Structural basis of TFIIH activation for nucleotide excision repair.

Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large multisubunit transcription factor IIH (TFIIH). Here we report the cryo-EM structure of an NER intermediate containing TFIIH and the NER factor XPA. Compared to its transcription conformation, the TFIIH structure is rearranged such that its ATPase subunits XPB and XPD bind double- and single-stranded DNA, consistent with their translocase and helicase activities, respectively. XPA releases the inhibitory kinase module of TFIIH, displaces a 'plug' element from the DNA-binding pore in XPD, and together with the NER factor XPG stimulates XPD activity. Our results explain how TFIIH is switched from a transcription to a repair factor, and provide the basis for a mechanistic analysis of the NER pathway

Structural basis of human transcription–DNA repair coupling

Transcription-coupled DNA repair removes bulky DNA lesions from the genome1,2 and protects cells against ultraviolet (UV) irradiation3. Transcription-coupled DNA repair begins when RNA polymerase II (Pol II) stalls at a DNA lesion and recruits the Cockayne syndrome protein CSB, the E3 ubiquitin ligase, CRL4CSA and UV-stimulated scaffold protein A (UVSSA)3. Here we provide five high-resolution structures of Pol II transcription complexes containing human transcription-coupled DNA repair factors and the elongation factors PAF1 complex (PAF) and SPT6. Together with biochemical and published3,4 data, the structures provide a model for transcription–repair coupling. Stalling of Pol II at a DNA lesion triggers replacement of the elongation factor DSIF by CSB, which binds to PAF and moves upstream DNA to SPT6. The resulting elongation complex, ECTCR, uses the CSA-stimulated translocase activity of CSB to pull on upstream DNA and push Pol II forward. If the lesion cannot be bypassed, CRL4CSA spans over the Pol II clamp and ubiquitylates the RPB1 residue K1268, enabling recruitment of TFIIH to UVSSA and DNA repair. Conformational changes in CRL4CSA lead to ubiquitylation of CSB and to release of transcription-coupled DNA repair factors before transcription may continue over repaired DNA

On the Properties of Two Pulses Propagating Simultaneously in Different Dispersion Regimes in a Nonlinear Planar Waveguide

Properties of two pulses propagating simultaneously in different dispersion regimes, anomalous and normal, in a Kerr-type planar waveguide are studied in the framework of the nonlinear Schroedinger equation. Catastrophic self-focusing and spatio-temporal splitting of the pulses is investigated. For the limiting case when the dispersive term of the pulse propagating in the normal dispersion regime can be neglected an indication of a possibility of a stable self-trapped propagation of both pulses is obtained.Comment: 18 pages (including 15 eps figures

X-wave mediated instability of plane waves in Kerr media

Plane waves in Kerr media spontaneously generate paraxial X-waves (i.e. non-dispersive and non-diffractive pulsed beams) that get amplified along propagation. This effect can be considered a form of conical emission (i.e. spatio-temporal modulational instability), and can be used as a key for the interpretation of the out of axis energy emission in the splitting process of focused pulses in normally dispersive materials. A new class of spatio-temporal localized wave patterns is identified. X-waves instability, and nonlinear X-waves, are also expected in periodical Bose condensed gases.Comment: 4 pages, 6 figure

Mg(2)Si(x)Sn(1-x)heterostructures on Si(111) substrate for optoelectronics and thermoelectronics

Thin (50-90 m) non-doped and doped (by Al atoms) Mg2Sn0.6Si0.4 and Mg(2)Sn(0.4)Si(0.6)films with roughness of 1.9-3.7 nm have been grown by multiple deposition and single annealing at 150 degrees C of multilayers formed by repetition deposition of three-layers (Si-Sn-Mg) on Si(111) p-type wafers with 45 cm resistivity. Transmission electron microscopy has shown that the first forming layer is an epitaxial layer of hex-Mg2Sn(300) on Si(111) substrate with thickness not more than 5-7 nm. Epitaxial relationships: hex-Mg2Sn(300)parallel to Si(111), hex-Mg2Sn[001]parallel to Si[-112] and hex-Mg2Sn[030]parallel to Si[110] have been found for the epitaxial layer. But inclusions of cub-Mg2Si were also observed inside hex-Mg2Sn layer. It was found that the remaining part of the film thickness is in amorphous state and has a layered distribution of major elements: Mg, Sn and Mg without exact chemical composition. It was established by optical spectroscopy data that both type films are semiconductor with undispersed region lower 0.18 eV with n(o) = 3.59 +/- 0.01, but only two direct interband transitions with energies 0.75-0.76 eV and 1.2 eV have been determined. The last interband transition has been confirmed by photoreflectance data at room temperature. Fourier transmittance spectroscopy and Raman spectroscopy data have established the formation of stannide, silicide and ternary compositions

Resonant raman scattering in complexes of nc-Si/SiO₂ quantum dots and oligonucleotides

We report on the functionalization of nanocrystalline nc-Si/SiO2 semiconductor quantum dots (QDs) by short d(20G, 20T) oligonucleotides. The obtained complexes have been studied by Raman spectroscopy techniques with high spectral and spatial resolution. A new phenomenon of multiband resonant light scattering on single oligonucleotide molecules has been discovered, and peculiarities of this effect related to the nonradiative transfer of photoexcitation from nc-Si/SiO2 quantum dots to d(20G, 20T) oligonucleotide molecules have been revealed