A Simple,High‐Yield Synthesis of DNA Duplexes Containing a Covalent,Thermally Cleavable Interstrand Cross‐Link at a Defined Location

Interstrand DNA–DNA cross‐links are highly toxic to cells because these lesions block the extraction of information from the genetic material. The pathways by which cells repair cross‐links are important, but not well understood. The preparation of chemically well‐defined cross‐linked DNA substrates represents a significant challenge in the study of cross‐link repair. Here a simple method is reported that employs “post‐synthetic” modifications of commercially available 2′‐deoxyoligonucleotides to install a single cross‐link in high yield at a specified location within a DNA duplex. The cross‐linking process exploits the formation of a hydrazone between a non‐natural N⁴‐amino‐2′‐deoxycytidine nucleobase and the aldehyde residue of an abasic site in duplex DNA. The resulting cross‐link is stable under physiological conditions, but can be readily dissociated and re‐formed through heating–cooling cycles.     

A Simple,High‐Yield Synthesis of DNA Duplexes Containing a Covalent,Thermally Cleavable Interstrand Cross‐Link at a Defined Location

Interstrand DNA–DNA cross‐links are highly toxic to cells because these lesions block the extraction of information from the genetic material. The pathways by which cells repair cross‐links are important, but not well understood. The preparation of chemically well‐defined cross‐linked DNA substrates represents a significant challenge in the study of cross‐link repair. Here a simple method is reported that employs “post‐synthetic” modifications of commercially available 2′‐deoxyoligonucleotides to install a single cross‐link in high yield at a specified location within a DNA duplex. The cross‐linking process exploits the formation of a hydrazone between a non‐natural N⁴‐amino‐2′‐deoxycytidine nucleobase and the aldehyde residue of an abasic site in duplex DNA. The resulting cross‐link is stable under physiological conditions, but can be readily dissociated and re‐formed through heating–cooling cycles.     

Light-activated reassembly of split green fluorescent protein

Truncated green fluorescent protein (GFP) with the 11th β-strand removed is potentially interesting for bioconjugation, imaging, and the preparation of semisynthetic proteins with novel spectroscopic or functional properties. Surprisingly, the truncated GFP generated by removing the 11th strand, once refolded, does not reassemble with a synthetic peptide corresponding to strand 11 but does reassemble following light activation. The mechanism of this process has been studied in detail by absorption, fluorescence, and Raman spectroscopy. The chromophore in this refolded truncated GFP is found to be in the trans configuration. Upon exposure to light a photostationary state is formed between the trans and cis conformations of the chromophore, and only truncated GFP with the cis configuration of the chromophore binds the peptide. A kinetic model describing the light-activated reassembly of this split GFP is discussed. This unique light-driven reassembly is potentially useful for controlling protein-protein interactions.     

Faster proton transfer dynamics of water on SnO2 compared to TiO2

Proton jump processes in the hydration layer on the iso-structural TiO(2) rutile (110) and SnO(2) cassiterite (110) surfaces were studied with density functional theory molecular dynamics. We find that the proton jump rate is more than three times faster on cassiterite compared with rutile. A local analysis based on the correlation between the stretching band of the O-H vibrations and the strength of H-bonds indicates that the faster proton jump activity on cassiterite is produced by a stronger H-bond formation between the surface and the hydration layer above the surface. The origin of the increased H-bond strength on cassiterite is a combined effect of stronger covalent bonding and stronger electrostatic interactions due to differences of its electronic structure. The bridging oxygens form the strongest H-bonds between the surface and the hydration layer. This higher proton jump rate is likely to affect reactivity and catalytic activity on the surface. A better understanding of its origins will enable methods to control these rates.     

Light harvesting in microscale metal-organic frameworks by energy migration and interfacial electron transfer quenching

Microscale metal-organic frameworks (MOFs) were synthesized from photoactive Ru(II)-bpy building blocks with strong visible light absorption and long-lived triplet metal-to-ligand charge transfer ((3)MLCT) excited states. These MOFs underwent efficient luminescence quenching in the presence of either oxidative or reductive quenchers. Up to 98% emission quenching was achieved with either an oxidative quencher (1,4-benzoquinone) or a reductive quencher (N,N,N',N'-tetramethylbenzidine), as a result of rapid energy migration over several hundred nanometers followed by efficient electron transfer quenching at the MOF/solution interface. The photoactive MOFs act as an excellent light-harvesting system by combining intraframework energy migration and interfacial electron transfer quenching.     

Preconditioning trace coupled 3d‐1d systems using fractional Laplacian

Multiscale or multiphysics problems often involve coupling of partial differential equations posed on domains of different dimensionality. In this work, we consider a simplified model problem of a 3d‐1d coupling and the main objective is to construct algorithms that may utilize standard multilevel algorithms for the 3d domain, which has the dominating computational complexity. Preconditioning for a system of two elliptic problems posed, respectively, in a three‐dimensional domain and an embedded one dimensional curve and coupled by the trace constraint is discussed. Investigating numerically the properties of the well‐defined discrete trace operator, it is found that negative fractional Sobolev norms are suitable preconditioners for the Schur complement of the system. The norms are employed to construct a robust block diagonal preconditioner for the coupled problem.     

An unusual structure of the hydrated sodium chloride complex of cryptand [2.2.2]

The solid state structure of the Na[2.2.2]C1 · 3H₂O complex has the sodium ion displaced towards one of the cryptand nitrogens and the chloride and water molecules associated by hydrogen bonds to form a pseudo cube with two chloride ions at opposite corners of the cube and water oxygens at the other six corners.     

Energy Dispersive X-Ray Spectrometry by Microcalorimetry for the SEM

 Analytical X-ray spectrometry for electron beam instruments has advanced significantly with the development of the microcalorimeter energy dispersive X-ray spectrometer (μcal EDS). The μcal EDS operates by measuring the temperature rise when a single photon is absorbed in a metal target. A cryoelectronic circuit with electrothermal feedback and a superconducting transition edge sensor serves as the thermometer. Spectral resolution approaching 4.5 eV for high energy photons (6000 eV) and 2 eV for low energy photons below 2000 eV has been demonstrated in energy dispersive operation across a photon energy range from 250 eV to 8 keV. Spectra of a variety of materials demonstrate the power of the μcal EDS to solve practical problems while operating on a scanning electron microscope platform.     

Principal minors, Part I: A method for computing all the principal minors of a matrix

An order O(2ⁿ) algorithm for computing all the principal minors of an arbitrary n × n complex matrix is motivated and presented, offering an improvement by a factor of n³ over direct computation. The algorithm uses recursive Schur complementation and submatrix extraction, storing the answer in a binary order. An implementation of the algorithm in MATLAB® is also given and practical considerations are discussed and treated accordingly.