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J F Marko

Publications and source records attributed to J F Marko.

23 records · Page 2Linked to original sources
PubMed1997

Extension of torsionally stressed DNA by external force.

Metropolis Monte Carlo simulation was used to study the elasticity of torsionally stressed double-helical DNA. Equilibrium distributions of DNA conformations for different values of linking deficit, external force, and ionic conditions were simulated using the discrete wormlike chain model. Ionic conditions were specified in terms of DNA effective diameter, i.e., hard-core radius of the model chain. The simulations show that entropic elasticity of the double helix depends on how much it is twisted. For low amounts of twisting (less than about one turn per twist persistence length) the force versus extension is nearly the same as in the completely torsionally relaxed case. For more twisting than this, the molecule starts to supercoil, and there is an increase in the force needed to realize a given extension. For sufficiently large amounts of twist, the entire chain is plectonemically supercoiled at low extensions; a finite force must be applied to obtain any extension at all in this regime. The simulation results agree well with the results of recent micromanipulation experiments.

Computer Simulation↗
PubMed1997

Driving proteins off DNA using applied tension.

Proteins that bind DNA so as to reduce its end-to-end length can be dissociated by application of force. The thermodynamics of this process are discussed, with special attention to the case of histones bound to DNA (i.e., a string of nucleosomes, or chromatin fiber). The histone octamer is predicted to be driven off chromatin fiber for tensions >2 piconewtons.

Biophysical Phenomena↗
PubMed1997

Polymer models of meiotic and mitotic chromosomes.

Polymers tied together by constraints exhibit an internal pressure; this idea is used to analyze physical properties of the bottle-brush-like chromosomes of meiotic prophase that consist of polymer-like flexible chromatin loops, attached to a central axis. Using a minimal number of experimental parameters, semiquantitative predictions are made for the bending rigidity, radius, and axial tension of such brushes, and the repulsion acting between brushes whose bristles are forced to overlap. The retraction of lampbrush loops when the nascent transcripts are stripped away, the oval shape of diplotene bivalents between chiasmata, and the rigidity of pachytene chromosomes are all manifestations of chromatin pressure. This two-phase (chromatin plus buffer) picture that suffices for meiotic chromosomes has to be supplemented by a third constituent, a chromatin glue to understand mitotic chromosomes, and explain how condensation can drive the resolution of entanglements. This process resembles a thermal annealing in that a parameter (the affinity of the glue for chromatin and/or the affinity of the chromatin for buffer) has to be tuned to achieve optimal results. Mechanical measurements to characterize this protein-chromatin matrix are proposed. Finally, the propensity for even slightly chemically dissimilar polymers to phase separate (cluster like with like) can explain the apparent segregation of the chromatin into A + T- and G + C-rich regions revealed by chromosome banding.

Animals↗
PubMed1994

Fluctuations and supercoiling of DNA.

Frequently, DNA in vivo is organized into loops that are partially underwound and consequently form interwound helical supercoils. Methods from polymer statistical mechanics are used to show how the competition between entropy (thermal fluctuations) and elastic energy determines supercoil radius and pitch, in good agreement with recent experiments and simulations. Supercoil reorganization by means of slithering (reptation) of the DNA along the supercoil is argued to be a slow process. Extension of supercoiled DNA by an applied force shows a number of unexpected features, including coexistence of interwound and helical states.

DNA, Superhelical↗