Buckling transitions in superhelical DNA: Dependence on the elastic constants and DNA size

G. Ramachandran, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

Buckling transitions in superhelical DNA are sudden changes in shape that accompany a smooth variation in a key parameter, such as superhelical density. Here we explore the dependence of these transitions on the elastic constants for bending and twisting, A and C, important characteristics of DNA's bending and twisting persistence lengths. The large range we explore extends to other elastic materials with self-contact interactions, modeled here by a Debye-Huckel electrostatic potential. Our collective description of DNA shapes and energies over a wide range of ρ = A/C reveals a dramatic dependence of DNA shape and associated configurational transitions on ρ: transitions are sharp for large ρ but masked for small ρ. In particular, at small ρ, a nonplanar circular family emerges, in agreement with Julicher's recent analytical predictions; a continuum of forms (and associated writhing numbers) is also observed. The relevance of these buckling transitions to DNA in solution is examined through studies of size dependence and thermal effects. Buckling transitions smooth considerably as size increases, and this can be explained in part by the lower curvature in larger plasmids. This trend suggests that buckling transitions should not be detectable for isolated (i.e., unbound) DNA plasmids of biological interest, except possibly for very large ρ. Buckling phenomena would nonetheless be relevant for small DNA loops, particularly for higher values of ρ, and might have a role in regulatory mechanisms: a small change in superhelical stress could lead to a large configurational change. Writhe distributions as a function of ρ, generated by Langevin dynamics simulations, reveal the importance of thermal fluctuations. Each distribution range (and multipeaked shape) can be interpreted by our buckling profiles. Significantly, the distributions for moderate to high superhelical densities are most sensitive to ρ, isolating different distribution patterns. If this effect could be captured experimentally for small plasmids by currently available imaging techniques, such results suggest a slightly different experimental procedure for estimating the torsional stiffness of supercoiled DNA than considered to date.

Original languageEnglish (US)
Pages (from-to)5-25
Number of pages21
JournalBiopolymers - Peptide Science Section
Volume41
Issue number1
DOIs
StatePublished - Jan 1997

Fingerprint

Superhelical DNA
Elastic constants
Buckling
DNA
Plasmids
Hot Temperature
Static Electricity
Thermal effects
Electrostatics
Stiffness
Imaging techniques
Computer simulation

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

Buckling transitions in superhelical DNA : Dependence on the elastic constants and DNA size. / Ramachandran, G.; Schlick, Tamar.

In: Biopolymers - Peptide Science Section, Vol. 41, No. 1, 01.1997, p. 5-25.

Research output: Contribution to journalArticle

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