Direct Capture and Amplification of Small Fragmented DNAs Using Nitrogen-Mustard-Coated Microbeads

Circulating cell-free DNA (cfDNA) has been implicated as an important biomarker and has been intensively studied for “liquid biopsy” applications in cancer diagnostics. Owing to its small fragment size and its low concentration in circulation, cfDNA extraction and purification from serum samples are...

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Bibliographic Details
Published in:Analytical chemistry (Washington) 2022-05, Vol.94 (21), p.7594-7600
Main Authors: Hapsianto, Benediktus N., Kojima, Naoshi, Kurita, Ryoji, Yamagata, Hitoshi, Fujita, Hiroyuki, Fujii, Teruo, Kim, Soo Hyeon
Format: Article
Language:English
Subjects:
Amplification
Analytical chemistry
Beads
Biomarkers
Biopsy
Chemistry
Deoxyribonucleic acid
Diagnostic software
DNA
Microspheres
Mustard
Nanoparticles
Nitrogen
Polymerase chain reaction
Purification
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Summary:Circulating cell-free DNA (cfDNA) has been implicated as an important biomarker and has been intensively studied for “liquid biopsy” applications in cancer diagnostics. Owing to its small fragment size and its low concentration in circulation, cfDNA extraction and purification from serum samples are complicated, and the extraction yield affects the precision of subsequent molecular diagnostic tests. Here, we report a novel approach using nitrogen-mustard-coated DNA capture beads (NMD beads) that covalently capture DNA and allow direct subsequent polymerase chain reaction (PCR) amplification from the NMD bead without elusion. The complex DNA extraction and purification processes are not required. To illustrate the diagnostic use of the NMD beads, we detected short DNA fragments (142 bp) that were spiked into fetal bovine serum (as a model serum sample). The spiked DNAs were captured directly from serum samples and detected using real-time PCR at concentrations as low as 10 fg/mL. We anticipate that this DNA capture bead technique has the potential to simplify the preanalytical processes required for cfDNA detection, which could significantly expand the diagnostic applications of liquid biopsy.
ISSN:0003-2700
1520-6882
DOI:10.1021/acs.analchem.2c00531