Literature DB >> 23765314

Physical chemistry of nucleic acids and their complexes.

Rodolfo Ghirlando1, Gary Felsenfeld.   

Abstract

Studies of the physical properties of nucleic acids began almost immediately following the discovery of the DNA structure. Early investigations focused on the stability and specificity of multi-strand polynucleotide complexes, then gradually on their interaction with other molecules, particularly proteins. As molecular and structural biology expanded to provide detailed information about biochemical mechanisms, physical studies eventually acquired the additional constraint that they should be relevant to functioning biological systems. We describe work in our laboratory that began with investigations of relatively simple questions about the role of electrostatic interactions in the stabilization of multi-strand nucleic acid structures, and evolved to studies of chromatin structure in vitro and within the nucleus.
Copyright © 2013 Wiley Periodicals, Inc.

Entities:  

Keywords:  DNA; chromatin; polynucleotide structures

Mesh:

Substances:

Year:  2013        PMID: 23765314      PMCID: PMC4563860          DOI: 10.1002/bip.22311

Source DB:  PubMed          Journal:  Biopolymers        ISSN: 0006-3525            Impact factor:   2.505


  43 in total

1.  Transitions in histone acetylation reveal boundaries of three separately regulated neighboring loci.

Authors:  M D Litt; M Simpson; F Recillas-Targa; M N Prioleau; G Felsenfeld
Journal:  EMBO J       Date:  2001-05-01       Impact factor: 11.598

2.  Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene.

Authors:  A C Bell; G Felsenfeld
Journal:  Nature       Date:  2000-05-25       Impact factor: 49.962

3.  Transcription through the nucleosome by mRNA-producing RNA polymerases.

Authors:  W Walter; M Kashlev; V M Studitsky
Journal:  Methods Enzymol       Date:  2004       Impact factor: 1.600

4.  Perturbation of nucleosome structure by the erythroid transcription factor GATA-1.

Authors:  J Boyes; J Omichinski; D Clark; M Pikaart; G Felsenfeld
Journal:  J Mol Biol       Date:  1998-06-12       Impact factor: 5.469

5.  Capturing chromosome conformation.

Authors:  Job Dekker; Karsten Rippe; Martijn Dekker; Nancy Kleckner
Journal:  Science       Date:  2002-02-15       Impact factor: 47.728

6.  The preferential interactions of polylysine and polyarginine with specific base sequences in DNA.

Authors:  M Leng; G Felsenfeld
Journal:  Proc Natl Acad Sci U S A       Date:  1966-10       Impact factor: 11.205

7.  A study of polyadenylic acid at neutral pH.

Authors:  M Leng; G Felsenfeld
Journal:  J Mol Biol       Date:  1966-02       Impact factor: 5.469

8.  Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus.

Authors:  M D Litt; M Simpson; M Gaszner; C D Allis; G Felsenfeld
Journal:  Science       Date:  2001-08-09       Impact factor: 47.728

9.  Functional association of CTCF with the insulator upstream of the H19 gene is parent of origin-specific and methylation-sensitive.

Authors:  C Kanduri; V Pant; D Loukinov; E Pugacheva; C F Qi; A Wolffe; R Ohlsson; V V Lobanenkov
Journal:  Curr Biol       Date:  2000-07-13       Impact factor: 10.834

10.  Visualization of chromatin domains created by the gypsy insulator of Drosophila.

Authors:  Keith Byrd; Victor G Corces
Journal:  J Cell Biol       Date:  2003-08-18       Impact factor: 10.539

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  2 in total

1.  Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting.

Authors:  Magdalena Gebala; George M Giambaşu; Jan Lipfert; Namita Bisaria; Steve Bonilla; Guangchao Li; Darrin M York; Daniel Herschlag
Journal:  J Am Chem Soc       Date:  2015-11-12       Impact factor: 15.419

2.  A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.

Authors:  Christopher Maffeo; Thuy T M Ngo; Taekjip Ha; Aleksei Aksimentiev
Journal:  J Chem Theory Comput       Date:  2014-06-03       Impact factor: 6.006

  2 in total

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