Recruitment of UvrBC complexes to UV-induced damage in the absence of UvrA increases cell survival

Nucleotide excision repair (NER) is the primary mechanism for removal of ultraviolet light (UV)-induced DNA photoproducts and is mechanistically conserved across all kingdoms of life. Bacterial NER involves damage recognition by UvrA2 and UvrB, followed by UvrC-mediated incision either side of the lesion. Here, using a combination of in vitro and in vivo single-molecule studies we show that a UvrBC complex is capable of lesion identification in the absence of UvrA. Single-molecule analysis of eGFP-labelled UvrB and UvrC in living cells showed that UV damage caused these proteins to switch from cytoplasmic diffusion to stable complexes on DNA. Surprisingly, ectopic expression of UvrC in a uvrA deleted strain increased UV survival. These data provide evidence for a previously unrealized mechanism of survival that can occur through direct lesion recognition by a UvrBC complex

Imperfect Forward Secrecy: How Diffie-Hellman Fails in Practice

International audienceWe investigate the security of Diffie-Hellman key exchange as used in popular Internet protocols and find it to be less secure than widely believed. First, we present Logjam, a novel flaw in TLS that lets a man-in-the-middle downgrade connections to " export-grade " Diffie-Hellman. To carry out this attack, we implement the number field sieve discrete log algorithm. After a week-long precomputation for a specified 512-bit group, we can compute arbitrary discrete logs in that group in about a minute. We find that 82% of vulnerable servers use a single 512-bit group, allowing us to compromise connections to 7% of Alexa Top Million HTTPS sites. In response, major browsers are being changed to reject short groups. We go on to consider Diffie-Hellman with 768-and 1024-bit groups. A small number of fixed or standardized groups are in use by millions of servers. Performing precomputations for just ten of these groups would allow a passive eavesdropper to decrypt traffic to up to 66% of IPsec VPN servers, 26% of SSH servers, 24% of popular HTTPS sites, or 16% of SMTP servers. In the 1024-bit case, we estimate that such computations are plausible given nation-state resources, and a close reading of published NSA leaks shows that the agency's attacks on VPNs are consistent with having achieved such a break. We conclude that moving to stronger key exchange methods should be a priority for the Internet community

Imperfect forward secrecy: How Diffie-Hellman fails in practice

International audienceWe investigate the security of Diffie-Hellman key exchange as used in popular Internet protocols and find it to be less secure than widely believed. First, we present Logjam, a novel flaw in TLS that lets a man-in-the-middle downgrade connections to "export-grade" Diffie-Hellman. To carry out this attack, we implement the number field sieve discrete logarithm algorithm. After a week-long precomputation for a specified 512-bit group, we can compute arbitrary discrete logarithms in that group in about a minute. We find that 82% of vulnerable servers use a single 512-bit group, and that 8.4% of Alexa Top Million HTTPS sites are vulnerable to the attack. a In response, major browsers have changed to reject short groups. We go on to consider Diffie-Hellman with 768-and 1024-bit groups. We estimate that even in the 1024-bit case, the computations are plausible given nation-state resources. A small number of fixed or standardized groups are used by millions of servers; performing precomputation for a single 1024-bit group would allow passive eavesdropping on 18% of popular HTTPS sites, and a second group would allow decryption of traffic to 66% of IPsec VPNs and 26% of SSH servers. A close reading of published NSA leaks shows that the agency's attacks on VPNs are consistent with having achieved such a break. We conclude that moving to stronger key exchange methods should be a priority for the Internet community

DNA-Protein Interactions Studied Directly Using Single Molecule Fluorescence Imaging of Quantum Dot Tagged Proteins Moving on DNA Tightropes

Many protein interactions with DNA require specific sequences; however, how these sequences are located remains uncertain. DNA normally appears bundled in solution but, to study DNA-protein interactions, the DNA needs to be elongated. Using fluidics single DNA strands can be efficiently and rapidly elongated between beads immobilized on a microscope slide surface. Such "DNA tightropes" offer a valuable method to study protein search mechanisms. Real-time fluorescence imaging of these interactions provides quantitative descriptions of search mechanism at the single molecule level. In our lab, we use this method to study the complex process of nucleotide excision DNA repair to determine mechanisms of damage detection, lesion removal, and DNA excision

mNG-tagged fusion proteins and nanobodies to visualize tropomyosins in yeast and mammalian cells

Tropomyosins are structurally conserved α-helical coiled-coil proteins that bind along the length of filamentous actin (F-actin) in fungi and animals. Tropomyosins play essential roles in the stability of actin filaments and in regulating myosin II contractility. Despite the crucial role of tropomyosin in actin cytoskeletal regulation, in vivo investigations of tropomyosin are limited, mainly due to the suboptimal live-cell imaging tools currently available. Here, we report on an mNeonGreen (mNG)-tagged tropomyosin, with native promoter and linker length configuration, that clearly reports tropomyosin dynamics in Schizosaccharomyces pombe (Cdc8), Schizosaccharomyces japonicus (Cdc8) and Saccharomyces cerevisiae (Tpm1 and Tpm2). We also describe a fluorescent probe to visualize mammalian tropomyosin (TPM2 isoform). Finally, we generated a camelid nanobody against S. pombe Cdc8, which mimics the localization of mNG–Cdc8 in vivo. Using these tools, we report the presence of tropomyosin in previously unappreciated patch-like structures in fission and budding yeasts, show flow of tropomyosin (F-actin) cables to the cytokinetic actomyosin ring and identify rearrangements of the actin cytoskeleton during mating. These powerful tools and strategies will aid better analyses of tropomyosin and F-actin cables in vivo