1bcb

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(New page: 200px<br /><applet load="1bcb" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bcb" /> '''INTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES''...)
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'''INTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES'''<br />
 
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==Overview==
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==INTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES==
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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 &gt;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.
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<StructureSection load='1bcb' size='340' side='right'caption='[[1bcb]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1bcb]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BCB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BCB FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bcb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bcb OCA], [https://pdbe.org/1bcb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bcb RCSB], [https://www.ebi.ac.uk/pdbsum/1bcb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bcb ProSAT]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The solution conformations of the intramolecular triple helices d(AGAAGA-X-TCTTCT-X-TC+TTC+T) and d(AAGGAA-X-TTCCTT-X-TTC+C+TT) (X = non-nucleotide linker) have been determined by NMR.1H NMR spectra in H2O showed that the third strand cytosine residues are fully paired with the guanine residues, each using two Hoogsteen hydrogen bonds. Determination of the13C chemical shifts of the cytosine C6 and C5 and their one-bond coupling constants (1 J CH) conclusively showed that the Hoogsteen cytosine residues are protonated at N3. The global conformations of the two molecules determined with &gt;19 restraints per residue are very similar (RMSD = 0.96 A). However, some differences in local conformation and dynamics were observed for the central two base triplets of the two molecules. The C N3H were less labile in adjacent CG.C+triplets than in non-adjacent ones, indicating that the adjacent charge does not kinetically destabilize these triplets. The sugar conformations of the two adjacent cytosine residues were different and the 5'-residue was atypical of protonated cytosine. Hence, there are subtle effects of the interaction between two adjacent cytosine residues. The central two purines in each sequence showed non-standard backbone conformations, averaging between gamma approximately 60 degrees and gamma approximately 180 degrees. This may be related to the difference in the dependence of the thermodynamic stability on pH observed for these two sequences.
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==About this Structure==
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Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG.C+ triplets.,Asensio JL, Brown T, Lane AN Nucleic Acids Res. 1998 Aug 15;26(16):3677-86. PMID:9685482<ref>PMID:9685482</ref>
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1BCB 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BCB OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9480771 9480771]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 1bcb" style="background-color:#fffaf0;"></div>
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[[Category: Asensio, J.L.]]
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== References ==
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[[Category: Brown, T.]]
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<references/>
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[[Category: Lane, A.N.]]
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__TOC__
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[[Category: deoxyribonucleic acid]]
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</StructureSection>
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[[Category: dna triplex]]
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[[Category: Large Structures]]
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[[Category: Asensio JL]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:59:59 2007''
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[[Category: Brown T]]
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[[Category: Lane AN]]

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INTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES

PDB ID 1bcb

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