Journal Article

FZJ-2018-03175

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Preferential Binding of Urea to Single-Stranded DNA Structures: A Molecular Dynamics Study

Oprzeska-Zingrebe, E. A. ; Smiatek, J. (Corresponding author)FZJ*

2018
Cell Press Cambridge, Mass.

This record in other databases:      

Please use a persistent id in citations: doi:10.1016/j.bpj.2018.02.013

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.

---

Contributing Institute(s):

1. Helmholtz-Institut Münster Ionenleiter für Energiespeicher (IEK-12)

Research Program(s):

1. 131 - Electrochemical Storage (POF3-131) (POF3-131)

Appears in the scientific report 2018

---

Database coverage:
; BIOSIS Previews ; Current Contents - Life Sciences ; IF < 5 ; JCR ; NCBI Molecular Biology Database ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

---