Membranes / Biomolecules

Free energy landscape


Free energy landscape of cytosine rich DNA strands


Our group is specialized in studying the microscopic properties of complex systems via computer simulations. We analyze DNA and DNA-polymer hybrid systems employing high performance calculations. More specifically, we examine the folding and unfolding dynamics and the thermodynamic properties of tetrameric DNA as well as for DNA-polymer hybrid systems, for different external conditions, with enhanced sampling methods on a microscopic level.

I-motif 100

We focus on the cytosine rich DNA sequences that form four stranded structures (i-motif) under acidic conditions. The i-motif is an intercalated structure formed by association in a head to tail orientation of two parallel duplexes whose strands are held together by hemiprotonated cytosine•cytosine(+) pairs. Our theoretical work examines how point defects in the central strands and variations of the cytosine sequences’ length affect the thermodynamical stability of the i-motif structure. In this project, we employ the fully atomistic molecular dynamics method with an explicit solvent model. Furthermore, in order to enhance the conformational sampling and to compute the thermodynamic stability of the new "mutated" i-motif structures, we use metadynamics, replica-exchange and steered molecular dynamics.
The outcome of our computer simulations is compared with experiments conducted by an experimental group of Prof. Dongsheng Liu, working on proton-driven DNA nanomotors and bio-sensors, e.g. by exploring the sensitivity of the stability of the i-motif on pH-value.

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J. Smiatek, A. Heuer
Deprotonation mechanism of a single-stranded DNA i-motif
RSC Advances 4, 17110-17113 (2014)

J. Smiatek, D. Janssen-Mueller, R. Friedrich, A. Heuer
Systematic detection of hidden complexities in the unfolding mechanism of a cytosine-rich DNA strand
arXiv: 1109.5474, Physica A 394, 136–144 (2014)

J. Smiatek, D. Liu, A. Heuer
High temperature unfolding simulations of a single-stranded DNA i-motif.
arxiv:1103.5932, Current Physical Chemistry 2, 115-123 (2012)

J. Smiatek, C. Chen, D. Liu, A. Heuer

Stable conformations of a single stranded deprotonated DNA i-motif
J. Phys. Chem. B, 2011, 115 (46), 13788–13795 (2011)

J. Smiatek, A. Heuer
Calculation of free energy landscapes: A Histogram Reweighted Metadynamics approach
arXiv:1006.4308v1, Journal of Computational Chemistry 32/10, 2084–2096 ( 2011)


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Institut für Physikalische Chemie
Prof. Dr. Andreas Heuer

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· D-48149 Münster
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