Literature DB >> 15728387

DNA coiled coils.

J L Campos1, L Urpí, T Sanmartín, C Gouyette, J A Subirana.   

Abstract

We report the coiled-coil structure of DNA, which is generated by the dodecanucleotide d(ATATATATATAT). The structure has been determined by single-crystal x-ray crystallography. The molecules form duplexes with single-stranded overhangs, which associate with neighbor molecules and give rise to infinite double helices in a coiled-coil conformation, with staggered nicks in both strands. The coiled coils have six dodecamer duplexes per turn. Despite the presence of nicks, the structure is very rigid. Statistical disorder is present, which gives rise to continuous scattering along the layer lines. This observation can be interpreted by the classical theory of coiled coils developed for proteins, which we apply here to a DNA structure. A clear splitting of the original layer lines of the DNA double helix is detected. The structure we have found adds a previously unrecognized element to the architectures that can be built from DNA oligonucleotides. Any duplex with complementary single-strand overhangs should be expected to give rise to regular coiled-coil structures.

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Year:  2005        PMID: 15728387      PMCID: PMC553320          DOI: 10.1073/pnas.0500496102

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  26 in total

1.  Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix.

Authors:  Karen A Bunting; S Mark Roe; Anthony Headley; Tom Brown; Renos Savva; Laurence H Pearl
Journal:  Nucleic Acids Res       Date:  2003-03-15       Impact factor: 16.971

2.  Scanning human gene deserts for long-range enhancers.

Authors:  Marcelo A Nobrega; Ivan Ovcharenko; Veena Afzal; Edward M Rubin
Journal:  Science       Date:  2003-10-17       Impact factor: 47.728

3.  Analysis of alpha-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation.

Authors:  Sergei V Strelkov; Peter Burkhard
Journal:  J Struct Biol       Date:  2002 Jan-Feb       Impact factor: 2.867

Review 4.  At the crossroads of chemistry, biology, and materials: structural DNA nanotechnology.

Authors:  Nadrian C Seeman
Journal:  Chem Biol       Date:  2003-12

5.  Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs).

Authors:  I Liebich; J Bode; I Reuter; E Wingender
Journal:  Nucleic Acids Res       Date:  2002-08-01       Impact factor: 16.971

6.  Linker histone interaction shows divalent character with both supercoiled and linear DNA.

Authors:  Thomas P Ellen; K E van Holde
Journal:  Biochemistry       Date:  2004-06-22       Impact factor: 3.162

7.  Single-stranded breaks relax intrinsic curvature in DNA?

Authors:  Dimitri E Kamashev; Alexey K Mazur
Journal:  Biochemistry       Date:  2004-06-29       Impact factor: 3.162

8.  Stacked-unstacked equilibrium at the nick site of DNA.

Authors:  Ekaterina Protozanova; Peter Yakovchuk; Maxim D Frank-Kamenetskii
Journal:  J Mol Biol       Date:  2004-09-17       Impact factor: 5.469

9.  X-ray and NMR studies of the DNA oligomer d(ATATAT): Hoogsteen base pairing in duplex DNA.

Authors:  Nicola G A Abrescia; Carlos González; Catherine Gouyette; Juan A Subirana
Journal:  Biochemistry       Date:  2004-04-13       Impact factor: 3.162

10.  Nature of conformational changes in poly[d(A-T)-d(A-T)] in the premelting region.

Authors:  S Brahms; J Brahms; K E Van Holde
Journal:  Proc Natl Acad Sci U S A       Date:  1976-10       Impact factor: 11.205

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  1 in total

1.  Overview of the structure of all-AT oligonucleotides: organization in helices and packing interactions.

Authors:  Lourdes Campos; Núria Valls; Lourdes Urpí; Catherine Gouyette; Trinidad Sanmartín; Michael Richter; Elida Alechaga; Alicia Santaolalla; Roberto Baldini; Marc Creixell; Ruth Ciurans; Petr Skokan; Joan Pous; Juan A Subirana
Journal:  Biophys J       Date:  2006-05-12       Impact factor: 4.033

  1 in total

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