Bubbles and denaturation in DNA
نویسندگان
چکیده
منابع مشابه
Bubbles and denaturation in DNA.
The local opening of DNA is an intriguing phenomenon from a statistical-physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code cannot take place without the unwinding of the DNA double helix. Although these biological processes are driven by proteins, there might well be a relation between these biological op...
متن کاملDNA denaturation bubbles at criticality.
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of nonlinear base-stacking interactions. Small bubbles extending over fewer than ten base pairs are associated with much larger free energies of formation per site than...
متن کاملQuantifying supercoiling-induced denaturation bubbles in DNA
In both eukaryotic and prokaryotic DNA sequences of 30–100 base-pairs rich in AT base-pairs have been identified at which the double helix preferentially unwinds. Such DNA unwinding elements are commonly associated with origins for DNA replication and transcription, and with chromosomal matrix attachment regions. Here we present a quantitative study of local DNA unwinding based on extensive sin...
متن کاملDenaturation Bubbles in Fluctuating Dna Chains
– A statistical model of DNA, coupling base pair states (unbroken or broken) and thermal chain fluctuations, is formulated and then investigated using an exact solution obtained by transfer kernel techniques. The dependence on temperature and DNA length of the fraction of denaturation bubbles and their correlation length are deduced. Novel results include (i) the melting temperature emerges nat...
متن کاملPlectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA
We predict a novel conformational regime for DNA, where denaturation bubbles form at the tips of plectonemes, and study its properties using coarse-grained simulations. For negative supercoiling, this regime lies between bubble-dominated and plectoneme-dominated phases, and explains the broad transition between the two observed in experiment. Tip bubbles cause localisation of plectonemes within...
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ژورنال
عنوان ژورنال: The European Physical Journal E
سال: 2006
ISSN: 1292-8941,1292-895X
DOI: 10.1140/epje/i2006-10032-2