Solution structure of an intramolecular DNA triplex containing 5-(1-propynyl)-2'-deoxyuridine residues in the third strand

Biochemistry
A K PhippsJ Feigon

Abstract

Incorporation of the modified base 5-(1-propynl)-2'-deoxyuridine (propynylU) in the third strand of a triplex leads to enhanced triplex stabilization. To investigate effects of the propyne nucleotide on triplex structure and the factors underlying the increased stability, we have determined the solution structure of the intramolecular DNA pyrmidine-purine-pyrimdine d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-PCPCPCPP) (PDD-EG), which contains 5-(1-propynl)-2'-deoxyuridine (P) in the third strand and hexakis(ethylene glycol) linkers [(EG)6]. The structure was calculated using X-PLOR with distance and dihedral angle restraints obtained from two-dimensional NMR experiments and refined with the direct relaxation matrix method. The structures show that the extended aromatic electron cloud of the propynylU nucleotide stacks well over the 5'-neighboring nucleotides, resulting in increased stabilization. The propynylU nucleotides also affect the overall structure of the triple helix. A comparison of the structure to that of the nonmodified intramolecular DNA triplex of the same sequence, d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT) (DDD-EG), shows that PDD-EG has a more A-DNA like X displacement and inclination than DDD-EG yet still maintains predomi...Continue Reading

References

Jan 1, 1992·Annual Review of Pharmacology and Toxicology·S T Crooke
Aug 1, 1988·Journal of Biomolecular Structure & Dynamics·R Lavery, H Sklenar
Sep 1, 1983·Journal of Medicinal Chemistry·J GoodchildH J Wadsworth
Jan 7, 1997·Proceedings of the National Academy of Sciences of the United States of America·C GiovannangeliC Helene
Nov 1, 1995·Journal of Biomolecular NMR·K P NeidigH R Kalbitzer

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Citations

Mar 14, 2002·Biopolymers·J Sühnel
Jun 8, 2002·Journal of Molecular Biology·Paula Rodrigues Hoyne, L James Maher
Mar 17, 2012·Journal of the American Chemical Society·Annalisa ArcellaModesto Orozco
Nov 18, 2003·Journal of Biomolecular Structure & Dynamics·Thibault MichelElaine Taillandier
Nov 10, 2000·Nucleic Acids Research·R SolivaM Orozco
Dec 17, 2005·Nucleic Acids Research·Kristin EisenschmidtAlfred Pingoud
Nov 16, 2010·Accounts of Chemical Research·Dev P Arya
Apr 24, 1999·FEBS Letters·M KepplerK R Fox
Nov 24, 2006·Chembiochem : a European Journal of Chemical Biology·Ivan TrkuljaRobert Häner
Dec 4, 2014·Chembiochem : a European Journal of Chemical Biology·Takashi KanamoriKohji Seio
Jun 11, 1999·Current Opinion in Structural Biology·D E Gilbert, J Feigon
Oct 9, 2001·Chemistry & Biology·P R HardwidgeL J Maher
Nov 27, 2001·Nucleosides, Nucleotides & Nucleic Acids·B CatalanottiM Varra
Jun 6, 2003·Journal of the American Chemical Society·Brent M ZnoskoDouglas H Turner
Dec 18, 2003·Journal of the American Chemical Society·Anna AviñóModesto Orozco

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