We  report calculations of position- and size-dependent opening probabilities for bubbles in double-stranded DNA . Our results are obtained from transfer-matrix solutions of (i) the Zimm-Bragg model for unconstrained DNA and of (ii) a self-consistent linearization of the Benham model for DNA under a superhelical constraint . The numerical efficiency of our method allows for the analysis of entire genomes and of random sequences of corresponding length (10^6-10^9 bp). At physiological temperatures and superhelical densities, opening is strongly cooperative with average bubble sizes of %DIFDELCMD < {\cal %%% O (100-1000) bp. In general, their statistics and location are dominated by sequence heterogeneity. For genomic DNA , bubbles are frequently located directly upstream of transcription start sites.
We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence . Our results are obtained from transfer-matrix solutions of the Zimm-Bragg model for unconstrained DNA and of a self-consistent linearization of the Benham model for superhelical DNA . The numerical efficiency of our method allows for the analysis of entire genomes and of random sequences of corresponding length (10^6-10^9 base pairs). We show that, at physiological conditions, opening in superhelical DNA is strongly cooperative with average bubble sizes of %DIFDELCMD < {\cal %%% 10^2-10^3 base pairs (bp), and orders of magnitude higher than in unconstrained DNA. In heterogeneous sequences, the average degree of base-pair opening is self-averaging, while bubble localization and statistics are dominated by sequence disorder. Compared to random sequences with identical GC-content, genomic DNA has a significantly increased probability to open large bubbles under superhelical stress. These bubbles are frequently located directly upstream of transcription start sites.
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present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We
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in double-stranded DNA
along the sequence
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(i)
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(ii)
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DNA under a superhelical constraint
superhelical DNA
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bp). At physiological temperatures and superhelical densities, opening
base pairs). We show that, at physiological conditions, opening in superhelical DNA
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(100-1000) bp. In general, their statistics and location
10^2-10^3 base pairs (bp), and orders of magnitude higher than in unconstrained DNA. In heterogeneous sequences, the average degree of base-pair opening is self-averaging, while bubble localization and statistics
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heterogeneity. For genomic DNA ,
disorder. Compared to random sequences with identical GC-content, genomic DNA has a significantly increased probability to open large bubbles under superhelical stress. These