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@ARTICLE{OprzeskaZingrebe:846003,
      author       = {Oprzeska-Zingrebe, Ewa Anna and Smiatek, Jens},
      title        = {{P}referential {B}inding of {U}rea to {S}ingle-{S}tranded
                      {DNA} {S}tructures: {A} {M}olecular {D}ynamics {S}tudy},
      journal      = {Biophysical journal},
      volume       = {114},
      number       = {7},
      issn         = {0006-3495},
      address      = {Cambridge, Mass.},
      publisher    = {Cell Press},
      reportid     = {FZJ-2018-03175},
      pages        = {1551 - 1562},
      year         = {2018},
      abstract     = {In nature, a wide range of biological processes such as
                      transcription termination and intermolecular binding depend
                      on the formation of specific DNA secondary and tertiary
                      structures. These structures can be both stabilized or
                      destabilized by different cosolutes coexisting with nucleic
                      acids in the cellular environment. In our molecular dynamics
                      simulation study, we investigate the binding of urea at
                      different concentrations to short 7-nucleotide
                      single-stranded DNA structures in aqueous solution. The
                      local concentration of urea around a native DNA hairpin in
                      comparison to an unfolded DNA conformation is analyzed by a
                      preferential binding model in light of the Kirkwood-Buff
                      theory. All our findings indicate a pronounced accumulation
                      of urea around DNA that is driven by a combination of
                      electrostatic and dispersion interactions and accomplished
                      by a significant replacement of hydrating water molecules.
                      The outcomes of our study can be regarded as a first step
                      into a deeper mechanistic understanding toward
                      cosolute-induced effects on nucleotide structures in
                      general.},
      cin          = {IEK-12},
      ddc          = {570},
      cid          = {I:(DE-Juel1)IEK-12-20141217},
      pnm          = {131 - Electrochemical Storage (POF3-131)},
      pid          = {G:(DE-HGF)POF3-131},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:29642026},
      UT           = {WOS:000430214500006},
      doi          = {10.1016/j.bpj.2018.02.013},
      url          = {https://juser.fz-juelich.de/record/846003},
}