Lengthscales and cooperativity in DNA bubble formation

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Lengthscales and Cooperativity in DNA Bubble Formation

Z. Rapti, A. Smerzi, K. Ø. Rasmussen and A. R. Bishop 1 Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and School of Mathematics, Institute for Advanced Study, Einstein Drive 1, Princeton, New Jersey 08540 2 Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 and 3 Istituto Nazionale di ...

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Bubble nucleation and cooperativity in DNA melting.

Bubbles in DNA are related to fundamental processes such as duplication and transcription. Using a new ensemble technique to trap intermediate states, we present direct measurements of the average length of the denaturation bubble and the statistical weights of the bubble states in the temperature-driven melting of DNA oligomers. For a bubble flanked by double-stranded regions, we find a nuclea...

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Comment on "bubble nucleation and cooperativity in DNA melting".

The conclusions presented by Ares et al. [1] rely on not converged calculations and should be considered with caution. Zeng et al. investigated the temperature evolution of the length of bubbles close to the melting of short DNA sequences and concluded that the average size of ‘‘bubbles in the middle’’ reaches a plateau equal to the number of AT pairs before the two strands separate [2]. Ares e...

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Theory of Bubble Nucleation and Cooperativity in DNA Melting

Saúl Ares, 2 N. K. Voulgarakis, K. Ø. Rasmussen, and A. R. Bishop Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA Grupo Interdisciplinar de Sistemas Complejos (GISC) and Departamento de Matemáticas, Universidad Carlos III de Madrid, Avenida de la Universidad 30, 28911 Leganés, Madrid, Spain Department of Physics, Universit...

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Helix untwisting and bubble formation in circular DNA.

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ژورنال

عنوان ژورنال: Europhysics Letters (EPL)

سال: 2006

ISSN: 0295-5075,1286-4854

DOI: 10.1209/epl/i2005-10543-x