Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userQuantitative analysis of reptation of partially extended DNA in sub-30 nm nanoslits
446
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
We observed reptation of single DNA molecules in fused silica nanoslits of sub-30 nm height. The reptation behavior and the effect of confinement are quantitatively characterized using orientation correlation and transverse fluctuation analysis. We show tube-like polymer motion arises for a tense polymer under strong quasi-2D confinement and interaction with surface- passivating polyvinylpyrrolidone (PVP) molecules in nanoslits, while etching- induced device surface roughness, chip bonding materials and DNA-intercalated dye-surface interaction, play minor roles. These findings have strong implications for the effect of surface modification in nanofluidic systems with potential applications for single molecule DNA analysis.
rate research
Read More
Biological materials are self-assembled with near-atomic precision in living cells, whereas synthetic 3D structures generally lack such precision and controllability. Recently, DNA nanotechnology, especially DNA origami technology, has been useful in the bottom-up fabrication of well-defined nanostructures ranging from tens of nanometres to sub-micrometres. In this Primer, we summarize the methodologies of DNA origami technology, including origami design, synthesis, functionalization and characterization. We highlight applications of origami structures in nanofabrication, nanophotonics and nanoelectronics, catalysis, computation, molecular machines, bioimaging, drug delivery and biophysics. We identify challenges for the field, including size limits, stability issues and the scale of production, and discuss their possible solutions. We further provide an outlook on next-generation DNA origami techniques that will allow in vivo synthesis and multiscale manufacturing.
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this melting transition have been intensively investigated. Recently there has been a surge of interest in this question, caused by experiments determining the properties of partially bound DNA confined to nanochannels. But how does such confinement affect the melting transition? To answer this question we introduce, and solve a model predicting how confinement affects the melting transition for a simple model system by first disregarding the effect of self-avoidance. We find that the transition is smoother for narrower channels. By means of Monte-Carlo simulations we then show that a model incorporating self-avoidance shows qualitatively the same behaviour and that the effect of confinement is stronger than in the ideal case.
The role of thermal pressure fluctuation excited within tightly packaged DNA prior to ejection from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of parallel segments that forms an equilibrium conformation at minimum free energy, which presses tightly against internal capsid walls. Using a canonical ensemble at temperature T we calculate internal pressure fluctuations against a slowly moving or static capsid mantle for an elastic continuum model of the folded DNA bundle. It is found that fluctuating pressure on the capsid internal wall from thermal excitation of longitudinal acoustic vibrations in the bundle may have root-mean-square values which are several tens of atmospheres for typically small phage dimensions. Comparisons are given with measured data on three mutants of lambda phage with different base pair lengths and total genome ejection pressures.
Semiflexible polymers characterized by the contour length $L$ and persistent length $ell_p$ confined in a spatial region $D$ have been described as a series of ``{em spherical blobs} and ``{em deflecting lines} by de Gennes and Odjik for $ell_p < D$ and $ell_p gg D$ respectively. Recently new intermediate regimes ({em extended de Gennes} and {em Gauss-de Gennes}) have been investigated by Tree {em et al.} [Phys. Rev. Lett. {bf 110}, 208103 (2013)]. In this letter we derive scaling relations to characterize these transitions in terms of universal scaled fluctuations in $d$-dimension as a function of $L,ell_p$, and $D$, and show that the Gauss-de Gennes regime is absent and extended de Gennes regime is vanishingly small for polymers confined in a 2D strip. We validate our claim by extensive Brownian dynamics (BD) simulation which also reveals that the prefactor $A$ used to describe the chain extension in the Odjik limit is independent of physical dimension $d$ and is the same as previously found by Yang {em et al.}[Y. Yang, T. W. Burkhardt, G. Gompper, Phys. Rev. E {bf 76}, 011804 (2007)]. Our studies are relevant for optical maps of DNA stretched inside a nano-strip.
Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous recombination, the mechanism of homology recognition is still an unsolved puzzle. While specific proteins are known to play a role at later stages of recombination, an initial coarse grained recognition step has been proposed. This relies on the sequence dependence of the DNA structural parameters, such as twist and rise, mediated by intermolecular interactions, in particular electrostatic ones. In this proposed mechanism, sequences having the same base pair text, or are homologous, have lower interaction energy than those sequences with uncorrelated base pair texts; the difference termed the recognition energy. Here, we probe how the recognition energy changes when one DNA fragment slides past another, and consider, for the first time, homologous sequences in antiparallel alignment. This dependence on sliding was termed the recognition well. We find that there is recognition well for anti-parallel, homologous DNA tracts, but only a very shallow one, so that their interaction will differ little from the interaction between two nonhomologous tracts. This fact may be utilized in single molecule experiments specially targeted to test the theory. As well as this, we test previous theoretical approximations in calculating the recognition well for parallel molecules against MC simulations, and consider more rigorously the optimization of the orientations of the fragments about their long axes. The more rigorous treatment affects the recognition energy a little, when the molecules are considered rigid. However when torsional flexibility of the DNA molecules is introduced, we find excellent agreement between analytical approximation and simulation.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
