title: How topological constraints facilitate growth and stability of bubbles in DNA.
abstract: The bubbles in double-stranded DNA, essential for gene transcription and replication, occur in mechanically constrained situations. Through an elastic model incorporating topological constraint, we show that, when a stretched double helix is underwound above a critical value of twist, a bubble can spontaneously form, yielding extension and torque behaviors quantitatively in agreement with magnetic tweezers experiments. We find that, unlike thermal bubble in an unconstrained DNA, the bubbles in these constrained states can grow and stabilize, provided that tension and length of DNA are above critical values.
authors.affiliation: Department of Physics and POSTECH Center for Theoretical Physics, Pohang University of Science and Technology, Pohang, Republic of Korea.
authors.forename: Jae-Hyung
authors.initials: JH
authors.lastname: Jeon
authors.forename: Wokyung
authors.initials: W
authors.lastname: Sung
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D013816:Thermodynamics; D019415:Torque
chemical_list: D004247:DNA