Sequence dependence of DNA bending rigidity

Abstract

For many aspects of DNA-protein interaction, it is vital to know how DNA bending rigidity (or persistence length, a) depends on its sequence. We addressed this problem using the method based on cyclization of short DNA fragments, which allows very accurate determination of a. Our approach was based on assigning specific values of a to each of 10 distinct dinucleotide steps. We prepared DNA fragments, each about 200 bp in length, with various quasiperiodic sequences, measured their cyclization efficiencies (j factors), and fitted the data by the theoretical equation to obtain the values of a for each fragment. From these data, we obtained a set of a for the dinucleotide steps. To test this set, we used it to design DNA sequences that should correspond to very low and very high values of a, prepared the corresponding fragments, and determined their values of a experimentally. The measured and calculated values of a were very close to one another, confirming that we have found the correct solution to this long-standing problem. The same experimental data also allowed us to determine the sequence dependence of DNA helical repeat.DNA elasticity | DNA persistence length T he value of DNA persistence length, a, closely related to the bending rigidity of the double helix, is very important for quantitative analysis of many aspects of DNA functioning. Many different methods were applied over the last decades to determine this value and its dependence on ionic conditions (1). These studies showed that under near physiological ionic conditions the value of a is close to 50 nm (1-3). They also showed that, in a good approximation, the value of a does not depend on DNA sequence, because many studies that use different DNA molecules gave very close values of a. However, the sequence dependence of DNA bending rigidity is vital for many aspects of DNAprotein interaction, and is particularly important for understanding how nucleosomes position along DNA molecules (4, 5). Despite its importance, the problem has formerly remained unsolved, although a few research groups have tried various approaches (6-8). The data that are generally considered most reliable were obtained from statistical analysis of DNA-protein crystal structures (9, 10). The large volume of available structural data allowed this group of researchers to present a very detailed picture of the sequence dependence of DNA conformational properties. This analysis, however, is based on the assumption that variations of the DNA bend angles in the crystals correspond to the amplitudes of thermal fluctuations of these angles in solution. It is hard to justify this assumption.The major obstacle in determining the sequence dependence of a is the necessity of highly accurate measurements of a for different sequences. The majority of methods applied for the measurements of a do not provide the necessary level of accuracy. The only known method that allows one to measure a with the required accuracy is based on cyclization of short DNA fragments by DNA ligase (2,3,11,12). It i...

DNA Looping in Prokaryotes: Experimental and Theoretical Approaches

“…This distance is the minimum observed in naturally occurring DNA loops, although smaller loops have been shown to function in artificial lac constructs (89). Ninety base pairs is distinctly shorter than the persistence length for DNA, which is about 150 bp for naked DNA (90), as usually measured in vitro by cyclization assays (91,92). To make smaller loops, the curvature energy of the DNA becomes too great and the formation of the loop is not favorable.…”

Stiffer double-stranded DNA in two-dimensional confinement due to bending anisotropy

“…Other bulk experiments, such as DNA-cyclization [13,18] and gel electro-phoretic mobility [10,22], also result in a value in this range (Table I).…”

“…The most convenient measure of bending flexibility of a polymer is the "persistence length" (P ), which is defined as the correlation length of the tangent unit vector along the contour length [1]. Many experimental and simulational techniques have been performed to measure this quantity of the DNA molecule [2][3][4][5][6][7][8][9][10][11][12][13][14][15][16], and characterize its dependence on the ionic strength [2,10,11,17], temperature [12], sequence [18] and length scale [19][20][21]. In the single molecule stretching experiment, Baumann et al have shown that the persistence length of a random DNA sequence in moderate salt buffer is around 45−50 nm [11].…”

High-Mobility-Group A-Like CarD Binds to a DNA Site Optimized for Affinity and Position and to RNA Polymerase To Regulate a Light-Inducible Promoter in Myxococcus xanthus

“…The importance of the location of the CarD binding site relative to the P QRS promoter region still remained to be addressed. We checked this by generating variants of the CarD binding site which moved the site by 5 bp or 10 bp upstream of the natural site at P QRS , corresponding to displacements of approximately one-half or one helical turn, respectively (28)(29)(30). Figure 5A depicts the specific site displacement variants that were examined.…”