated, in a so-called i-motif, first observed serendipitously in [d(TC5)]4. RESULTS: A high-definition structure of [d(TCC)]4 was computed on the basis of inter-residue distances corresponding to 21 NOESY cross-peaks measured at short mixing times. A similarly defined structure of [d(5mCCT)]4 was also obtained. A small number of very characteristic (amino proton)-(sugar proton) cross-peaks entails the intercalation topology. The structure is generally similar to that of [d(TC5)]4. The sequence d(T5mCC) forms two tetramers in comparable proportions. The intercalation topologies are read off the two patterns of (amino proton)-(sugar proton) cross-peaks: one is the same as in the d(TCC) tetramer, the other has the intercalated strands shifted by one base, which avoids the steric hindrance between the methyl groups of the 5mC pairs of the two duplexes. CONCLUSIONS: The structures obtained in this work and the procedures introduced to characterize them and to solve the problems linked to the symmetry of the structure provide tools for further exploring the conditions required for formation of the i-motif.
About this StructureAbout this Structure
106D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Solution structures of the i-motif tetramers of d(TCC), d(5methylCCT) and d(T5methylCC): novel NOE connections between amino protons and sugar protons., Leroy JL, Gueron M, Structure. 1995 Jan 15;3(1):101-20. PMID:7743125
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