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1. Osmotically Driven and Detected DNA Translocations

   https://doi.org/10.1038/s41598-019-51049-4  

   McMullen, Angus; Araujo, George; Winter, Michele; Stein, Derek (October 2019, Scientific Reports)

   Abstract A salinity gradient propels a DNA molecule through a solid-state nanopore and generates an ionic current whose change allows for the detection of the translocation. Measurements and theoretical analyses reveal the role of diffusio-osmosis in driving these phenomena: After accounting for known salinity-dependent electrode effects, the measured current change caused by the presence of a DNA molecule inside the nanopore and the DNA translocation speed through it both increase with the magnitude of the applied salinity gradients. The effects are consistent with the theory of diffuisio-osmosis and strong enough to enable DNA translocations to overcome an applied retarding potential of tens of millivolts. This work illustrates how salinity gradients can be used to power and operate a nanopore sensor. 

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2. Multi-resolution simulation of DNA transport through large synthetic nanostructures

   https://doi.org/10.1039/d1cp04589j  

   Choudhary, Adnan; Maffeo, Christopher; Aksimentiev, Aleksei (February 2022, Physical Chemistry Chemical Physics)

   Modeling and simulation has become an invaluable partner in development of nanopore sensing systems. The key advantage of the nanopore sensing method – the ability to rapidly detect individual biomolecules as a transient reduction of the ionic current flowing through the nanopore – is also its key deficiency, as the current signal itself rarely provides direct information about the chemical structure of the biomolecule. Complementing experimental calibration of the nanopore sensor readout, coarse-grained and all-atom molecular dynamics simulations have been used extensively to characterize the nanopore translocation process and to connect the microscopic events taking place inside the nanopore to the experimentally measured ionic current blockades. Traditional coarse-grained simulations, however, lack the precision needed to predict ionic current blockades with atomic resolution whereas traditional all-atom simulations are limited by the length and time scales amenable to the method. Here, we describe a multi-resolution framework for modeling electric field-driven passage of DNA molecules and nanostructures through to-scale models of synthetic nanopore systems. We illustrate the method by simulating translocation of double-stranded DNA through a solid-state nanopore and a micron-scale slit, capture and translocation of single-stranded DNA in a double nanopore system, and modeling ionic current readout from a DNA origami nanostructure passage through a nanocapillary. We expect our multi-resolution simulation framework to aid development of the nanopore field by providing accurate, to-scale modeling capability to research laboratories that do not have access to leadership supercomputer facilities. 

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3. Combining dynamic Monte Carlo with machine learning to study nanoparticle translocation

   https://doi.org/10.1039/D2SM00431C  

   Vieira, Luiz Fernando; Weinhofer, Alexandra C.; Oltjen, William C.; Yu, Cindy; de Souza Mendes, Paulo Roberto; Hore, Michael J. (July 2022, Soft Matter)

   Resistive pulse sensing (RPS) measurements of nanoparticle translocation have the ability to provide information on single-particle level characteristics, such as diameter or mobility, as well as ensemble averages. However, interpreting these measurements is complex and requires an understanding of nanoparticle dynamics in confined spaces as well as the ways in which nanoparticles disrupt ion transport while inside a nanopore. Here, we combine Dynamic Monte Carlo (DMC) simulations with Machine Learning (ML) and Poisson–Nernst–Planck calculations to simultaneously simulate nanoparticle dynamics and ion transport during hundreds of independent particle translocations as a function of nanoparticle size, electrophoretic mobility, and nanopore length. The use of DMC simulations allowed us to explicitly investigate the effects of Brownian motion and nanoparticle/nanopore characteristics on the amplitude and duration of translocation signals. Simulation results were verified with experimental RPS measurements and found to be in quantitative agreement. 

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4. Chromosome painting reveals inter‐chromosomal rearrangements and evolution of subgenome D of wheat

   https://doi.org/10.1111/tpj.15926  

   Shi, Peiyao; Sun, Haojie; Liu, Guanqing; Zhang, Xu; Zhou, Jiawen; Song, Rongrong; Xiao, Jin; Yuan, Chunxia; Sun, Li; Wang, Zongkuan; et al (August 2022, The Plant Journal)

   SUMMARY Aegilopsspecies represent the most important gene pool for breeding bread wheat (Triticum aestivum). Thus, understanding the genome evolution, including chromosomal structural rearrangements and syntenic relationships amongAegilopsspecies or betweenAegilopsand wheat, is important for both basic genome research and practical breeding applications. In the present study, we attempted to develop subgenome D‐specific fluorescencein situhybridization (FISH) probes by selecting D‐specific oligonucleotides based on the reference genome of Chinese Spring. The oligo‐based chromosome painting probes consisted of approximately 26 000 oligos per chromosome and their specificity was confirmed in both diploid and polyploid species containing the D subgenome. Two previously reported translocations involving two D chromosomes have been confirmed in wheat varieties and their derived lines. We demonstrate that the oligo painting probes can be used not only to identify the translocations involving D subgenome chromosomes, but also to determine the precise positions of chromosomal breakpoints. Chromosome painting of 56 accessions ofAe. tauschiifrom different origins led us to identify two novel translocations: a reciprocal 3D‐7D translocation in two accessions and a complex 4D‐5D‐7D translocation in one accession. Painting probes were also used to analyze chromosomes from more diverseAegilopsspecies. These probes produced FISH signals in four different genomes. Chromosome rearrangements were identified inAegilops umbellulata,Aegilops markgrafii, andAegilops uniaristata, thus providing syntenic information that will be valuable for the application of these wild species in wheat breeding. 

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5. LD-CNV: rapid and simple discovery of chromosomal translocations using linkage disequilibrium between copy number variable loci

   https://doi.org/10.1093/genetics/iyab137  

   Comai, Luca; Amundson, Kirk R; Ordoñez, Benny; Zhao, Xin; Braz, Guilherme Tomaz; Jiang, Jiming; Henry, Isabelle M (August 2021, Genetics)

   Abstract Large-scale structural variations, such as chromosomal translocations, can have profound effects on fitness and phenotype, but are difficult to identify and characterize. Here, we describe a simple and effective method aimed at identifying translocations using only the dosage of sequence reads mapped on the reference genome. We binned reads on genomic segments sized according to sequencing coverage and identified instances when copy number segregated in populations. For each dosage-polymorphic 1 Mb bin, we tested independence, effectively an apparent linkage disequilibrium (LD), with other variable bins. In nine potato (Solanum tuberosum) dihaploid families translocations affecting pericentromeric regions were common and in two cases were due to genomic misassembly. In two populations, we found evidence for translocation affecting euchromatic arms. In cv. PI 310467, a nonreciprocal translocation between chromosomes (chr.) 7 and 8 resulted in a 5–3 copy number change affecting several Mb at the respective chromosome tips. In cv. “Alca Tarma,” the terminal arm of chr. 4 translocated to the tip of chr. 1. Using oligonucleotide-based fluorescent in situ hybridization painting probes (oligo-FISH), we tested and confirmed the predicted arrangement in PI 310467. In 192 natural accessions of Arabidopsis thaliana, dosage haplotypes tended to vary continuously and resulted in higher noise, while apparent LD between pericentromeric regions suggested the effect of repeats. This method, LD-CNV, should be useful in species where translocations are suspected because it tests linkage without the need for genotyping. 

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