1p3x
From Proteopedia
|
INTRAMOLECULAR DNA TRIPLEX WITH 1-PROPYNYL DEOXYURIDINE IN THE THIRD STRAND, NMR, 10 STRUCTURES
Overview
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 predominantly S-type sugar puckers as found in DDD-EG and other, DNA triplexes.
About this Structure
1P3X is a Protein complex structure of sequences from [1] with PDU as ligand. Full crystallographic information is available from OCA.
Reference
Solution structure of an intramolecular DNA triplex containing 5-(1-propynyl)-2'-deoxyuridine residues in the third strand., Phipps AK, Tarkoy M, Schultze P, Feigon J, Biochemistry. 1998 Apr 28;37(17):5820-30. PMID:9558315
Page seeded by OCA on Sun Nov 25 01:56:56 2007
Categories: Protein complex | Feigon, J. | Phipps, A.K. | Schultze, P. | Tarkoy, M. | PDU | Oligonucleotide | Propyne | Triplex
