'''DNA TRIPLEX WITH 5' AND 3' JUNCTIONS, NMR, 10 STRUCTURES'''
===DNA TRIPLEX WITH 5' AND 3' JUNCTIONS, NMR, 10 STRUCTURES===
==Overview==
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BACKGROUND: Polypurine x polypyrimidine sequences of DNA can form parallel triple helices via Hoogsteen hydrogen bonds with a third DNA strand that is complementary to the purine strand. The triplex prevents transcription and could therefore potentially be used to regulate specific genes. The determination of the structures of triplex-duplex junctions can help us to understand the structural basis of specificity, and aid in the design of optimal antigene oligonucleotides. RESULTS: The solution structures of the junction triplexes d(GAGAGACGTA)-X-(TACGTCTCTC)-X-(CTCTCT) and d(CTCTCT)-X-(TCTCTCAGTC)-X-(GACTGAGAGA) (where X is bis(octylphosphate) and nucleotides in the triplex regions are underlined) have been solved using nuclear magnetic resonance (NMR) spectroscopy. The structure is characterised by significant changes in the conformation of the purine residues, asymmetry of the 5' and 3' junctions, and variations in groove widths associated with the positive charge of the protonated cytosine residues in the third strand. The thermodynamic stability of triplexes with either a 5' or a 3'CH+ is higher than those with a terminal thymidine. CONCLUSIONS: The observed sequence dependence of the triplex structure, and the distortions of the DNA at the 5' and 3' termini has implications for the design of optimal triplex-forming sequences, both in terms of the terminal bases and the importance of including positive charges in the third strand. Thus, triplex-stabilising ligands might be designed that can discriminate between TA x T-rich and CG x C+-rich sequences that depend not only on charge, but also on local groove widths. This could improve the stabilisation and specificity of antigene triplex formation.
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(as it appears on PubMed at http://www.pubmed.gov), where 10368268 is the PubMed ID number.
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{{ABSTRACT_PUBMED_10368268}}
==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BWG OCA].
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BWG OCA].
==Reference==
==Reference==
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[[Category: Dna triplex]]
[[Category: Dna triplex]]
[[Category: Triplex-duplex junction]]
[[Category: Triplex-duplex junction]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 19:49:27 2008''
Revision as of 19:49, 30 June 2008
This article has been automatically seeded. Changes to this page should pertain to the PDB entry only and not to the protein or biomolecule in general.
Full experimental information is available from OCA.
ReferenceReference
Solution conformation of a parallel DNA triple helix with 5' and 3' triplex-duplex junctions., Asensio JL, Brown T, Lane AN, Structure. 1999 Jan 15;7(1):1-11. PMID:10368268
