DNA melting in small-molecule-DNA-hybrid dimer structures: Experimental characterization and coarse-grained molecular dynamics simulations

Tatiana R. Prytkova, Ibrahim Eryazici, Brian Stepp, Son Binh Nguyen, George C Schatz

Research output: Contribution to journalArticle

41 Citations (Scopus)

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 l, 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 coarsegrained 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.

Original languageEnglish
Pages (from-to)2627-2634
Number of pages8
JournalJournal of Physical Chemistry B
Volume114
Issue number8
DOIs
Publication statusPublished - Mar 4 2010

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Dimers
Molecular dynamics
Melting
DNA
deoxyribonucleic acid
dimers
melting
molecular dynamics
Molecules
Computer simulation
molecules
simulation
Ions
strands
ions
hybrid structures
Benzene
Analytical models
benzene
Thermodynamics

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Materials Chemistry
  • Surfaces, Coatings and Films

Cite this

DNA melting in small-molecule-DNA-hybrid dimer structures : Experimental characterization and coarse-grained molecular dynamics simulations. / Prytkova, Tatiana R.; Eryazici, Ibrahim; Stepp, Brian; Nguyen, Son Binh; Schatz, George C.

In: Journal of Physical Chemistry B, Vol. 114, No. 8, 04.03.2010, p. 2627-2634.

Research output: Contribution to journalArticle

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