2,534 research outputs found
Dynamics of a bubble formed in double stranded DNA
We study the fluctuational dynamics of a tagged base-pair in double stranded
DNA. We calculate the drift force which acts on the tagged base-pair using a
potential model that describes interactions at base pairs level and use it to
construct a Fokker-Planck equation.The calculated displacement autocorrelation
function is found to be in very good agreement with the experimental result of
Altan-Bonnet {\it et. al.} Phys. Rev. Lett. {\bf 90}, 138101 (2003) over the
entire time range of measurement. We calculate the most probable displacements
which predominately contribute to the autocorrelation function and the
half-time history of these displacements.Comment: 11 pages, 4 figures. submitted to Phys. Rev. Let
DNA bubble dynamics as a quantum Coulomb problem
We study the dynamics of denaturation bubbles in double-stranded DNA on the
basis of the Poland-Scheraga model. We demonstrate that the associated
Fokker-Planck equation is equivalent to a Coulomb problem. Below the melting
temperature the bubble lifetime is associated with the continuum of scattering
states of the repulsive Coulomb potential, at the melting temperature the
Coulomb potential vanishes and the underlying first exit dynamics exhibits a
long time power law tail, above the melting temperature, corresponding to an
attractive Coulomb potential, the long time dynamics is controlled by the
lowest bound state. Correlations and finite size effects are discussed.Comment: 4 pages, 3 figures, revte
Dynamics of DNA-breathing: Weak noise analysis, finite time singularity, and mapping onto the quantum Coulomb problem
We study the dynamics of denaturation bubbles in double-stranded DNA on the
basis of the Poland-Scheraga model. We show that long time distributions for
the survival of DNA bubbles and the size autocorrelation function can be
derived from an asymptotic weak noise approach. In particular, below the
melting temperature the bubble closure corresponds to a noisy finite time
singularity. We demonstrate that the associated Fokker-Planck equation is
equivalent to a quantum Coulomb problem. Below the melting temperature the
bubble lifetime is associated with the continuum of scattering states of the
repulsive Coulomb potential; at the melting temperature the Coulomb potential
vanishes and the underlying first exit dynamics exhibits a long time power law
tail; above the melting temperature, corresponding to an attractive Coulomb
potential, the long time dynamics is controlled by the lowest bound state.
Correlations and finite size effects are discussed.Comment: 12 pages, 10 figures, revte
Two-Dimensional Crystallography of TFIIB– and IIE–RNA Polymerase II Complexes: Implications for Start Site Selection and Initiation Complex Formation
AbstractTranscription factors IIB (TFIIB) and IIE (TFIIE) bound to RNA polymerase II have been revealed by electron crystallography in projection at 15.7 Å resolution. The results lead to simple hypotheses for the roles of these factors in the initiation of transcription. TFIIB is suggested to define the distance from TATA box to transcription start site by bringing TATA DNA in contact with polymerase at that distance from the active center of the enzyme. TFIIE is suggested to participate in a key conformational switch occurring at the active center upon polymerase–DNA interaction
Master equation approach to DNA-breathing in heteropolymer DNA
After crossing an initial barrier to break the first base-pair (bp) in
double-stranded DNA, the disruption of further bps is characterized by free
energies between less than one to a few kT. This causes the opening of
intermittent single-stranded bubbles. Their unzipping and zipping dynamics can
be monitored by single molecule fluorescence or NMR methods. We here establish
a dynamic description of this DNA-breathing in a heteropolymer DNA in terms of
a master equation that governs the time evolution of the joint probability
distribution for the bubble size and position along the sequence. The transfer
coefficients are based on the Poland-Scheraga free energy model. We derive the
autocorrelation function for the bubble dynamics and the associated relaxation
time spectrum. In particular, we show how one can obtain the probability
densities of individual bubble lifetimes and of the waiting times between
successive bubble events from the master equation. A comparison to results of a
stochastic Gillespie simulation shows excellent agreement.Comment: 12 pages, 8 figure
Dynamical scaling of the DNA unzipping transition
We report studies of the equilibrium and the dynamics of a general set of
lattice models which capture the essence of the force-induced or mechanical DNA
unzipping transition. Besides yielding the whole equilibrium phase diagram in
the force vs temperature plane, which reveals the presence of an interesting
re-entrant unzipping transition for low T, these models enable us to
characterize the dynamics of the process starting from a non-equilibrium
initial condition. The thermal melting of the DNA strands displays a model
dependent time evolution. On the contrary, our results suggest that the
dynamical mechanism for the unzipping by force is very robust and the scaling
behaviour does not depend on the details of the description we adopt.Comment: 6 pages, 4 figures, A shorter version of this paper appeared in Phys.
Rev. Lett. 88, 028102 (2002
iciA, an Escherichia coli gene encoding a specific inhibitor of chromosomal initiation of replication in vitro.
Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms
Recent evidence suggests that transcript elongation by RNA polymerase II (RNAPII) is regulated by mechanical cues affecting the entry into, and exit from, transcriptionally inactive states, including pausing and arrest. We present a single-molecule optical-trapping study of the interactions of RNAPII with transcription elongation factors TFIIS and TFIIF, which affect these processes. By monitoring the response of elongation complexes containing RNAPII and combinations of TFIIF and TFIIS to controlled mechanical loads, we find that both transcription factors are independently capable of restoring arrested RNAPII to productive elongation. TFIIS, in addition to its established role in promoting transcript cleavage, is found to relieve arrest by a second, cleavage-independent mechanism. TFIIF synergistically enhances some, but not all, of the activities of TFIIS. These studies also uncovered unexpected insights into the mechanisms underlying transient pauses. The direct visualization of pauses at near-base-pair resolution, together with the load dependence of the pause-entry phase, suggests that two distinct mechanisms may be at play: backtracking under forces that hinder transcription and a backtrack-independent activity under assisting loads. The measured pause lifetime distributions are inconsistent with prevailing views of backtracking as a purely diffusive process, suggesting instead that the extent of backtracking may be modulated by mechanisms intrinsic to RNAPII. Pauses triggered by inosine triphosphate misincorporation led to backtracking, even under assisting loads, and their lifetimes were reduced by TFIIS, particularly when aided by TFIIF. Overall, these experiments provide additional insights into how obstacles to transcription may be overcome by the concerted actions of multiple accessory factors
The democratic engagement of Britain's ethnic minorities
Democratic engagement is a multi-faceted phenomenon that embraces citizens' involvement with electoral politics, their participation in ‘conventional’ extra-parliamentary political activity, their satisfaction with democracy and trust in state institutions, and their rejection of the use of violence for political ends. Evidence from the 2010 BES and EMBES shows that there are important variations in patterns of democratic engagement across Britain's different ethnic-minority groups and across generations. Overall, ethnic-minority engagement is at a similar level to and moved by the same general factors that influence the political dispositions of whites. However, minority democratic engagement is also strongly affected by a set of distinctive ethnic-minority perceptions and experiences, associated particularly with discrimination and patterns of minority and majority cultural engagement. Second-generation minorities who grew up in Britain are less, rather than more, likely to be engaged
Diverse phenotypes resulting from polyphosphate kinase gene (ppk1) inactivation in different strains of Helicobacter pylori
Connections among biochemical pathways should help buffer organisms against environmental stress and affect the pace and trajectory of genome evolution. To explore these ideas, we studied consequences of inactivating the gene for polyphosphate kinase 1 (ppk1) in strains of Helicobacter pylori, a genetically diverse gastric pathogen. The PPK1 enzyme catalyzes synthesis of inorganic polyphosphate (poly P), a reservoir of high-energy phosphate bonds with multiple roles. Prior analyses in less-fastidious microbes had implicated poly P in stress resistance, motility, and virulence. In our studies, ppk1 inactivation caused the expected near-complete absence of poly P (>250-fold decrease) but had phenotypic effects that differed markedly among unrelated strains: (i) poor initial growth on standard brain heart infusion agar (five of six strains tested); (ii) weakened colonization of mice (4 of 5 strains); (iii) reduced growth on Ham's F-12 agar, a nutritionally limiting medium (8 of 11 strains); (iv) heightened susceptibility to metronidazole (6 of 17 strains); and (v) decreased motility in soft agar (1 of 13 strains). Complementation tests confirmed that the lack of growth of one Δppk1 strain on F-12 agar and the inability to colonize mice of another were each due to ppk1 inactivation. Thus, the importance of ppk1 to H. pylori differed among strains and the phenotypes monitored. We suggest that quantitative interactions, as seen here, are common among genes that affect metabolic pathways and that H. pylori's high genetic diversity makes it well suited for studies of such interactions, their underlying mechanisms, and their evolutionary consequences
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