Ibrahim Eryazici - DNA Melting in Small-Molecule−DNA-Hybrid Dimer Structures: Experimental Characterization and Coarse-Grained Molecular Dynamics Simulations

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  Publication Details (including relevant citation   information):

  Prytkova,T. R.,   Eryazici, I., Stepp, B., Nguyen, S. T., Schatz, G. C.,   Journal of Physical Chemistry B, 2010,   114(8), 2627-2634.

  Abstract:

  When DNA hybridization is used to link together nanoparticles or   molecules, the melting transition of the resulting DNA-linked   material often is very sharp. In this paper, we study a   particularly simple version of this class of material based on a   small-molecule−DNA-hybrid (SMDH) structure that has three DNA   strands per 1,3,5-tris(phenylethynyl)benzene core. By varying the   concentration of the SMDHs, it is possible to produce either SMDH   dimers or bulk aggregates, with the former having highly packed   duplex DNA while the latter has an extended network. Melting   measurements that we present show that the dimers exhibit sharp   melting while the extended aggregates show broad melting. To   interpret these results, we have performed coarse-grained   molecular dynamics (CGMD) studies of the dimer melting and also   of isolated duplex melting using CGMD potentials that have either   implicit or explicit ions. Details of the melting simulation   technology demonstrate that the simulations properly describe   equilibrium transitions in isolated duplexes. The results show   that the SMDH dimer has much sharper melting than the isolated   duplex. Both implicit and explicit ion calculations show this   effect, but the explicit ion results are sharper. An analytical   model of the melting thermodynamics is developed which shows that   the sharp melting is entropically driven and can be understood   primarily in terms of the differences between the effective   concentrations of the DNA strands for intracomplex hybridization   events compared to intermolecular hybridization.

  Address (URL): http://pubs.acs.org/doi/abs/10.1021/jp910395k

 

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