English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

We present a general framework to study the thermodynamic denaturation ofdouble-stranded DNA under superhelical stress. We report calculations ofposition- and size-dependent opening probabilities for bubbles along thesequence. Our results are obtained from transfer-matrix solutions of theZimm-Bragg model for unconstrained DNA and of a self-consistent linearizationof the Benham model for superhelical DNA. The numerical efficiency of ourmethod allows for the analysis of entire genomes and of random sequences ofcorresponding length ($10^6-10^9$ base pairs). We show that, at physiologicalconditions, opening in superhelical DNA is strongly cooperative with averagebubble sizes of $10^2-10^3$ base pairs (bp), and orders of magnitude higherthan in unconstrained DNA. In heterogeneous sequences, the average degree ofbase-pair opening is self-averaging, while bubble localization and statisticsare dominated by sequence disorder. Compared to random sequences with identicalGC-content, genomic DNA has a significantly increased probability to open largebubbles under superhelical stress. These bubbles are frequently locateddirectly upstream of transcription start sites.

Bubble statistics and positioning in superhelically stressed DNA