Spontaneous Sharp Bending of Double-Stranded DNA

Abstract

Sharply bent DNA is essential for gene regulation in prokaryotes and is a major feature of eukaryotic nucleosomes and viruses. The explanation normally given for these phenomena is that specific proteins sharply bend DNA by application of large forces, while the DNA follows despite its intrinsic inflexibility. Here we show that DNAs that are 94 bp in length-comparable to sharply looped DNAs in vivo-spontaneously bend into circles. Proteins can enhance the stability of such loops, but the loops occur spontaneously even in naked DNA. Random DNA sequences cyclize 10(2)-10(4) times more easily than predicted from current theories of DNA bending, while DNA sequences that position nucleosomes cyclize up to 10(5) times more easily. These unexpected results establish DNA as an active participant in the formation of looped regulatory complexes in vivo, and they point to a need for new theories of DNA bending.

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

“…Difference free energies for wrapping of different 94 bp DNAs around the core histone H32H42 tetramer are plotted against the difference free energies of cyclization for these same DNAs. 74 The line illustrates the least-squares fit to the data. The slope of the line is one, implying that the entirety of the difference in affinity for wrapping around histones can be explained by the difference in the ability to cyclize.…”

Critical Torque for Kink Formation in Double-Stranded DNA

“…This form of the energy must break down for R sufficiently small, but this is not seen in the DNA stretching experiments where the highcurvature configurations are irrelevant [11]. In contrast, cyclization experiments initially suggested [12] that the high-curvature states of DNA are much more flexible than predicted by (1). There is some controversy about the exact range of validity of (1).…”

“…There is some controversy about the exact range of validity of (1). If we write this range of validity as R > Cl p =ð2 Þ, where C is a numerical factor (of order 1), then the initial suggestion from cyclization experiments [12] was C % 0:7, whereas Du et al argued that C is lower [13]; using DNA minicircles the study [14] found that C % 0:5. Other studies also reported softening of the DNA at small scales [15]; in particular, the Atomic Force Microscopy (AFM) study [11] reported that the measured correlation functions are best described by a linear (rather than quadratic) dependence of the energy on the bending angle.…”

“…The structural transition responsible for this softening is likely to involve formation of a small bubble (single-stranded or ss region) in the DNA, as pointed out by Yan and Marko [16]. Cyclization experiments [12] and AFM imaging experiments [11] rely on thermal fluctuations to realize the highcurvature states; one difficulty is then that the probability of these states is small. In our approach, the high-curvature states are designed into a mechanically constrained molecule [17], and the elastic energy is measured by thermodynamics methods [18,19].…”

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

“…100 bp),5 dsDNA bending has been a central debate in the field 4b. 6 Recently, a single‐molecule study showed extreme dsDNA bendability at less than 100 bp by analyzing real‐time cyclization kinetics 7.…”