To this end, we introduce local surface-induced static bends leading to an averaged heteropolymer WLC model ( 3–5,13). A modification of the homopolymer WLC model was required to provide an adequate description of the DNA configuration in plane. By extending the number of statistical quantities, we prove a two-dimensional equilibrium state of immobilized molecules. We will show that DNA immobilized onto a surface can exhibit a notable variation in persistence length, yet showing its chain statistics as expected over long separation distances (in EM from 10 to 120 nm and in AFM from 10 to 300 nm) along the contour. In this article, we will argue that successful analysis of two-dimensional data sets requires both dedicated image processing and a model describing the statistical behavior of DNA molecules confined to a plane. Even the breakdown of the conventional elastic rod model is suggested for short DNA fragments ( 27). In this line, recent studies show that DNA flexibility may vary in a length-dependent manner, exhibiting an increased flexibility (via spontaneous large-angle bends) over distances <5 nm ( 16). Both EM and AFM provide evidence(s) for a two-dimensional state ( 10,11,19) and a three-dimensional one ( 11,20,26). Molecules are captured (i.e., trapped) by the imaging surface without their equilibration, leading to the conformation reflecting a projection of three-dimensional conformation in solution onto a two-dimensional plane (called the three-dimensional state).Ī mixture of both two-dimensional and three-dimensional states can be present for each molecule or their ensemble, depending on the deposition procedure and DNA length. In addition, there is disagreement about the state of the deposited molecules: However, smaller values (36 nm ( 23)) and larger values (∼80–140 nm ( 9,11,24,25)) were reported as well. In many instances, the persistence length calculated close to 50 nm ( 10–14,16,21,22), a generally accepted value determined by other techniques exploiting mainly bulk measurements ( 15,17,18). Numerous examples demonstrate the power of EM and AFM in determination of DNA persistence length and the conformational state of DNA confined to an imaging plane ( 9–20). Several extensions were made toward a more realistic model, such as the inclusion of static bends or kinks distributed randomly (in position and orientation) along the polymer chain ( 4–9). The main statistical quantities describing behavior of homopolymers by either model have similar analytical expressions, allowing the use of either description for the analysis purposes. Similar to the WLC model, the discrete model describes DNA as a homopolymer. Another model is based on a discrete description of a DNA polymer chain attributing its conformational flexibility to the thermal fluctuations in the angles between adjacent basepairs ( 3). The wormlike chain (WLC) model treats DNA as a continuous, inextensible (elastic) rod and considers the deformations occurring at each infinitesimal point following Hooke's law ( 1,2). Potential distortions of the DNA double helix reflected in notable alterations in DNA conformation(s), which may lead to a change in the apparent persistence length.Ī quantitative description of the apparent DNA conformation confined to a plane requires invoking the existing models for DNA conformation in solution (three-dimensional) and in plane as well.
Implications of this finding are discussed. We therefore argue that adhesion of DNA to a charged surface may lead to additional static bending (kinking) of ∼5 degrees per dinucleotide step without impairing the dynamic behavior of the DNA backbone. Analysis of local bending on short length scales (down to 6 nm in the EM study) shows that DNA flexibility behaves as predicted by the wormlike chain model. However, in contrast to AFM, the EM mounting leads to a noticeable decrease in DNA persistence length together with decreased kurtosis. Automated procedures for the extraction of DNA contours (∼10–120 nm for EM data and ∼10–300 nm for AFM data) combined with new statistical chain descriptors indicate a uniquely two-dimensional equilibration of the molecules on the substrate surface regardless of the procedure of molecule mounting. We use electron (EM) and atomic force microscopy (AFM) to characterize the flexibility of double-stranded DNA (∼150–950 nm long) close to a charged surface. DNA is a very important cell structural element, which determines the level of expression of genes by virtue of its interaction with regulatory proteins.
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