Related papers: Characterizing the Interaction Between DNA and Gel…
The dynamics of particles interacting by key-lock binding of attached biomolecules are studied theoretically. Experimental realizations of such systems include colloids grafted with complementary single-stranded DNA (ssDNA), and particles…
Discontinuous shear thickening (DST) is associated with a sharp rise of a suspension's viscosity with increasing applied shear rate. A key signature of DST, highlighted in recent studies, is the very large fluctuations of the measured…
Single-molecule FRET is widely used to study helicases by detecting distance changes between a fluorescent donor and an acceptor anchored to overhangs of a forked DNA duplex. However, it has lacked single-base pair (1-bp) resolution…
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
The extension of DNA confined to nanochannels has been studied intensively and in detail. Yet quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined…
The rapid worldwide spread of severe viral infections, often involving novel modifications of viruses, poses major challenges to our health care systems. This means that tools that can efficiently and specifically diagnose viruses are much…
In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones)…
The dependence of DNA assemblies conductance on relative humidity is investigated theoretically. Following earlier suggestions, we consider the ionic conductivity through the layers of water adsorbed by DNA molecules. The increase in…
We report a comparison of two photonic techniques for single-molecule sensing: fluorescence nanoscopy and optoplasmonic sensing. As the test system, oligonucleotides with and without fluorescent labels are transiently hybridized to…
Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…
We report a structural polymorphism of the S-DNA when a canonical B-DNA is stretched under different pulling protocols and provide a fundamental molecular understanding of the DNA stretching mechanism. Extensive all atom molecular dynamics…
The supra-molecular structure of a liquid is strongly connected to its dynamics which in turn controls macroscopic properties such as viscosity. Consequently, detailed knowledge about how this structure changes with temperature is essential…
Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…
The dynamics of loops at the DNA denaturation transition is studied. A scaling argument is used to evaluate the asymptotic behavior of the autocorrelation function of the state of complementary bases (either open or closed). The long-time…
Recent experiments have shown that the force-extension (F-x) curve for single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is significantly different from thymine [poly(dT)]. Here, we show that the base stacking interaction is…
Ring polymers exhibit unique flow properties due to their closed chain topology. Despite recent progress, we have not yet achieved a full understanding of the nonequilibrium flow behavior of rings in nondilute solutions where intermolecular…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We consider DNA-cationic lipid complexes that form lamellar stacks of lipid bilayers with parallel DNA strands intercalated in between. We calculate the electrostatically induced elastic deformations of the lipid bilayers. It is found that…