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Evidence for intrinsic DNA dynamics and deformability in damage sensing by the Rad4/XPC nucleotide excision repair complex.
Nucleic Acids Res
January 2025
Department of Physics, 845 W Taylor St, University of Illinois Chicago, Chicago, IL 60607, USA.
Altered DNA dynamics at lesion sites are implicated in how DNA repair proteins sense damage within genomic DNA. Using laser temperature-jump (T-jump) spectroscopy combined with cytosine-analog Förster Resonance Energy Transfer (FRET) probes that sense local DNA conformations, we measured the intrinsic dynamics of DNA containing 3 base-pair mismatches recognized in vitro by Rad4 (yeast ortholog of XPC). Rad4/XPC recognizes diverse lesions from environmental mutagens and initiates nucleotide excision repair.
View Article and Find Full Text PDFA novel algorithm for the detection of microsatellite instability in endometrial cancer using next‑generation sequencing data.
Oncol Lett
February 2025
Department of Pathology, Yijishan Hospital, The First Affiliated Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China.
The molecular-based detection of microsatellite instability (MSI) in endometrial cancer is complex, due to the low sensitivity of PCR and a lack of standardization in next-generation sequencing (NGS) methods. In the present study, sequenced data were obtained from an NGS panel following the addition of five commonly used microsatellite loci. Subsequently, a novel algorithm, namely MSIPeak, was developed for data analysis.
View Article and Find Full Text PDFImmune Dysregulation in a Child With SOD1-Related Neurological Disease.
Am J Med Genet A
December 2024
Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada.
Article Synopsis
- Spastic tetraplegia and axial hypotonia (STAHP) is a rare neurological disorder in children linked to biallelic SOD1 deficiency, marked by progressive symptoms starting before age 2.
- Five studies have reported nine cases, primarily related to a common genetic variant in SOD1 that disrupts enzyme function, with one case involving a novel SOD1 variant in a 19-year-old male.
- The patient exhibited significant neurological decline and MRI findings of cerebellar atrophy, plus new symptoms including immune dysregulation and physical anomalies not previously associated with STAHP.
Stability and conformation of DNA-hairpin in cylindrical confinement.
Biophys Chem
January 2025
Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India. Electronic address:
We conducted atomistic Molecular Dynamics (MD) simulations of DNA-Hairpin molecules encapsulated within Single-Walled Carbon Nanotubes (SWCNTs) at a temperature of 300 K. Our investigation revealed that the structural integrity of the DNA-Hairpin can be maintained within SWCNTs, provided that the diameter of the SWCNT exceeds a critical threshold value. Conversely, when the SWCNT diameter falls below this critical threshold, the DNA-Hairpin undergoes denaturation, even at a temperature of 300 K.
View Article and Find Full Text PDFCombining Off-flow, a Nextflow-coded program, and whole genome sequencing reveals unintended genetic variation in CRISPR/Cas-edited iPSCs.
Comput Struct Biotechnol J
December 2024
The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas nucleases and human induced pluripotent stem cell (iPSC) technology can reveal deep insight into the genetic and molecular bases of human biology and disease. Undesired editing outcomes, both on-target (at the edited locus) and off-target (at other genomic loci) hinder the application of CRISPR-Cas nucleases. We developed Off-flow, a Nextflow-coded bioinformatic workflow that takes a specific guide sequence and Cas protein input to call four separate off-target prediction programs (CHOPCHOP, Cas-Offinder, CRISPRitz, CRISPR-Offinder) to output a comprehensive list of predicted off-target sites.
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