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      • Record: found
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      Conformational analysis of nucleic acids revisited: Curves+

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          Abstract

          We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamics.

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          The structure of DNA in the nucleosome core.

          Timothy Richmond, Curt Davey (2003)
          The 1.9-A-resolution crystal structure of the nucleosome core particle containing 147 DNA base pairs reveals the conformation of nucleosomal DNA with unprecedented accuracy. The DNA structure is remarkably different from that in oligonucleotides and non-histone protein-DNA complexes. The DNA base-pair-step geometry has, overall, twice the curvature necessary to accommodate the DNA superhelical path in the nucleosome. DNA segments bent into the minor groove are either kinked or alternately shifted. The unusual DNA conformational parameters induced by the binding of histone protein have implications for sequence-dependent protein recognition and nucleosome positioning and mobility. Comparison of the 147-base-pair structure with two 146-base-pair structures reveals alterations in DNA twist that are evidently common in bulk chromatin, and which are of probable importance for chromatin fibre formation and chromatin remodelling.
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            PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules.

            M Egholm, O Buchardt, L. Christensen … (1993)
            DNA analogues are currently being intensely investigated owing to their potential as gene-targeted drugs. Furthermore, their properties and interaction with DNA and RNA could provide a better understanding of the structural features of natural DNA that determine its unique chemical, biological and genetic properties. We recently designed a DNA analogue, PNA, in which the backbone is structurally homomorphous with the deoxyribose backbone and consists of N-(2-aminoethyl)glycine units to which the nucleobases are attached. We showed that PNA oligomers containing solely thymine and cytosine can hybridize to complementary oligonucleotides, presumably by forming Watson-Crick-Hoogsteen (PNA)2-DNA triplexes, which are much more stable than the corresponding DNA-DNA duplexes, and bind to double-stranded DNA by strand displacement. We report here that PNA containing all four natural nucleobases hybridizes to complementary oligonucleotides obeying the Watson-Crick base-pairing rules, and thus is a true DNA mimic in terms of base-pair recognition.
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              A standard reference frame for the description of nucleic acid base-pair geometry.

              E. Westhof, R Dickerson, Mayumi Suzuki … (2001)
              Article 0 comments Cited 144 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: September 2009
                Publication date (Print): September 2009
                Publication date (Electronic): 22 July 2009
                Publication date PMC-release: 22 July 2009
                Volume: 37
                Issue: 17
                Pages: 5917-5929
                Affiliations
                1Institut de Biologie et Chimie des Protéines, CNRS UMR 5086/Université de Lyon, 7 Passage du Vercors, 69367 Lyon, France, 2Laboratoire de Modélisation Mathématique et Numérique dans les Sciences de l'Ingénieur, Ecole Nationale d'Ingénieurs de Tunis, B.P. 37, 1002 Tunis-Belvédère, Tunisia and 3Institut de Mathématiques B, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
                Author notes
                *To whom correspondence should be addressed. Tel: +33 4 72 72 26 37; Fax: +33 4 72 72 26 04; Email: richard.lavery@ 123456ibcp.fr Correspondence may also be addressed to K. Zakrzewska. Tel: +33 4 72 72 26 37; Fax: +33 4 72 72 26 04; Email: krystyna.zakrzewska@ 123456ibcp.fr

                The authors wish it to be known that, in their opinion, the first and the last authors should be regarded as joint First Authors.

                Article
                Publisher ID: gkp608
                DOI: 10.1093/nar/gkp608
                PMC ID: 2761274
                PubMed ID: 19625494
                SO-VID: 53c79da6-90fa-44b9-9492-15ac0a195b68
                Copyright © © 2009 The Author(s)
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 22 April 2009
                Date revision received : 5 July 2009
                Date accepted : 6 July 2009
                Categories
                Subject: Structural Biology

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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