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Biomedical subjects

Oleg Krichevsky

Publications and source records attributed to Oleg Krichevsky.

5 recordsLinked to original sources

Sequence sensitivity of breathing dynamics in heteropolymer DNA.

We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a biological sequence of the T7 bacteriophage. Quantitative agreement with data from fluorescence correlation spectroscopy is demonstrated.

Bacteriophage T7↗

Fluorescence correlation spectroscopy analysis of segmental dynamics in actin filaments.

We adapt fluorescence correlation spectroscopy (FCS) formalism to the studies of the dynamics of semiflexible polymers and derive expressions relating FCS correlation function to the longitudinal and transverse mean-square displacements of polymer segments. The obtained relations do not depend on any specific model of polymer dynamics. We use the derived expressions to measure the dynamics of actin filaments in two experimental situations: filaments labeled at distinct positions and homogeneously labeled filaments. Both approaches give consistent results and allow to measure the temporal dependence of the segmental mean-square displacement over almost five decades in time, from approximately 40 micros to approximately 2 s. These noninvasive measurements allow for a detailed quantitative comparison of the experimental data to the current theories of semiflexible polymer dynamics. Good quantitative agreement is found between the experimental results and theories explicitly accounting for the hydrodynamic interactions between polymer segments.

Actin Cytoskeleton↗

Nuclear import of ho endonuclease utilizes two nuclear localization signals and four importins of the ribosomal import system.

Activity of Ho, the yeast mating switch endonuclease, is restricted to a narrow time window of the cell cycle. Ho is unstable and despite being a nuclear protein is exported to the cytoplasm for proteasomal degradation. We report here the molecular basis for the highly efficient nuclear import of Ho and the relation between its short half-life and passage through the nucleus. The Ho nuclear import machinery is functionally redundant, being based on two bipartite nuclear localization signals, recognized by four importins of the ribosomal import system. Ho degradation is regulated by the DNA damage response and Ho retained in the cytoplasm is stabilized, implying that Ho acquires its crucial degradation signals in the nucleus. Ho arose by domestication of a fungal VMA1 intein. A comparison of the primary sequences of Ho and fungal VMA1 inteins shows that the Ho nuclear localization signals are highly conserved in all Ho proteins, but are absent from VMA1 inteins. Thus adoption of a highly efficient import strategy occurred very early in the evolution of Ho. This may have been a crucial factor in establishment of homothallism in yeast, and a key event in the rise of the Saccharomyces sensu stricto.

Active Transport, Cell Nucleus↗

Monomer dynamics in double- and single-stranded DNA polymers.

We present the first measurements of the kinetics of random motion of individual monomers within large polymer coils. We use double- and single-stranded DNA (dsDNA and ssDNA) as models of semiflexible and flexible polymers, respectively. Fluorescence fluctuations of DNA fragments labeled specifically at a single position reveal the time dependence of the DNA monomer's mean-square displacement . The monomer motions within dsDNA and ssDNA coils are characterized by two qualitatively different kinetic regimes: close to proportional to t(2/3) for ssDNA and proportional to sqrt[t] for dsDNA. While the kinetic behavior of ssDNA is consistent with the generally accepted Zimm theory of polymer dynamics, the kinetic behavior of dsDNA monomers is in good agreement with the Rouse model.

DNA↗

Bubble dynamics in double-stranded DNA.

We report the first measurement of the dynamics of bubble formation in double-stranded DNA. Fluctuations of fluorescence of a synthetic DNA construct, internally tagged with a fluorophore and a quencher, are monitored by fluorescence correlation spectroscopy. The relaxation dynamics follow a multistate relaxation kinetics, with a characteristic time scale of 50 microseconds. A simple model of bubble dynamics based on constant zipping-unzipping rates is proposed to account for our experimental data. The role of different secondary structures stabilizing the open bubble is tested.

DNA↗