Search Results - "Vologodskii, Alexander V"

The Flexibility of DNA Double Crossover Molecules by Sa-Ardyen, Phiset, Vologodskii, Alexander V., Seeman, Nadrian C.

“…Double crossover molecules are DNA structures containing two Holliday junctions connected by two double helical arms. There are several types of double…”
Get full text

The kinetics of oligonucleotide replacements by Reynaldo, Luis P, Vologodskii, Alexander V, Neri, Bruce P, Lyamichev, Victor I

“…The formation of a duplex between two nucleic acid strands is restricted if one of the strands forms an intra- or intermolecular secondary structure. The…”
Get full text

Simplification of DNA Topology Below Equilibrium Values by Type II Topoisomerases by Rybenkov, Valentin V., Ullsperger, Christian, Vologodskii, Alexander V., Cozzarelli, Nicholas R.

“…Type II DNA topoisomerases catalyze the interconversion of DNA topoisomers by transporting one DNA segment through another. The steady-state fraction of…”
Get full text

Mechanism of Topology Simplification by Type II DNA Topoisomerases by Vologodskii, Alexander V., Zhang, Wentao, Rybenkov, Valentin V., Podtelezhnikov, Alexei A., Subramanian, Deepa, Griffith, Jack D., Cozzarelli, Nicholas R.

“…Type II DNA topoisomerases actively reduce the fractions of knotted and catenated circular DNA below thermodynamic equilibrium values. To explain this…”
Get full text

Topological Behavior of Plasmid DNA by Higgins, N Patrick, Vologodskii, Alexander V

“…The discovery of the B-form structure of DNA by Watson and Crick led to an explosion of research on nucleic acids in the fields of biochemistry, biophysics,…”
Get more information

Dynamics of DNA Loop Capture by the SfiI Restriction Endonuclease on Supercoiled and Relaxed DNA by Embleton, Michelle L., Vologodskii, Alexander V., Halford, Stephen E.

“…The SfiI endonuclease is a prototype for DNA looping. It binds two copies of its recognition sequence and, if Mg 2+ is present, cuts both concertedly. Looping…”
Get full text

Equilibrium Distributions of Topological States in Circular DNA: Interplay of Supercoiling and Knotting by Podtelezhnikov, Alexei A., Cozzarelli, Nicholas R., Vologodskii, Alexander V.

“…Two variables define the topological state of closed double-stranded DNA: the knot type, K, and Δ LK, the linking number difference from relaxed DNA. The…”
Get full text

Experimental and Theoretical Analysis of the Invasive Signal Amplification Reaction by Lyamichev, Victor I, Kaiser, Michael W, Lyamicheva, Natasha E, Vologodskii, Alexander V, Hall, Jeff G, Ma, Wu-Po, Allawi, Hatim T, Neri, Bruce P

“…The invasive signal amplification reaction is a sensitive method for single nucleotide polymorphism detection and quantitative determination of viral load and…”
Get full text

Positive Torsional Strain Causes the Formation of a Four-way Junction at Replication Forks by Postow, Lisa, Ullsperger, Chris, Keller, Rebecca W., Bustamante, Carlos, Vologodskii, Alexander V., Cozzarelli, Nicholas R.

“…The advance of a DNA replication fork requires an unwinding of the parental double helix. This in turn creates a positive superhelical stress, a (+)-ΔLk, that…”
Get full text

A Combined Wormlike-Chain and Bead Model for Dynamic Simulations of Long Linear DNA by Jian, Hongmei, Vologodskii, Alexander V., Schlick, Tamar

“…A carefully parameterized and tested simulation procedure for studying the dynamic properties of long linear DNA, based on a representation that combines…”
Get full text

Probability of DNA Knotting and the Effective Diameter of the DNA Double Helix by Rybenkov, Valentin V., Cozzarelli, Nicholas R., Vologodskii, Alexander V.

“…During the random cyclization of long polymer chains, knots of different types are formed. We investigated experimentally the distribution of knot types…”
Get full text

Sedimentation and electrophoretic migration of DNA knots and catenanes by Vologodskii, Alexander V., Crisona, Nancy J., Laurie, Ben, Pieranski, Piotr, Katritch, Vsevolod, Dubochet, Jacques, Stasiak, Andrzej

“…Various site-specific recombination enzymes produce different types of knots or catenanes while acting on circular DNA in vitro and in vivo. By analysing the…”
Get full text

Dynamics of Small Loops in DNA Molecules by Podtelezhnikov, Alexei A, Vologodskii, Alexander V

“…The kinetics and thermodynamics of loop formation by short segments of double-stranded DNA was studied by computer simulation. The DNA molecule was modeled as…”
Get full text

Conformational and thermodynamic properties of supercoiled DNA by Vologodskii, A V, Levene, S D, Klenin, K V, Frank-Kamenetskii, M, Cozzarelli, N R

“…We used Monte Carlo simulations to investigate the conformational and thermodynamic properties of DNA molecules with physiological levels of supercoiling…”
Get more information

The effect of ionic conditions on the conformations of supercoiled DNA. II. equilibrium catenation by Rybenkov, Valentin V, Vologodskii, Alexander V, Cozzarelli, Nicholas R

“…We studied the equilibrium formation of DNA catenanes to assess the conformational properties of supercoiled DNA as a function of ionic conditions and…”
Get full text

Torsional control of double-stranded DNA branch migration by Yang, Xiaoping, Vologodskii, Alexander V., Liu, Bing, Kemper, Börries, Seeman, Nadrian C.

“…DNA branched junctions are analogues of Holliday junction recombination intermediates. Partially mobile junctions contain a limited amount of homology flanking…”
Get full text

Monte Carlo analysis of the conformation of DNA catenanes by Vologodskii, A V, Cozzarelli, N R

“…We used a Monte Carlo method to study the conformational properties of catenanes between two nicked DNA rings. We calculated the writhe induced by catenation…”
Get more information

Thermodynamics of the B-Z transition in superhelical DNA by Frank-Kamenetskii, Maxim D, Vologodskii, Alexander V

“…One of the most exciting events in recent years in molecular biology was the discovery of the left-handed Z form of the DNA double helix. Originally found in…”
Get full text

Extension of torsionally stressed DNA by external force by Vologodskii, A.V., Marko, J.F.

“…Metropolis Monte Carlo simulation was used to study the elasticity of torsionally stressed double-helical DNA. Equilibrium distributions of DNA conformations…”
Get full text

The Effect of Ionic Conditions on DNA Helical Repeat, Effective Diameter and Free Energy of Supercoiling by Rybenkov, Valentin V., Vologodskii, Alexander V., Cozzarelli, Nicholas R.

“…We determined the free energy of DNA supercoiling as a function of the concentration of magnesium and sodium chloride in solution by measuring the variance of…”
Get full text