Chemical probing of the homopurine·homopyrimidine tract in supercoiled DNA at single-nucleotide resolution

AbstractLocal structure of the homopurine·homopyrimidine tract in a supercoiled plasmid pEJ4 was studied using chemical probes at single-nucleotide resolution. The conformation of the homopyrimidine strand was probed by osmium tetroxide, pyridine (Os,py) while that of the homopurine strand was tested by diethyl pyrocarbonate (DEPC), i.e. by probes reacting preferentially with single-stranded DNA. At weakly acidic pH values, a strong Os,py attack on three nucleotides at the centre of the (dC-dT)16 block and a weaker attack on two nucleotides at the end of the block were observed. DEPC modified adenines in the 5′-half of the homopurine strand. Os,py modification at the centre of the block corresponded to the loop of the hairpin formed by the homopyrimidine tract, while DEPC modification corresponded to the unstructured half of the homopurine strand in the model of protonated triplex H form of DNA

Long-Lasting, Patient-Controlled, Procedure-Free Contraception: A Review of Annovera with a Pharmacist Perspective

Annovera (segesterone acetate and ethinyl estradiol vaginal system) is a US Food and Drug Administration FDA-approved long-lasting, reversible contraceptive that is fully administered by the user and does not require a procedure for insertion or removal. The vaginal system is in the shape of a ring and contains low doses of a novel progestin, egesterone acetate, and ethinyl estradiol. It is made of silicone and is fully pliable and flexible. The vaginal system is reusable for 13 cycles, using a 21 days in/7 days out regimen, providing women with the ability to control their fertility. Particularly now during the COVID-19 pandemic when access to contraception has been further reduced, patients may benefit from a method that is both long-lasting and patient-controlled

Epitaxy: Programmable Atom Equivalents

The programmability of DNA makes it an attractive structure-directing ligand for the assembly of nanoparticle (NP) superlattices in a manner that mimics many aspects of atomic crystallization. However, the synthesis of multilayer single crystals of defined size remains a challenge. Though previous studies considered lattice mismatch as the major limiting factor for multilayer assembly, thin film growth depends on many interlinked variables. Here, a more comprehensive approach is taken to study fundamental elements, such as the growth temperature and the thermodynamics of interfacial energetics, to achieve epitaxial growth of NP thin films. Both surface morphology and internal thin film structure are examined to provide an understanding of particle attachment and reorganization during growth. Under equilibrium conditions, single crystalline, multilayer thin films can be synthesized over 500 × 500 μm² areas on lithographically patterned templates, whereas deposition under kinetic conditions leads to the rapid growth of glassy films. Importantly, these superlattices follow the same patterns of crystal growth demonstrated in atomic thin film deposition, allowing these processes to be understood in the context of well-studied atomic epitaxy and enabling a nanoscale model to study fundamental crystallization processes. Through understanding the role of epitaxy as a driving force for NP assembly, we are able to realize 3D architectures of arbitrary domain geometry and size.United States. Air Force Office of Scientific Research (AFOSR FA9550-11-1-0275)United States. Air Force Office of Scientific Research (FA9550-12-1-0280)United States. Department of Defense (N00014-15-1-0043)United States. Department of Energy (Grant DE-SC0000989-0002)National Science Foundation (U.S.) (Award DMR-1121262

Differences in behavior and distribution of permafrost-related lakes in Central Yakutia and their response to climatic drivers

The Central Yakutian permafrost landscape is rapidly being modified by land use and global warming, but small-scale thermokarst process variability and hydrological conditions are poorly understood. We analyze lake-area changes and thaw subsidence of young thermokarst lakes on ice-complex deposits (yedoma lakes) in comparison to residual lakes in alas basins during the last 70 years for a local study site and we record regional lake size and distribution on different ice-rich permafrost terraces using satellite and historical airborne imagery. Statistical analysis of climatic and ground-temperature data identified driving factors of yedoma- and alas-lake changes. Overall, lake area is larger today than in 1944 but alas-lake levels have oscillated greatly over 70 years, with a mean alas-lake-radius change rate of 1.663.0 m/yr. Anthropogenic disturbance and forest degradation initiated, and climate forced rapid, continuous yedoma-lake growth. The mean yedoma lake-radius change rate equals 1.261.0 m/yr over the whole observation period. Mean thaw subsidence below yedoma lakes is 6.261.4 cm/yr. Multiple regression analysis suggests that winter precipitation, winter temperature, and active-layer properties are primary controllers of area changes in both lake types; summer weather and permafrost conditions additionally influence yedoma-lake growth rates. The main controlling factors of alas-lake changes are unclear due to larger catchment areas and subsurface hydrological conditions. Increasing thermokarst activity is currently linked to older terraces with higher ground-ice contents, but thermokarst activity will likely stay high and wet conditions will persist within the near future in Central Yakutian alas basins

Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair

Carcinogenesis and neoplastic progression are mediated by the accumulation of somatic mutations. Here we report that the local density of somatic mutations in cancer genomes is highly reduced specifically in accessible regulatory DNA defined by DNase I hypersensitive sites. This reduction is independent of any known factors influencing somatic mutation density and is observed in diverse cancer types, suggesting a general mechanism. By analyzing individual cancer genomes1, we show that the reduced local mutation density within regulatory DNA is linked to intact global genome repair machinery, with nearly complete abrogation of the hypomutation phenomenon in individual cancers that possess mutations in multiple nucleotide excision repair components. Together, our results connect chromatin structure, gene regulation and cancer-associated somatic mutation

Checkpoints are blind to replication restart and recombination intermediates that result in gross chromosomal rearrangements

Replication fork inactivation can be overcome by homologous recombination, but this can cause gross chromosomal rearrangements that subsequently missegregate at mitosis, driving further chromosome instability. It is unclear when the chromosome rearrangements are generated and whether individual replication problems or the resulting recombination intermediates delay the cell cycle. Here we have investigated checkpoint activation during HR-dependent replication restart using a site-specific replication fork-arrest system. Analysis during a single cell cycle shows that HR-dependent replication intermediates arise in S phase, shortly after replication arrest, and are resolved into acentric and dicentric chromosomes in G2. Despite this, cells progress into mitosis without delay. Neither the DNA damage nor the intra-S phase checkpoints are activated in the first cell cycle, demonstrating that these checkpoints are blind to replication and recombination intermediates as well as to rearranged chromosomes. The dicentrics form anaphase bridges that subsequently break, inducing checkpoint activation in the second cell cycle

A Defective mRNA Cleavage and Polyadenylation Complex Facilitates Expansions of Transcribed (GAA) n Repeats Associated with Friedreich’s Ataxia

Expansions of microsatellite repeats are responsible for numerous hereditary diseases in humans, including myotonic dystrophy and Friedreich's ataxia. Whereas the length of an expandable repeat is the main factor determining disease inheritance, recent data point to genomic trans modifiers that can impact the likelihood of expansions and disease progression. Detection of these modifiers may lead to understanding and treating repeat expansion diseases. Here, we describe a method for the rapid, genome-wide identification of trans modifiers for repeat expansion in a yeast experimental system. Using this method, we found that missense mutations in the endoribonuclease subunit (Ysh1) of the mRNA cleavage and polyadenylation complex dramatically increase the rate of (GAA) n repeat expansions but only when they are actively transcribed. These expansions correlate with slower transcription elongation caused by the ysh1 mutation. These results reveal an interplay between RNA processing and repeat-mediated genome instability, confirming the validity of our approach. Keywords: genome instability; repeat expansion; RNA polyadenylation; RNA processing; transcription-replication conflicts; Friedreich’s ataxia; DNA double-strand breaks; trans-modifiers of repeat expansions; genetic screen; whole-genome sequencin

Towards a Tetravalent Chemistry of Colloids

We propose coating spherical particles or droplets with anisotropic nano-sized objects to allow micron-scale colloids to link or functionalize with a four-fold valence, similar to the sp3 hybridized chemical bonds associated with, e.g., carbon, silicon and germanium. Candidates for such coatings include triblock copolymers, gemini lipids, metallic or semiconducting nanorods and conventional liquid crystal compounds. We estimate the size of the relevant nematic Frank constants, discuss how to obtain other valences and analyze the thermal distortions of ground state configurations of defects on the sphere.Comment: Replaced to improve figures. 4 figures Nano Letter