ArticleBMC biology2021
Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA.
Article in BMC biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 43 citations in OpenAlex.
- Holistic determination of ends of cfDNA molecules.Cell genomics · 2026Article
- Extracellular heme:DNA complexes promote oxidative stress and inflammation during lupus-associated hemolysis.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Salivary biomarkers in oral cancer diagnosis: advancing conventional treatment strategies.Military Medical Research · 2026Review
- Amplification-free cancer diagnosis based on inhibition of Cas12a activity by site-specific 5mC-modified cfDNA.Nucleic acids research · 2025Article
- Characterization of Ultra-Short plasma Cell-Free DNA in maternal blood and its preliminary potential as a screening marker for preeclampsia.Molecular medicine (Cambridge, Mass.) · 2025Article
- Cell-Free DNA: Features and Attributes Shaping the Next Frontier in Liquid Biopsy.Molecular diagnosis & therapy · 2025Review
- Identification of an enzyme with strong single-stranded DNA ligation activity and its application for sequencing.Nucleic acids research · 2025Article
- Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA.Nucleic acids research · 2024Article
- Article
- A review on the impact of single-stranded library preparation on plasma cell-free diversity for cancer detection.Frontiers in oncology · 2024Review
- Distinct Features of Plasma Ultrashort Single-Stranded Cell-Free DNA as Biomarkers for Lung Cancer Detection.Clinical chemistry · 2023Article
- Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids.Human genomics · 2023Article
- Multi-faceted attributes of salivary cell-free DNA as liquid biopsy biomarkers for gastric cancer detection.Biomarker research · 2023Article
- A highly efficient scheme for library preparation from single-stranded DNA.Scientific reports · 2023Article
- Cross-platform comparisons for targeted bisulfite sequencing of MGISEQ-2000 and NovaSeq6000.Clinical epigenetics · 2023Article
- Saliva diagnostics: Salivaomics, saliva exosomics, and saliva liquid biopsy.Journal of the American Dental Association (1939) · 2023Review
- Genome-Wide Profiling of Endogenous Single-Stranded DNA Using the SSiNGLe-P1 Method.International journal of molecular sciences · 2023Article
- Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures.Diagnostics (Basel, Switzerland) · 2022Review
- Plasma contains ultrashort single-stranded DNA in addition to nucleosomal cell-free DNA.iScience · 2022Article
- Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA.Genome research · 2022Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCell-free DNA (cfDNA), which is extracellular DNA present in the circulating plasma and other body fluids, is currently investigated as a minimally invasive, highly informative biomarker. While nucleosome-sized cfDNA fragments have been investigated intensively, shorter DNA fragments in the plasma have not been studied due to several technical limitations.
resultsWe aimed to investigate the existence of shorter cfDNA fragments in the blood. Using an improved cfDNA purification protocol and a 3'-end-labeling method, we found DNA fragments of approximately 50 nucleotides in length in the human plasma, present at a molar concentration comparable to that of nucleosome-sized fragments. Unfortunately, these short fragments cannot be recovered by widely used cfDNA isolation methods. In addition, they are composed of single-stranded DNA (ssDNA), thus escaping detection in previous studies. Therefore, we established a library-preparation protocol based on our unique ssDNA ligation technique and applied it to the isolated cfDNA. Deep sequencing of these libraries revealed that the short fragments are derived from hundreds of thousands of genomic sites in open chromatin regions and enriched with transcription factor-binding sites. Remarkably, antisense strands of putative G-quadruplex motifs occupy as much as one-third of the peaks by these short fragments.
conclusionsWe propose a new class of plasma cfDNA composed of short single-stranded fragments that potentially form non-canonical DNA structures.
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