Literature DB >> 21047071

Counting ions around DNA with anomalous small-angle X-ray scattering.

Suzette A Pabit1, Steve P Meisburger, Li Li, Joshua M Blose, Christopher D Jones, Lois Pollack.   

Abstract

The majority of charge-compensating ions around nucleic acids form a diffuse counterion "cloud" that is not amenable to investigation by traditional methods that rely on rigid structural interactions. Although various techniques have been employed to characterize the ion atmosphere around nucleic acids, only anomalous small-angle X-ray scattering (ASAXS) provides information about the spatial distribution of ions. Here we present an experimentally straightforward extension of ASAXS that can be used to count the number of ions around nucleic acids.

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Year:  2010        PMID: 21047071      PMCID: PMC3012602          DOI: 10.1021/ja107259y

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  9 in total

1.  Counterion distribution around DNA probed by solution X-ray scattering.

Authors:  R Das; T T Mills; L W Kwok; G S Maskel; I S Millett; S Doniach; K D Finkelstein; D Herschlag; L Pollack
Journal:  Phys Rev Lett       Date:  2003-05-08       Impact factor: 9.161

Review 2.  A guide to ions and RNA structure.

Authors:  David E Draper
Journal:  RNA       Date:  2004-03       Impact factor: 4.942

3.  Ion effects on ligand-nucleic acid interactions.

Authors:  M T Record; M L Lohman; P De Haseth
Journal:  J Mol Biol       Date:  1976-10-25       Impact factor: 5.469

4.  Using anomalous small angle X-ray scattering to probe the ion atmosphere around nucleic acids.

Authors:  Suzette A Pabit; Kenneth D Finkelstein; Lois Pollack
Journal:  Methods Enzymol       Date:  2009-11-17       Impact factor: 1.600

Review 5.  Metal ions and RNA folding: a highly charged topic with a dynamic future.

Authors:  Sarah A Woodson
Journal:  Curr Opin Chem Biol       Date:  2005-04       Impact factor: 8.822

Review 6.  Salt effects on nucleic acids.

Authors:  K A Sharp; B Honig
Journal:  Curr Opin Struct Biol       Date:  1995-06       Impact factor: 6.809

7.  Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids.

Authors:  Yu Bai; Max Greenfeld; Kevin J Travers; Vincent B Chu; Jan Lipfert; Sebastian Doniach; Daniel Herschlag
Journal:  J Am Chem Soc       Date:  2007-11-09       Impact factor: 15.419

8.  Direct quantitation of Mg2+-RNA interactions by use of a fluorescent dye.

Authors:  Dan Grilley; Ana Maria Soto; David E Draper
Journal:  Methods Enzymol       Date:  2009       Impact factor: 1.600

9.  Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA.

Authors:  Suzette A Pabit; Xiangyun Qiu; Jessica S Lamb; Li Li; Steve P Meisburger; Lois Pollack
Journal:  Nucleic Acids Res       Date:  2009-04-24       Impact factor: 16.971

  9 in total
  42 in total

1.  RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations.

Authors:  Serdal Kirmizialtin; Suzette A Pabit; Steve P Meisburger; Lois Pollack; Ron Elber
Journal:  Biophys J       Date:  2012-02-21       Impact factor: 4.033

2.  The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations.

Authors:  Serdal Kirmizialtin; Alexander R J Silalahi; Ron Elber; Marcia O Fenley
Journal:  Biophys J       Date:  2012-02-21       Impact factor: 4.033

3.  The Role of Correlation and Solvation in Ion Interactions with B-DNA.

Authors:  Maria L Sushko; Dennis G Thomas; Suzette A Pabit; Lois Pollack; Alexey V Onufriev; Nathan A Baker
Journal:  Biophys J       Date:  2016-01-19       Impact factor: 4.033

4.  Multiscale methods for computational RNA enzymology.

Authors:  Maria T Panteva; Thakshila Dissanayake; Haoyuan Chen; Brian K Radak; Erich R Kuechler; George M Giambaşu; Tai-Sung Lee; Darrin M York
Journal:  Methods Enzymol       Date:  2015-01-22       Impact factor: 1.600

5.  Effects of a protecting osmolyte on the ion atmosphere surrounding DNA duplexes.

Authors:  Joshua M Blose; Suzette A Pabit; Steve P Meisburger; Li Li; Christopher D Jones; Lois Pollack
Journal:  Biochemistry       Date:  2011-09-15       Impact factor: 3.162

6.  Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids.

Authors:  Hung T Nguyen; Suzette A Pabit; Steve P Meisburger; Lois Pollack; David A Case
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

7.  Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting.

Authors:  Magdalena Gebala; Daniel Herschlag
Journal:  Biophys J       Date:  2019-08-12       Impact factor: 4.033

8.  Electrostatics of nucleic acid folding under conformational constraint.

Authors:  Peter C Anthony; Adelene Y L Sim; Vincent B Chu; Sebastian Doniach; Steven M Block; Daniel Herschlag
Journal:  J Am Chem Soc       Date:  2012-02-27       Impact factor: 15.419

9.  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

10.  DEAD-box protein CYT-19 is activated by exposed helices in a group I intron RNA.

Authors:  Inga Jarmoskaite; Hari Bhaskaran; Soenke Seifert; Rick Russell
Journal:  Proc Natl Acad Sci U S A       Date:  2014-07-07       Impact factor: 11.205

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