{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,9]],"date-time":"2026-05-09T15:18:11Z","timestamp":1778339891922,"version":"3.51.4"},"reference-count":34,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2016,8,9]],"date-time":"2016-08-09T00:00:00Z","timestamp":1470700800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Sensors"],"abstract":"<jats:p>Aberrant methylation of a crucial CpG island is the main mechanism for the inactivation of CDKN2A in the early stages of carcinogenesis. Therefore, the detection of DNA methylation with high sensitivity and specificity is important, and various detection methods have been developed. Recently, upconversion nanoparticles (UCNPs) have been found to display a high signal-to-noise ratio and no photobleaching, making them useful for diagnostic applications. In this pilot study, we applied UCNPs to the detection of CDKN2A methylation and evaluated the feasibility of this system for use in molecular diagnostics. DNA PCR was performed using biotinylated primers, and the PCR amplicon was then intercalated with SYTOX Orange dye, followed by incubation with streptavidin-conjugated UCNPs. Fluorescence detection of the F\u00f6rster resonance energy transfer (FRET) of the UCNPs (MS-UC-FRET) was then performed, and the results were compared to those from real-time PCR (RQ-PCR) and pyrosequencing. Detection by MS-UC-FRET was more sensitive than that by either RQ-PCR or pyrosequencing. Our results confirmed the success of our MS-UC-FRET system for detecting DNA methylation and demonstrated the potential application of this system in molecular diagnostics.<\/jats:p>","DOI":"10.3390\/s16081259","type":"journal-article","created":{"date-parts":[[2016,8,9]],"date-time":"2016-08-09T09:14:10Z","timestamp":1470734050000},"page":"1259","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Upconversion Nanoparticle-Based F\u00f6rster Resonance Energy Transfer for Detecting DNA Methylation"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3505-3914","authenticated-orcid":false,"given":"Seockjune","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul 05505, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3201-5728","authenticated-orcid":false,"given":"Sang-Hyun","family":"Hwang","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Center for Diagnostic Oncology, Research Institute and Hospital, National Cancer Center, Goyang-si 10408, Korea"},{"name":"Hematologic Malignancy Branch, Research Institute and Hospital, National Cancer Center, Goyang-si 10408, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Su-Gyeong","family":"Im","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Center for Diagnostic Oncology, Research Institute and Hospital, National Cancer Center, Goyang-si 10408, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Min-Ki","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Pusan National University School of Medicine and Biomedical Research Institute, Pusan National University Hospital, 179 Gudeok-ro, Seo-gu, Busan 602-739, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chang-Hun","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Pathology, Pusan National University School of Medicine and Biomedical Research Institute, Pusan National University Hospital, 179 Gudeok-ro, Seo-gu, Busan 602-739, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sang","family":"Son","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Gachon University, Seongnam, Gyeonggi, and Gachon Medical Research Institute, Gil Medical Center, Inchon 461-701, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Heung-Bum","family":"Oh","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul 05505, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2016,8,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Gao, D., Herman, J.G., and Guo, M. (2016). The clinical value of aberrant epigenetic changes of DNA damage repair genes in human cancer. Oncotarget.","DOI":"10.18632\/oncotarget.7949"},{"key":"ref_2","first-page":"4397","article-title":"Transcriptional Regulation of the p16 Tumor Suppressor Gene","volume":"35","author":"Kotake","year":"2015","journal-title":"Anticancer Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"11891","DOI":"10.1073\/pnas.95.20.11891","article-title":"Aberrant methylation of p16(INK4a) is an early event in lung cancer and a potential biomarker for early diagnosis","volume":"95","author":"Belinsky","year":"1998","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Zhang, L.R., Rong, Y., Ming, L., Xin, Y., Feng, J., and Lin, X. (2013). The prognostic value of epigenetic silencing of p16 gene in NSCLC patients: A systematic review and meta-analysis. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0054970"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.bios.2013.07.040","article-title":"A new strategy for methylated DNA detection based on photoelectrochemical immunosensor using Bi2S3 nanorods, methyl bonding domain protein and anti-his tag antibody","volume":"51","author":"Yin","year":"2014","journal-title":"Biosens. Bioelectron."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"17547","DOI":"10.1039\/C5NR04956C","article-title":"Highly sensitive detection of DNA methylation levels by using a quantum dot-based FRET method","volume":"7","author":"Ma","year":"2015","journal-title":"Nanoscale"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1373\/clinchem.2008.121962","article-title":"PCR-based methods for detecting single-locus DNA methylation biomarkers in cancer diagnostics, prognostics, and response to treatment","volume":"55","author":"Kristensen","year":"2009","journal-title":"Clin. Chem."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"9821","DOI":"10.1073\/pnas.93.18.9821","article-title":"Methylation-specific PCR: A novel PCR assay for methylation status of CpG islands","volume":"93","author":"Herman","year":"1996","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Eads, C.A., Danenberg, K.D., Kawakami, K., Saltz, L.B., Blake, C., Shibata, D., Danenberg, P.V., and Laird, P.W. (2000). MethyLight: A high-throughput assay to measure DNA methylation. Nucleic. Acids. Res., 28.","DOI":"10.1093\/nar\/28.8.e32"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"146","DOI":"10.2144\/03351md01","article-title":"Sensitive and quantitative universal Pyrosequencing methylation analysis of CpG sites","volume":"35","author":"Colella","year":"2003","journal-title":"BioTechniques"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1101\/gr.088831.108","article-title":"MS-qFRET: A quantum dot-based method for analysis of DNA methylation","volume":"19","author":"Bailey","year":"2009","journal-title":"Genome Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.bios.2014.03.033","article-title":"DNA methylation detection by a novel fluorimetric nanobiosensor for early cancer diagnosis","volume":"60","author":"Dadmehr","year":"2014","journal-title":"Biosens. Bioelectron."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"4709","DOI":"10.1021\/cr900323b","article-title":"Binary probes for nucleic acid analysis","volume":"110","author":"Kolpashchikov","year":"2010","journal-title":"Chem. Rev."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2781","DOI":"10.1002\/smll.201000418","article-title":"Small upconverting fluorescent nanoparticles for biomedical applications","volume":"6","author":"Chatterjee","year":"2010","journal-title":"Small"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1021\/cr020357g","article-title":"Upconversion and anti-Stokes processes with f and d ions in solids","volume":"104","author":"Auzel","year":"2004","journal-title":"Chem. Rev."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"5808","DOI":"10.1002\/anie.201005159","article-title":"Upconverting nanoparticles","volume":"50","author":"Haase","year":"2011","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1021\/jacs.5b10309","article-title":"Dual-Mode Ultrasensitive Quantification of MicroRNA in Living Cells by Chiroplasmonic Nanopyramids Self-Assembled from Gold and Upconversion Nanoparticles","volume":"138","author":"Li","year":"2016","journal-title":"J. Am. Chem. Soc."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"7622","DOI":"10.1039\/C5AN01634G","article-title":"An upconversion fluorescent resonant energy transfer biosensor for hepatitis B virus (HBV) DNA hybridization detection","volume":"140","author":"Zhu","year":"2015","journal-title":"Analyst"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.bios.2014.06.037","article-title":"Upconversion nanoparticle-based ligase-assisted method for specific and sensitive detection of T790M mutation in epidermal growth factor receptor","volume":"62","author":"Wang","year":"2014","journal-title":"Biosens. Bioelectron."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.bios.2013.09.011","article-title":"Upconversion nanoparticle-based Forster resonance energy transfer for detecting the IS6110 sequence of Mycobacterium tuberculosis complex in sputum","volume":"53","author":"Hwang","year":"2014","journal-title":"Biosens. Bioelectron."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1515\/CCLM.2011.108","article-title":"Detection of HOXA9 gene methylation in tumor tissues and induced sputum samples from primary lung cancer patients","volume":"49","author":"Hwang","year":"2011","journal-title":"Clin. Chem. Lab. Med."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Hwang, S.H., Im, S.G., Hah, S.S., Cong, V.T., Lee, E.J., Lee, Y.S., Lee, G.K., Lee, D.H., and Son, S.J. (2013). Effects of upconversion nanoparticles on polymerase chain reaction. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0073408"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"209","DOI":"10.2353\/jmoldx.2006.050135","article-title":"Precision and performance characteristics of bisulfite conversion and real-time PCR (MethyLight) for quantitative DNA methylation analysis","volume":"8","author":"Ogino","year":"2006","journal-title":"J. Mol. Diagn."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Nosho, K., Irahara, N., Shima, K., Kure, S., Kirkner, G.J., Schernhammer, E.S., Hazra, A., Hunter, D.J., Quackenbush, J., and Spiegelman, D. (2008). Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample. PLoS ONE, 3.","DOI":"10.1371\/journal.pone.0003698"},{"key":"ref_25","first-page":"469","article-title":"Level of HOXA5 hypermethylation in acute myeloid leukemia is associated with short-term outcome","volume":"30","author":"Kim","year":"2010","journal-title":"Korean J. Lab. Med."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"6989","DOI":"10.1039\/C5TB00885A","article-title":"Nanoparticle based fluorescence resonance energy transfer (FRET) for biosensing applications","volume":"3","author":"Shi","year":"2015","journal-title":"J. Mater. Chem. B"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.jmoldx.2012.06.007","article-title":"Conventional and nanotechniques for DNA methylation profiling","volume":"15","author":"Shanmuganathan","year":"2013","journal-title":"J. Mol. Diagn."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Gu, J., Wen, Y., Zhu, S., Hua, F., Zhao, H., Xu, H., You, J., Sun, L., Wang, W., and Chen, J. (2013). Association between P(16INK4a) promoter methylation and non-small cell lung cancer: a meta-analysis. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0060107"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1897","DOI":"10.1093\/carcin\/bgg169","article-title":"Hypermethylation of p16INK4a in Chinese lung cancer patients: biological and clinical implications","volume":"24","author":"Liu","year":"2003","journal-title":"Carcinogenesis"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.1056\/NEJMra072067","article-title":"Epigenetics in cancer","volume":"358","author":"Esteller","year":"2008","journal-title":"N. Engl. J. Med."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1158\/1055-9965.EPI-07-2518","article-title":"DNA methylation in tumor and matched normal tissues from non-small cell lung cancer patients","volume":"17","author":"Feng","year":"2008","journal-title":"Cancer Epidemiol. Biomarkers Prev."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"11","DOI":"10.4046\/trd.2012.73.1.11","article-title":"Promoter Methylation of CDKN2A, RAR\u03b2, and RASSF1A in Non-Small Cell Lung Carcinoma: Quantitative Evaluation Using Pyrosequencing","volume":"73","author":"Lee","year":"2012","journal-title":"Tuberc. Respir. Dis."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1586\/erm.10.65","article-title":"Developments in real-time PCR research and molecular diagnostics","volume":"10","author":"Bustin","year":"2010","journal-title":"Expert. Rev. Mol. Diagn."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1522","DOI":"10.1016\/j.bios.2008.08.023","article-title":"Highly sensitive and selective oligonucleotide sensor for sickle cell disease gene using photon upconverting nanoparticles","volume":"24","author":"Kumar","year":"2009","journal-title":"Biosens. Bioelectron."}],"container-title":["Sensors"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1424-8220\/16\/8\/1259\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T19:28:02Z","timestamp":1760210882000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1424-8220\/16\/8\/1259"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,8,9]]},"references-count":34,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2016,8]]}},"alternative-id":["s16081259"],"URL":"https:\/\/doi.org\/10.3390\/s16081259","relation":{},"ISSN":["1424-8220"],"issn-type":[{"value":"1424-8220","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,8,9]]}}}