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DNA Triplex with Propyne
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A.K. Phipps, M. Tarkoy, P. Schultze, and J. Feigon: "Solution structure of an intramolecular DNA triplex containing 5-(1-propynyl)-2'-deoxyuridine residues in the third strand", Biochemistry 37, 5820-5830 (1998). [abstract] PDB Code: 1P3X
(A) Stereoview of a superposition of all heavy atoms of the 10 lowest-energy structures of PDD-EG. The view is into the major groove. The Watson-Crick paired pyrimidine strand is green (T9-T16) and the purine strand blue (A1-A8); the Hoogsteen paired cytidines (C18, C20, and C22) are cyan and the Hoogsteen paired propynylU nucleotides (P17, P19, P21, P23, and P24) violet. Only the nucleotides are shown, since the ethylene glycol linkers were not included in the structure calculation. (B) Top and side view of the two triplets (P23.A7.T10 and P24.A8.T9) containing the consecutive propynylUs. The van der Waals radii for the bases are shown as a dotted surface. (C) Stacking of the 5-(1-propynyl)-2'-deoxyuridine-containing triplet (P21.A5.T12) on the neighboring triplet (C+20.G4.C13). |
