Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity

Abstract

The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA persistence length. Similarly, eukaryotic DNA is packed in DNA-protein complexes (nucleosomes) in which DNA is tightly bent around protein spools. DNA is also tightly bent by many proteins that regulate transcription, resulting in a variation in gene expression that is amenable to quantitative analysis. In these cases, DNA loops are formed with lengths that are comparable to or smaller than the DNA persistence length. The aim of this review is to describe the physical forces associated with tightly bent DNA in all of these settings and to explore the biological consequences of such bending, as increasingly accessible by single-molecule techniques.

Critical Torque for Kink Formation in Double-Stranded DNA

“…For the nicked molecule, the elastic energy of the kinked state is E 1 ðnÞ given in (7). For the circular molecule, the elastic energy of the kinked state contains the additional cost of forming a 3 bp bubble at the kink [16], i.e., E circ 1 ðnÞ ¼ 0 ðn 0 0 À nÞ 1=2 þ 3ð À TÞ ðfor n n 0 0 Þ: (9) In both cases, the elastic energy of the smoothly bent state is E 2 given in (8). For the linear molecule, E 2 ¼ E 1 ¼ 0.…”

“…For example, in the cases of viral genome packaging, eukaryotic nucleosome compaction, and many transcription regulation steps, the DNA is sharply bent over a range of tens to hundreds of base pairs. DNA bending therefore has a strong influence on the energy scales of many biological processes [8,9].…”

Nanofluidic structures for single biomolecule fluorescent detection

“…For DNA, structural properties govern actions such as packaging into chromatin and bacteriophage heads. [30][31][32] To elucidate mechanical properties, optically trapped or magnetically responsive beads can be conjugated to a single DNA strand, enabling controlled stretching and twisting of the molecule. [33][34][35][36] By fixing one end of a fluorescently labeled DNA strand in an elongational flow, it is also possible to observe inhomogenous hydrodynamic stretching, which is a theoretically interesting phenomenon.…”

Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks

“…The ability of dsDNA to bend with high curvature is important for many biological processes. For instance, approximately 147 base pairs (bp) of genomic DNA wraps 1.7 times around a nucleosome of 8.5 nm in diameter;1d, 2 viral DNA that is 16 μm long is packed into a tiny volume in viruses (ca. 5×10 4  nm 3 );1d and DNA looping with high curvature (a bending curvature of ca.…”