Biophysical and electrochemical studies of protein-nucleic acid interactions

This review is devoted to biophysical and electrochemical methods used for studying protein-nucleic acid (NA) interactions. The importance of NA structure and protein-NA recognition for essential cellular processes, such as replication or transcription, is discussed to provide background for description of a range of biophysical chemistry methods that are applied to study a wide scope of protein-DNA and protein-RNA complexes. These techniques employ different detection principles with specific advantages and limitations and are often combined as mutually complementary approaches to provide a complete description of the interactions. Electrochemical methods have proven to be of great utility in such studies because they provide sensitive measurements and can be combined with other approaches that facilitate the protein-NA interactions. Recent applications of electrochemical methods in studies of protein-NA interactions are discussed in detail

Oxidative DNA cleavage with clip‐phenanthroline triplex‐forming oligonucleotide hybrids

A systematic study of several new types of hybrids of Cu‐chelated clamped phenanthroline artificial metallonuclease (AMN) with triplex‐forming oligonucleotides (TFO) for sequence‐specific cleavage of double‐stranded DNA (dsDNA) is reported. The synthesis of these AMN–TFO hybrids is based on application of the alkyne–azide cycloaddition click reaction as the key step. The AMN was attached through different linkers at either the 5′‐ or 3′‐ends or in the middle of the TFO stretch. The diverse hybrids efficiently formed triplexes with the target purine‐rich sequence and their copper complexes were studied for their ability to cleave dsDNA in the presence of ascorbate as a reductant. In all cases, the influence of the nature and length of the AMN–TFO, time, conditions and amounts of ascorbate were studied, and optimum conjugates and a procedure that gave reasonably efficient (up to 34 %) cleavage of the target sequence, while rendering an off‐target dsDNA intact, were found. The footprint of cleavage on PAGE was identified only in one case, with low conversion; this means that cleavage does not proceed with single nucleotide precision. On the other hand, these AMN–TFO hybrids are useful for the selective degradation of target dsDNA sequences. Future improvements to this design may provide higher resolution and selectivity

A modular approach to aryl-C-ribonucleosides via the allylic substitution and ring-closing metathesis sequence: a stereocontrolled synthesis of all four α-/β- andd-/l-C-nucleoside stereoisomers

Iridium(I)-catalyzed allylation of the enantiopure monoprotected copper(I) alkoxide, generated from (S)-5a, with the enantiopure allylic carbonates (R)-9a,b has been developed as the key step in a new approach to C-nucleoside analogues. The anomeric center was thus constructed via a stereocontrolled formation of the C-O rather than C-C bond with retention of configuration. The resulting bisallyl ethers 15a,b (>= 90% de and >99% cc) were converted into C-ribosides 29a,b via the Ru-catalyzed ring-closing metathesis, followed by a diastereoselective dihydroxylation catalyzed by OsO(4) or RuO(4) and deprotection. Variation of the absolute configuration of the starting segments 5a and 9a,b allowed a stereocontrolled synthesis of all four alpha/beta-D/L-combinations

Einstein beams and the diffractive aspect of gravitationally-lensed light

The study of light lensed by cosmic matter has yielded much information about astrophysical questions. Observations are explained using geometrical optics following a ray-based description of light. After deflection the lensed light interferes, but observing this diffractive aspect of gravitational lensing has not been possible due to coherency challenges caused by the finite size of the sources or lack of near-perfect alignment. In this article, we report on the observation of these wave effects of gravitational lensing by recreating the lensing conditions in the laboratory via electro-optic deflection of coherent laser light. The lensed light produces a beam containing regularities, caustics, and chromatic modulations of intensity that depend on the symmetry and structure of the lensing object. We were also able to observe previous and new geometric-optical lensing situations that can be compared to astrophysical observations. This platform could be a useful tool for testing numerical/analytical simulations, and for performing analog simulations of lensing situations when they are difficult to obtain otherwise. We found that laboratory lensed beams constitute a new class of beams, with long-range, low expansion, and self-healing properties, opening new possibilities for non-astrophysical applications