Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes.

A-tracts are A:T rich DNA sequences that exhibit unique structural and mechanical properties associated with several functions in vivo. The crystallographic structure of A-tracts has been well characterized. However, the mechanical properties of these sequences is controversial and their response to force remains unexplored. Here, we rationalize the mechanical properties of in-phase A-tracts present in the Caenorhabditis elegans genome over a wide range of external forces, using single-molecule experiments and theoretical polymer models. Atomic Force Microscopy imaging shows that A-tracts induce long-range (∼200 nm) bending, which originates from an intrinsically bent structure rather than from larger bending flexibility. These data are well described with a theoretical model based on the worm-like chain model that includes intrinsic bending. Magnetic tweezers experiments show that the mechanical response of A-tracts and arbitrary DNA sequences have a similar dependence with monovalent salt supporting that the observed A-tract bend is intrinsic to the sequence. Optical tweezers experiments reveal a high stretch modulus of the A-tract sequences in the enthalpic regime. Our work rationalizes the complex multiscale flexibility of A-tracts, providing a physical basis for the versatile character of these sequences inside the cell.

Stabilization of RAD-51-DNA filaments via an interaction domain in Caenorhabditis elegans BRCA2.

Mutations in BRCA2 predispose individuals to breast cancer, a consequence of the role of BRCA2 in DNA repair. Human BRCA2 interacts with the recombinase RAD51 via eight BRC repeats. Controversy has existed, however, about whether the BRC interactions are primarily with RAD51 monomers or with the RAD51-DNA helical polymer, and whether there is a single interaction or multiple ones. We show here that the single BRC motif in the Caenorhabditis elegans BRCA2 homolog, CeBRC-2, contains two different RAD-51-binding regions. One of these regions binds only weakly to RAD-51-DNA filaments but strongly to RAD-51 alone and corresponds to the part of human BRC4 crystallized with RAD51. Injection of a peptide corresponding to this region into worms inhibits the normal formation of RAD-51 foci in response to ionizing radiation (IR). Conversely, peptides corresponding to the second region bind strongly to RAD-51-DNA filaments but do not bind to RAD-51 alone. Three-dimensional reconstructions from electron micrographs show that this peptide binds to the RAD-51 N-terminal domain, which has been shown to have a regulatory function. Injection of this peptide into worms before IR leads to a dramatic increase and persistence of IR-induced RAD-51 foci. This peptide also inhibits the RAD-51 ATPase activity, required for filament depolymerization. These results support a model where an interaction with RAD-51 alone is likely involved in filament nucleation, whereas a second independent interaction is involved in stabilization of RAD-51 filaments by BRCA2. The multiple interactions between BRCA2-like molecules and RAD51 provide insights into why mutations in BRCA2 lead to cancer.

Structural analysis of hyperperiodic DNA from Caenorhabditis elegans.

Several bioinformatics studies have identified an unexpected but remarkably prevalent approximately 10 bp periodicity of AA/TT dinucleotides (hyperperiodicity) in certain regions of the Caenorhabditis elegans genome. Although the relevant C.elegans DNA segments share certain sequence characteristics with bent DNAs from other sources (e.g. trypanosome mitochondria), the nematode sequences exhibit a much more extensive and defined hyperperiodicity. Given the presence of hyperperiodic structures in a number of critical C.elegans genes, the physical characteristics of hyperperiodic DNA are of considerable interest. In this work, we demonstrate that several hyperperiodic DNA segments from C.elegans exhibit structural anomalies using high-resolution atomic force microscopy (AFM) and gel electrophoresis. Our quantitative analysis of AFM images reveals that hyperperiodic DNA adopts a significantly smaller mean square end-to-end distance, hence a more compact coil structure, compared with non-periodic DNA of similar length. While molecules remain capable of adopting both bent and straight (rod-like) configurations, indicating that their flexibility is still retained, examination of the local curvatures along the DNA contour length reveals that the decreased mean square end-to-end distance can be attributed to the presence of long-scale intrinsic bending in hyperperiodic DNA. Such bending is not detected in non-periodic DNA. Similar studies of shorter, nucleosome-length DNAs that survived micrococcal nuclease digestion show that sequence hyperperiodicity in short segments can likewise induce strong intrinsic bending. It appears, therefore, that regions of the C.elegans genome display a significant correlation between DNA sequence and unusual mechanical properties.