Article thumbnail
Location of Repository

Susceptibility to Superhelically Driven DNA Duplex Destabilization: A Highly Conserved Property of Yeast Replication Origins

By Prashanth Ak and Craig J Benham


Strand separation is obligatory for several DNA functions, including replication. However, local DNA properties such as A+T content or thermodynamic stability alone do not determine the susceptibility to this transition in vivo. Rather, superhelical stresses provide long-range coupling among the transition behaviors of all base pairs within a topologically constrained domain. We have developed methods to analyze superhelically induced duplex destabilization (SIDD) in genomic DNA that take into account both this long-range stress-induced coupling and sequence-dependent local thermodynamic stability. Here we apply this approach to examine the SIDD properties of 39 experimentally well-characterized autonomously replicating DNA sequences (ARS elements), which function as replication origins in the yeast Saccharomyces cerevisiae. We find that these ARS elements have a strikingly increased susceptibility to SIDD relative to their surrounding sequences. On average, these ARS elements require 4.78 kcal/mol less free energy to separate than do their immediately surrounding sequences, making them more than 2,000 times easier to open. Statistical analysis shows that the probability of this strong an association between SIDD sites and ARS elements arising by chance is approximately 4 × 10(−10). This local enhancement of the propensity to separate to single strands under superhelical stress has obvious implications for origin function. SIDD properties also could be used, in conjunction with other known origin attributes, to identify putative replication origins in yeast, and possibly in other metazoan genomes

Topics: Research Article
Publisher: Public Library of Science
Year: 2005
DOI identifier: 10.1371/journal.pcbi.0010007
OAI identifier:
Provided by: PubMed Central

Suggested articles


  1. (1993). A DNA unwinding element and an ARS consensus comprise a replication origin within a yeast chromosome.
  2. (1992). A yeast chromosomal origin of DNA replication defined by multiple functional elements.
  3. (1998). Activation of gene expression by a novel DNA structural transmission mechanism that requires supercoiling-induced DNA duplex destabilization in an upstream activating sequence.
  4. (1987). Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis.
  5. (1996). DNA replication in yeast. In:
  6. (2002). DNA replication joins the revolution: Wholegenome views of DNA replication in budding yeast.
  7. (1982). DNA sequence required for efficient transcription termination in yeast.
  8. (1996). Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions.
  9. (1993). Ease of DNA unwinding is a conserved property of yeast replication origins.
  10. (1992). Energetics of the strand separation transition in superhelical DNA.
  11. (1999). Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA.
  12. (2001). Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: Highresolution mapping of replication origins.
  13. (1967). Handbook of methods of applied statistics,
  14. (1999). Inhibition of supercoilingdependent transcriptional activation by a distant B-DNA to Z-DNA transition.
  15. (2004). Prediction of Saccharomyces cerevisiae replication origins.
  16. (1975). Probability and statistics.
  17. (2001). Replication dynamics of the yeast genome.
  18. (2004). Role for a region of helically unstable DNA within the Epstein-Barr virus latent cycle origin of DNA replication in origin function.
  19. (2004). Saccharomyces Genome Database [database].
  20. (1993). Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci.
  21. (1988). Stable DNA unwinding, not ‘‘breathing,’’ accounts for single-strand-specific nuclease hypersensitivity of specific AþT-rich sequences.
  22. (2004). The analysis of stress-induced duplex destabilization in long genomic DNA sequences.
  23. (2002). The B2 element of the Saccharomyces cerevisiae ARS1 origin of replication requires specific sequences to facilitate pre-RC formation.
  24. (1989). The DNA unwinding element: A novel, cisacting component that facilitates opening of the Escherichia coli replication origin.
  25. (2004). The dynamic response of upstream DNA to transcription-generated torsional stress.
  26. (2003). Unpaired structures in SCA10 (ATTCT)n.(AGAAT)n repeats.
  27. (2003). WEB-THERMODYN [Web-based computer program].
  28. (2003). WEB-THERMODYN: Sequence analysis software for profiling DNA helical stability.

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.