PDBsum entry 149d

DNA

PDB id: 149d

Contents

DNA/RNA

References listed in PDB file

Key reference

Title

Solution structure of a pyrimidine.Purine.Pyrimidine DNA triplex containing t.At, C+.Gc and g.Ta triples.

Authors

I.Radhakrishnan, D.J.Patel.

Ref.

Structure, 1994, 2, 17-32. [DOI no: 10.1016/S0969-2126(00)00005-8]

PubMed id

8075980

Abstract

BACKGROUND: Under certain conditions, homopyrimidine oligonucleotides can bind to complementary homopurine sequences in homopurine-homopyrimidine segments of duplex DNA to form triple helical structures. Besides having biological implications in vivo, this property has been exploited in molecular biology applications. This approach is limited by a lack of knowledge about the recognition by the third strand of pyrimidine residues in Watson-Crick base pairs. RESULTS: We have therefore determined the solution structure of a pyrimidine.purine.pyrimidine (Y.RY) DNA triple helix containing a guanine residue in the third strand which was postulated to specifically recognize a thymine residue in a Watson-Crick TA base pair. The structure was solved by combining NMR-derived restraints with molecular dynamics simulations conducted in the presence of explicit solvent and counter ions. The guanine of the G-TA triple is tilted out of the plane of its target TA base pair towards the 3'-direction, to avoid a steric clash with the thymine methyl group. This allows the guanine amino protons to participate in hydrogen bonds with separate carbonyls, forming one strong bond within the G-TA triple and a weak bond to an adjacent T.AT triple. Dramatic variations in helical twist around the guanine residue lead to a novel stacking interaction. At the global level, the Y.RY DNA triplex shares several structural features with the recently solved solution structure of the R.RY DNA triplex. CONCLUSIONS: The formation of a G.TA triple within an otherwise pyrimidine.purine.pyrimidine DNA triplex causes conformational realignments in and around the G.TA triple. These highlight new aspects of molecular recognition that could be useful in triplex-based approaches to inhibition of gene expression and site-specific cleavage of genomic DNA.

Figure 10.
Figure 10. Stereo views of the (T17–G18–T19) segment in the Y·RY triplex. Views parallel to the helix axis are shown to emphasize the stacking pattern between bases in this segment and the large variations in helical twist. Figure 10. Stereo views of the (T17–G18–T19) segment in the Y·RY triplex. Views parallel to the helix axis are shown to emphasize the stacking pattern between bases in this segment and the large variations in helical twist.

Figure 12.
Figure 12. Stacking patterns at (a)(C2–T3)·(A12–G13), (b)(T3–A4)·(T11–A12), and (c)(A4–T5)·(A10–T11) base pair steps in the Watson–Crick duplex segment in the Y·RY triplex. Figure 12. Stacking patterns at (a)(C2–T3)·(A12–G13), (b)(T3–A4)·(T11–A12), and (c)(A4–T5)·(A10–T11) base pair steps in the Watson–Crick duplex segment in the Y·RY triplex.

The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 17-32) copyright 1994.

Secondary reference #1

Title

Three-Dimensional homonuclear noesy-Tocsy of an intramolecular pyrimidine.Purine.Pyrimidine DNA triplex containing a central g.Ta triple: nonexchangeable proton assignments and structural implications.

Authors

I.Radhakrishnan, D.J.Patel, X.Gao.

Ref.

Biochemistry, 1992, 31, 2514-2523. [DOI no: 10.1021/bi00124a011]

PubMed id

1547235

Secondary reference #2

Title

Solution conformation of a g(dot)ta triple in an intramolecular pyrimidine(dot)purine(dot)pyrimidine DNA triplex

Authors

I.Radhakrishnan, D.J.Patel, J.M.Veal, X.Gao.

Ref.

j am chem soc, 1992, 114, 6913.

Secondary reference #3

Title

Nmr structural studies of intramolecular (y+)n.(R+)n(y-)Ndna triplexes in solution: imino and amino proton and nitrogen markers of g.Ta base triple formation.

Authors

I.Radhakrishnan, X.Gao, C.De los santos, D.Live, D.J.Patel.

Ref.

Biochemistry, 1991, 30, 9022-9030. [DOI no: 10.1021/bi00101a016]

PubMed id

1654085