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| | {{STRUCTURE_1bcb| PDB=1bcb | SCENE= }} | | {{STRUCTURE_1bcb| PDB=1bcb | SCENE= }} |
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| - | '''INTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES'''
| + | ===INTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES=== |
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| - | ==Overview==
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| - | The influence of the position of the CG.C+ triplet and the contribution of protonation at the N3 of the Hoogsteen cytosine residue on the stability of various sequences of parallel triple helices having the general composition d[(A5G)-x-(T5C)-x-(T5C)] and d[(A4G2)-x-(T4C2)-x-(T4C2)], where x is the hexaethylene glycol linker, has been determined by NMR, ultraviolet melting and absorbance spectrophotometry. The apparent pK value, i.e. the pH at which the observable has changed by 50% of its range, was typically in the range 6 to 7. However, the NMR spectra unequivocally showed that the pK of the protonated cytosine residue must be at least 9.5 for internal positions. This is five units above the pK of the free nucleotide, and represents a free energy of stabilisation from protonation of >11.5 RT. The pK of terminal cytosine residues is much lower, in the range 6.2 to 7.2, accounting for a free energy of stabilisation from protonation of 3.6 to 6 RT. The van't Hoff enthalpies were determined for the dissociation of the protonated triplex into the duplex+strand, and for the duplex to strand transition. The mean value for the duplexes were 23 to 27 kJ mol-1 base-pair, and 25 to 30 kJ mol-1 for the triplexes containing internal CG.C+ triplets. Good agreement was obtained for the thermodynamic parameters by the different methods. Free energy differences for the transition between the protonated triplex and the duplex+protonated strand were calculated at 298 K. The DeltaG of stabilisation of an internal CG.C triplet compared with a terminal CG.C triplet was about 6 kJ mol-1 ; a similar stabilisation was observed for the triplexes containing two CG.C triplets compared with those containing a single CG.C triplet. The very large stabilisation from protonation is too large to be accounted for by a single hydrogen bond, and is likely to include contributions from electrostatic interactions of the positive charge with the phosphate backbone, and more favourable interactions between neighbouring bases owing to the very different electronic properties of the protonated C.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_9480771}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 9480771 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_9480771}} |
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| | ==About this Structure== | | ==About this Structure== |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BCB OCA]. | + | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BCB OCA]. |
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| | ==Reference== | | ==Reference== |
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| | [[Category: Deoxyribonucleic acid]] | | [[Category: Deoxyribonucleic acid]] |
| | [[Category: Dna triplex]] | | [[Category: Dna triplex]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 11:20:01 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 18:49:01 2008'' |
Revision as of 15:49, 30 June 2008
Template:STRUCTURE 1bcb
INTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES
Template:ABSTRACT PUBMED 9480771
About this Structure
Full experimental information is available from OCA.
Reference
The contribution of cytosine protonation to the stability of parallel DNA triple helices., Asensio JL, Lane AN, Dhesi J, Bergqvist S, Brown T, J Mol Biol. 1998 Feb 6;275(5):811-22. PMID:9480771
Page seeded by OCA on Mon Jun 30 18:49:01 2008
