Publication

array(14 items)
   uid => 9 (integer)
   title => 'Salt corrections for RNA secondary structures in the ViennaRNA package' (70 chars)
   abstract => 'Background RNA features a highly negatively charged phosphate backbone that 
      attracts a of cloud counter-ions that reduce the electrostatic repulsion in 
      a concentration dependent manner. Ion concentrations thus have a large influ
      ence on folding and stability of RNA structures. Despite their well-document
      ed effects, salt effects are not handled by currently available secondary st
      ucture prediction algorithms. Combining Debye-Hückel potentials for line ch
      arges and Manning’s counter-ion condensation theory, Einert et al. [ Bioph
      ys. J. 100: 2745-2753 (2011)] modeled the energetic effects contributions mo
      novalent cations on loops and helices.  Results The model of Einert et al. i
      s adapted to match the structure of the dynamic programming recursion of RNA
       secondary structure prediction algorithms. An empirical term describing the
       dependence salt dependence of the duplex initiation energy is added to impr
      ove co-folding predictions for two or more RNA strands. The slightly modifie
      d model is implemented in the ViennaRNApackage in such way that only the ene
      rgy parameters but not the algorithmic structure is affected. A comparison w
      ith data from the literature show that predicted free energies and melting t
      emperatures are in reasonable agreement with experiments.  Conclusion The ne
      w feature in the ViennaRNApackage makes it possible to study effects of salt
       concentrations on RNA folding in a systematic manner. Strictly speaking, th
      e model pertains only to mono-valent cations, and thus covers the most impor
      tant parameter, i.e., the NaCl concentration. It remains a question for futu
      re research to what extent unspecific effects of bi- and tri-valent cations 
      can be approximated in a similar manner.  Availability Corrections for the c
      oncentration of monovalent cations are available in the ViennaRNApackage sta
      rting from version 2.6.0.' (1849 chars)
   authors => array(4 items)
      0 => array(3 items)
         last_name => 'Yao' (3 chars)
         first_name => 'Hua Ting' (8 chars)
         sorting => 1 (integer)
      1 => array(3 items)
         last_name => 'Lorenz' (6 chars)
         first_name => 'Ronny' (5 chars)
         sorting => 2 (integer)
      2 => array(3 items)
         last_name => 'Hofacker' (8 chars)
         first_name => 'Ivo L.' (6 chars)
         sorting => 3 (integer)
      3 => array(3 items)
         last_name => 'Stadler' (7 chars)
         first_name => 'Peter Florian' (13 chars)
         sorting => 4 (integer)
   type => '0' (1 chars)
   keywords => '' (0 chars)
   year => 2023 (integer)
   affiliation => 0 (integer)
   link_paper => 'https://syndication.highwire.org/content/doi/10.1101/2023.04.07.536000' (70 chars)
   link_supplements => '' (0 chars)
   file_published => 0 (integer)
   journal => '' (0 chars)
   doi => '10.1101/2023.04.07.536000' (25 chars)
   preprint => '-1' (2 chars)