Methylated DNA plays an important role in epigenetic gene regulation, and could therefore serve as a potentially promising biomarker for the diagnosis of cancer and other diseases. Therefore, the development of a simple method for analyzing cytosine methylation in a target gene is required. Here, we report on a new method for the sequence-selective chemical modification of a single cytosine in single-stranded DNA (ssDNA). This method is based on the formation of a DNA three-way junction of the ssDNA and two ssDNA probes, and was successfully applied for a simple polymerase chain reaction (PCR)-based assay for 'pinpoint' methylation analysis.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.2116/analsci.30.371 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Precise modelling of mitochondrial diseases using optimized mitoBEs.
Nature
January 2025
Changping Laboratory, Beijing, The People's Republic of China.
The development of animal models is crucial for studying and treating mitochondrial diseases. Here we optimized adenine and cytosine deaminases to reduce off-target effects on the transcriptome and the mitochondrial genome, improving the accuracy and efficiency of our newly developed mitochondrial base editors (mitoBEs). Using these upgraded mitoBEs (version 2 (v2)), we targeted 70 mouse mitochondrial DNA mutations analogous to human pathogenic variants, establishing a foundation for mitochondrial disease mouse models.
View Article and Find Full Text PDFDimerizing DNA-AgNCs a C-Ag-C structure for fluorescence sensing with dual-output signals.
Chem Commun (Camb)
January 2025
Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, People's Republic of China.
The unique insertion capability of Ag into cytosine-cytosine (C-Ag-C) mismatch-base pairs enables precise fabrication of DNA-trapped silver nanoclusters (DNA-AgNCs) through varying the DNA sequences, thereby offering precise assembly of DNA-AgNCs and demonstrating great fluorescence applications. However, most of the DNA-AgNC-based fluorescence sensors have a single output signal. Herein, we developed a dimerized DNA-AgNC system through C-Ag-C connection at the 3'-end of a designed DNA.
View Article and Find Full Text PDFThe topography of nullomer-emerging mutations and their relevance to human disease.
Comput Struct Biotechnol J
December 2024
Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
Nullomers are short DNA sequences (11-18 base pairs) that are absent from a genome; however, they can emerge due to mutations. Here, we characterize all possible putative human nullomer-emerging single base pair mutations, population variants and disease-causing mutations. We find that the primary determinants of nullomer emergence in the human genome are the presence of CpG dinucleotides and methylated cytosines.
View Article and Find Full Text PDFIn vivo base editing extends lifespan of a humanized mouse model of prion disease.
Nat Med
January 2025
Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Prion disease is a fatal neurodegenerative disease caused by the misfolding of prion protein (PrP) encoded by the PRNP gene. While there is currently no cure for the disease, depleting PrP in the brain is an established strategy to prevent or stall templated misfolding of PrP. Here we developed in vivo cytosine and adenine base strategies delivered by adeno-associated viruses to permanently modify the PRNP locus to achieve PrP knockdown in the mouse brain.
View Article and Find Full Text PDFFragment-specific Quantification of 5hmC by qPCR via a Combination of Enzymatic Digestion and Deamination: Extreme Specificity, High Sensitivity, and Clinical Applicability.
Anal Chem
January 2025
School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
Accurate identification and quantification of 5-hydroxymethylcytosine (5hmC) can help elucidate its function in gene expression and disease pathogenesis. Current 5hmC analysis methods still present challenges, especially for clinical applications, such as having a risk of false-positive results and a lack of sufficient sensitivity. Herein, a 5hmC quantification method for fragment-specific DNA sequences with extreme specificity, high sensitivity, and clinical applicability was established using a quantitative real-time PCR (qPCR)-based workflow through the combination of enzymatic digestion and biological deamination strategy (EDD-5hmC assay).
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!