In vivo detection of DNA secondary structures using permanganate/S1 footprinting with direct adapter ligation and sequencing (PDAL-Seq)

Methods in enzymology on CD-ROM/Methods in enzymology, Journal Year: 2024, Volume and Issue: unknown, P. 159 - 191

Published: Jan. 1, 2024

Language: Английский

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Advancements in molecular disassembly of optical probes: a paradigm shift in sensing, bioimaging, and therapeutics

Nanoscale Horizons, Journal Year: 2024, Volume and Issue: 9(9), P. 1390 - 1416

Published: Jan. 1, 2024

Molecular disassembly is pioneering a new route to refined diagnostic and therapeutic solutions. This approach breaks down self-assembled molecules, offering enhanced precision efficiency in various bio-oriented applications.

Language: Английский

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Centromere Plasticity With Evolutionary Conservation and Divergence Uncovered by Wheat 10+ Genomes

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(8)

Published: Aug. 1, 2023

Abstract Centromeres (CEN) are the chromosomal regions that play a crucial role in maintaining genomic stability. The underlying highly repetitive DNA sequences can evolve quickly most eukaryotes, and promote karyotype evolution. Despite their variability, it is not fully understood how these widely variable ensure homeostasis of centromere function. In this study, we investigated genetics epigenetics CEN population wheat lines from global breeding programs. We captured high degree sequences, positioning, epigenetic variations large complex CEN. found CENH3-associated repeats Cereba element retrotransposons exhibit phylogenetic homogenization across different lines, but less-associated repeat diverge on own way each line, implying specific mechanisms for selecting certain types as functional core Furthermore, observed CENH3 nucleosome structures display looser wrapping termini centromeric repeats, including repositioned also strict positioning intrinsic features determining identity among lines. Specific non-B form DNAs were substantially associated with nucleosomes centromeres. These findings suggest multiple involved adaptation stabilize Ultimately, proposed remarkable plasticity chromatin within diverse context, robustness function genome stability 10+ result past selections.

Language: Английский

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The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 1, 2023

Abstract Apes possess two sex chromosomes—the male-specific Y and the X shared by males females. The chromosome is crucial for male reproduction, with deletions linked to infertility. carries genes vital reproduction cognition. Variation in mating patterns brain function among great apes suggests corresponding differences their structure evolution. However, due highly repetitive nature incomplete reference assemblies, ape chromosomes have been challenging study. Here, using state-of-the-art experimental computational methods developed telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of five (chimpanzee, bonobo, gorilla, Bornean Sumatran orangutans) a lesser ape, siamang gibbon. These completely resolved ampliconic, palindromic, satellite sequences, including entire centromeres, allowing us untangle intricacies We found that, compared X, vary greatly size low alignability high levels structural rearrangements. This divergence on arises from accumulation lineage-specific ampliconic regions palindromes (which are more broadly species X) abundance transposable elements satellites lower representation X). Our analysis revealed expansions multi-copy gene families signatures purifying selection. In summary, exhibits dynamic evolution, while stable. Finally, mapping short-read sequencing data >100 individuals diversity selection chromosomes, demonstrating utility these studies expected further inform conservation genetics nonhuman apes, all which endangered species.

Language: Английский

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Non-B-form DNA is associated with centromere stability in newly-formed polyploid wheat

Science China Life Sciences, Journal Year: 2024, Volume and Issue: 67(7), P. 1479 - 1488

Published: April 16, 2024

Language: Английский

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Structural variation in humans and our primate kin in the era of telomere-to-telomere genomes and pangenomics

Current Opinion in Genetics & Development, Journal Year: 2024, Volume and Issue: 87, P. 102233 - 102233

Published: July 23, 2024

Structural variants (SVs) account for the majority of base pair differences both within and between primate species. However, our understanding inter- intra-species SV has been historically hampered by quality draft genomes absence genome resources key taxa. Recently, advances in long-read sequencing assembly have begun to radically reshape SVs. Two landmark achievements include publication a human telomere-to-telomere (T2T) as well development first pangenome reference. In this review, we look back major works laying foundation these projects. We then examine ways which T2T assemblies pangenomes are transforming approach SV. Finally, discuss what future research may like era pangenomics.

Language: Английский

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Sub-femtomolar drug monitoring via co-calibration mechanism with nanoconfined DNA probes

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 21, 2025

Abstract Synthetic drugs fundamentally reshape the illicit drug market due to their low cost, ease of production, and rapid manufacturing processes. However, current detection methods, which rely on complex instruments, have limited applicability often neglect influence pH fluctuations, leading potential bias unreliable results. Herein, we propose co-calibration DNA probes a nanoconfined biosensor (N C B S ), covering range sweat 3–8 achieve significantly enhanced target signal recognition. The N exhibits linear response 10 3 -10 8 fM with limit (LOD) 3.58 in artificial sweat. Compared single-aptamer , dual-aptamer offers broader range, primarily synergistic effects changes surface wettability capture hydrion, together reduce interference proton transport. doubles, its sensitivity improves by 4–5 orders magnitude compared existing methods. This sensing strategy expands application scope aptamer-based composite probes, offering an approach for ultra-sensitive demonstrating significant monitoring fields.

Language: Английский

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Characterization of a Novel Sequence

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 21 - 34

Published: Jan. 1, 2025

Language: Английский

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New acridone derivatives to target telomerase and oncogenes – an anticancer approach

RSC Medicinal Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

G4 stabilization by acridone derivatives to indirectly regulate pancreatic cell growth.

Language: Английский

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Replicative DNA polymerase epsilon and delta holoenzymes show wide-ranging inhibition at G-quadruplexes in the human genome

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(8)

Published: April 17, 2025

G-quadruplexes (G4s) are functional elements of the human genome, some which inhibit DNA replication. We investigated replication G4s within highly abundant microsatellite (GGGA, GGGT) and transposable element (L1 SVA) sequences. found that genome-wide, numerous motifs located preferentially on leading strand transcribed templates. directly tested replicative polymerase ϵ δ holoenzyme inhibition at these G4s, compared to low motifs. For all synthesis was higher G-rich than C-rich or control sequence. No single G4 an absolute block for either holoenzyme; however, inhibitory potential varied over order magnitude. Biophysical analyses showed form varying topologies, but did not correlate with a specific structure. Addition stabilizer pyridostatin severely inhibited forward specifically strand, enhancing G/C asynchrony. Our results reveal every examined is distinct, causing complementary become asynchronous, could contribute slowed fork elongation. Altogether, we provide critical information regarding how eukaryotic holoenzymes navigate through naturally occurring thousands times in regions genome.

Language: Английский

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