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Irradiation of the major conformation of duplex DNA found in cells (B form) produces cyclobutane pyrimidine dimers (CPDs) from adjacent pyrimidines in a head-to-head orientation (syn) with the C5 substituents in a cis stereochemistry. These CPDs have crucial implications in skin cancer. Irradiation of G-quadruplexes and other non-B DNA conformations in vitro produces, however, CPDs between non-adjacent pyrimidines in nearby loops with syn and head-to-tail orientations (anti) with both cis and trans stereochemistry to yield a mixture of six possible isomers of the T=T dimer. This outcome is further complicated by formation of mixtures of non-adjacent CPDs of dC=dT, dT=dC, and dC=dC, and successful analysis depends on development of specific and sensitive methods. Towards meeting this need, we investigated whether ion mobility mass spectrometry (IMMS) and MS/MS can distinguish the cis,syn and trans-anti T=T CPDs. Ion mobility can afford base-line separation and give relative mobilities that are in accord with predicted cross sections. Complementing this ability to distinguish isomers is MS/MS collisional activation where fragmentation also distinguishes the two isomers and confirms conclusions drawn from ion mobility analysis. The observations offer early support that ion mobility and MS/MS can enable the distinction of DNA photoproduct isomers. 

ABSTRACT Chemical abundance anomalies in twin stars have recently been considered tell-tale signs of interactions between stars and planets. While such signals are prevalent, their nature remains a subject of debate. On the one hand, exoplanet formation may induce chemical depletion in host stars by locking up refractory elements. On the other hand, exoplanet engulfment can result in chemical enrichment, and both processes potentially produce similar differential signals. In this study, we aim to observationally disentangle these processes by using the Ca ii infrared triplet to measure the magnetic activity of 125 co-moving star pairs with high signal-to-noise ratio, and high-resolution spectra from the Magellan, Keck, and VLT (Very Large Telescope) telescopes. We find that co-natal star pairs in which the two stars exhibit significant chemical abundance differences also show differences in their magnetic activity, with stars depleted in refractories being magnetically more active. Furthermore, the strength of this correlation between differential chemical abundances and differential magnetic activity increases with condensation temperature. One possible explanation is that the chemical anomaly signature may be linked to planet formation, wherein refractory elements are locked into planets, and the host stars become more active due to more efficient contraction during the pre-main-sequence phase or star–planet tidal and magnetic interactions. 

G-quadruplexes are thought to play an important role in gene regulation and telomere maintenance, but developing probes for their presence and location is challenging due to their transitory and highly dynamic nature. The majority of probes for G-quadruplexes have relied on antibody or small-molecule binding agents, many of which can also alter the dynamics and relative populations of G-quadruplexes. Recently, it was discovered that ultraviolet B (UVB) irradiation of human telomeric DNA and various G-quadruplex forming sequences found in human promoters, as well as reverse Hoogsteen hairpins, produces a unique class of non-adjacent anti cyclobutane pyrimidine dimers (CPDs). Therefore, one can envision using a pulse of UVB light to irreversibly trap these non-B DNA structures via anti CPD formation without perturbing their dynamics, after which the anti CPDs can be identified and mapped. As a first step toward this goal, we report radioactive post- and pre-labeling assays for the detection of non-adjacent CPDs and illustrate their use in detecting trans,anti T=(T) CPD formation in a human telomeric DNA sequence. Both assays make use of snake venom phosphodiesterase (SVP) to degrade the trans,anti T=(T) CPD-containing DNA to the tetranucleotide pTT=(pTT) corresponding to CPD formation between the underlined T's of two separate dinucleotides while degrading the adjacent syn TT CPDs to the trinucleotide pGT=T. In the post-labeling assay, calf intestinal phosphodiesterase is used to dephosphorylate the tetranucleotides, which are then rephosphorylated with kinase and [32P]-ATP to produce radiolabeled mono- and diphosphorylated tetranucleotides. The tetranucleotides are confirmed to be non-adjacent CPDs by 254 nm photoreversion to the dinucleotide p*TT. In the pre-labeling assay, radiolabeled phosphates are introduced into non-adjacent CPD-forming sites by ligation prior to irradiation, thereby eliminating the dephosphorylation and rephosphorylation steps. The assays are also demonstrated to detect the stereoisomeric cis,anti T=(T) CPD. 

Abstract Submesoscale processes provide a pathway for energy to transfer from the balanced circulation to turbulent dissipation. One class of submesoscale phenomena that has been shown to be particularly effective at removing energy from the balanced flow is centrifugal–symmetric instabilities (CSIs), which grow via geostrophic shear production. CSIs have been observed to generate significant mixing in both the surface boundary layer and bottom boundary layer flows along bathymetry, where they have been implicated in the mixing and water mass transformation of Antarctic Bottom Water. However, the mixing efficiency (i.e., the fraction of the energy extracted from the flow used to irreversibly mix the fluid) of these instabilities remains uncertain, making estimates of mixing and energy dissipation due to CSI difficult. In this work we use large-eddy simulations to investigate the mixing efficiency of CSIs in the submesoscale range. We find that centrifugally dominated CSIs (i.e., CSI mostly driven by horizontal shear production) tend to have a higher mixing efficiency than symmetrically dominated ones (i.e., driven by vertical shear production). The mixing efficiency associated with CSIs can therefore alternately be significantly higher or significantly lower than the canonical value used by most studies. These results can be understood in light of recent work on stratified turbulence, whereby CSIs control the background state of the flow in which smaller-scale secondary overturning instabilities develop, thus actively modifying the characteristics of mixing by Kelvin–Helmholtz instabilities. Our results also suggest that it may be possible to predict the mixing efficiency with more readily measurable parameters (viz., the Richardson and Rossby numbers), which would allow for parameterization of this effect.