Photosystem trap energies and spectrally-dependent energy-storage efficiencies in the Chl d-utilizing cyanobacterium, Acaryochloris marina.

Acaryochloris marina is the only species known to utilize chlorophyll (Chl) d as a principal photopigment. The peak absorption wavelength of Chl d is redshifted ≈40nm in vivo relative to Chl a, enabling this cyanobacterium to perform oxygenic phototrophy in niche environments enhanced in far-red light. We present measurements of the in vivo energy-storage (E-S) efficiency of photosynthesis in A.

Persistence lengths of DNA obtained from Brownian dynamics simulations.

The persistence length of DNA has been studied for decades; however, experimentally obtained values of this quantity have not been entirely consistent. We report results from Brownian dynamics simulations that address this issue, validating and demonstrating the utility of an explicitly double-stranded model for mesoscale DNA dynamics. We find that persistence lengths calculated from rotational relaxation increase with decreasing ionic strength, corroborating experimental evidence, but contradicting results obtained from wormlike coil assumptions.

Visualization of the detailed structure of plasmid DNA.

We report results from scanning tunneling microscopy experiments in which supercoiling of the plasmid, pTNT, leads to localized duplex denaturation at a single location. Measurements of the imaged strand-separated region suggest an extent of approximately 60 base pairs (bp's), in excellent agreement with the prediction of a statistical mechanical analysis of the pTNT base sequence that accounts for the topology-mediated global coupling of melting behaviors. Notwithstanding that the sequence of pTNT includes a 30-bp run of poly-A, where thermodynamic considerations alone predict significant instability, based on the statistical result, we propose the location of denaturation is an approximately 60-bp run, spanning positions 2050-2110, that is 82% AT-rich, terminally flanks the beta-lactamase coding region, and is known to contain two sites susceptible to cleavage by the DraI restriction enzyme.

Brownian dynamics of double-stranded DNA in periodic systems with discrete salt.

Numerical models of mesoscale DNA dynamics relevant to in vivo scenarios require methods that incorporate important features of the intracellular environment, while maintaining computational tractability. Because the explicit inclusion of ions leads to electrostatic calculations that scale as the square of the number of charged particles, such models typically handle these calculations using low-potential, mean-field approaches, rather than by considering the discrete interactions of ions. This allows approximation of the long-range, screened self-repulsion of DNA, but is unable to capture detailed electrostatic phenomena, such as short-range attractions mediated by ion-ion correlations.

Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA.

The topological state of DNA in vivo is dynamically regulated by a number of processes that involve interactions with bound proteins. In one such process, the tracking of RNA polymerase along the double helix during transcription, restriction of rotational motion of the polymerase and associated structures, generates waves of overtwist downstream and undertwist upstream from the site of transcription. The resulting superhelical stress is often sufficient to drive double-stranded DNA into a denatured state at locations such as promoters and origins of replication, where sequence-specific duplex opening is a prerequisite for biological function.

DNA mechanics.

We review the history of DNA mechanics and its analysis. We evaluate several methods to analyze the structures of superhelical DNA molecules, each predicated on the assumption that DNA can be modeled with reasonable accuracy as an extended, linearly elastic polymer. Three main approaches are considered: mechanical equilibrium methods, which seek to compute minimum energy conformations of topologically constrained molecules; statistical mechanical methods, which seek to compute the Boltzmann distribution of equilibrium conformations that arise in a finite temperature environment; and dynamic methods, which seek to compute deterministic trajectories of the helix axis by solving equations of motion.

Transcription-driven twin supercoiling of a DNA loop: a Brownian dynamics study.

The torque generated by RNA polymerase as it tracks along double-stranded DNA can potentially induce long-range structural deformations integral to mechanisms of biological significance in both prokaryotes and eukaryotes. In this paper, we introduce a dynamic computer model for investigating this phenomenon. Duplex DNA is represented as a chain of hydrodynamic beads interacting through potentials of linearly elastic stretching, bending, and twisting, as well as excluded volume.