{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T10:47:22Z","timestamp":1784630842024,"version":"3.55.0"},"reference-count":44,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2024,1,12]],"date-time":"2024-01-12T00:00:00Z","timestamp":1705017600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"\u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, Cluj-Napoca, Romania","award":["35\/172\/17.12.2021"],"award-info":[{"award-number":["35\/172\/17.12.2021"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biosensors"],"abstract":"<jats:p>This study delves into the intricate interaction between DNA and nanosystems, exploring its potential implications for biomedical applications. The focus lies in understanding the adsorption geometry of DNA when in proximity to plasmonic nanoparticles, utilizing ultrasensitive vibrational spectroscopy techniques. Employing a combined Raman-SERS analysis, we conducted an in-depth examination to clarify the molecular geometry of interactions between DNA and silver nanoparticles. Our findings also reveal distinctive spectral features regarding DNA samples due to their distinctive genome stability. To understand the subtle differences occurring between normal and cancerous DNA, their thermal stability was investigated by means of SERS measurement performed before and after a thermal treatment at 94 \u00b0C. It was proved that thermal treatment did not affect DNA integrity in the case of normal cells. On the other hand, due to epimutation pattern that characterizes cancerous DNA, variations between spectra recorded before and after heat treatment were observed, suggesting genome instability. These findings highlight the potential of DNA analysis using SERS for cancer detection. They demonstrate the applicability of this approach to overcoming challenges associated with low DNA concentrations (e.g., circulating tumor DNA) that occur in biofluids. In conclusion, this research contributes significant insights into the nanoscale behavior of DNA in the presence of nanosystems.<\/jats:p>","DOI":"10.3390\/bios14010041","type":"journal-article","created":{"date-parts":[[2024,1,12]],"date-time":"2024-01-12T11:43:53Z","timestamp":1705059833000},"page":"41","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Understanding DNA Epigenetics by Means of Raman\/SERS Analysis for Cancer Detection"],"prefix":"10.3390","volume":"14","author":[{"given":"Luca","family":"David","sequence":"first","affiliation":[{"name":"Faculty of Medicine, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anca","family":"Onaciu","sequence":"additional","affiliation":[{"name":"MedFuture\u2014Research Center for Advanced Medicine, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"},{"name":"Department of Pharmaceutical Physics & Biophysics, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8322-1180","authenticated-orcid":false,"given":"Valentin","family":"Toma","sequence":"additional","affiliation":[{"name":"MedFuture\u2014Research Center for Advanced Medicine, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-1754-2681","authenticated-orcid":false,"given":"Rare\u0219-Mario","family":"Bor\u0219a","sequence":"additional","affiliation":[{"name":"MedFuture\u2014Research Center for Advanced Medicine, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"},{"name":"Department of Maxillofacial Surgery and Implantology, \u201cIuliu Ha\u021bieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristian","family":"Moldovan","sequence":"additional","affiliation":[{"name":"MedFuture\u2014Research Center for Advanced Medicine, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"},{"name":"Department of Pharmaceutical Physics & Biophysics, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9397-0791","authenticated-orcid":false,"given":"Adrian-Bogdan","family":"\u021aigu","sequence":"additional","affiliation":[{"name":"MedFuture\u2014Research Center for Advanced Medicine, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana","family":"Cenariu","sequence":"additional","affiliation":[{"name":"MedFuture\u2014Research Center for Advanced Medicine, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ioan","family":"\u0218imon","sequence":"additional","affiliation":[{"name":"Department of Surgery, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriela-Fabiola","family":"\u0218tiufiuc","sequence":"additional","affiliation":[{"name":"Faculty of Physics, \u201cBabes Bolyai\u201d University, 400084 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2808-7019","authenticated-orcid":false,"given":"Eugen","family":"Carasevici","sequence":"additional","affiliation":[{"name":"Nanotechnology Laboratory, TRANSCEND Research Center, Regional Institute of Oncology, 700483 Iasi, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Br\u00eendu\u0219a","family":"Dr\u0103goi","sequence":"additional","affiliation":[{"name":"Nanotechnology Laboratory, TRANSCEND Research Center, Regional Institute of Oncology, 700483 Iasi, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5500-1519","authenticated-orcid":false,"given":"Ciprian","family":"Tomuleasa","sequence":"additional","affiliation":[{"name":"MedFuture\u2014Research Center for Advanced Medicine, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"},{"name":"Department of Hematology, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"},{"name":"Department of Hematology, \u201cIon Chiricuta\u201d Clinical Cancer Center, 400015 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6769-1545","authenticated-orcid":false,"given":"Rare\u0219-Ionu\u021b","family":"\u0218tiufiuc","sequence":"additional","affiliation":[{"name":"MedFuture\u2014Research Center for Advanced Medicine, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"},{"name":"Department of Pharmaceutical Physics & Biophysics, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania"},{"name":"Nanotechnology Laboratory, TRANSCEND Research Center, Regional Institute of Oncology, 700483 Iasi, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,1,12]]},"reference":[{"key":"ref_1","unstructured":"(2023, November 20). Globocan Cancer Observatory. Available online: https:\/\/Gco.Iarc.Fr\/."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"209","DOI":"10.3322\/caac.21660","article-title":"Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries","volume":"71","author":"Sung","year":"2021","journal-title":"CA Cancer J. Clin."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1158\/2159-8290.CD-14-0943","article-title":"Synthetic Lethal Approaches Exploiting DNA Damage in Aggressive Myeloma","volume":"5","author":"Cottini","year":"2015","journal-title":"Cancer Discov."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Botrugno, O.A., and Tonon, G. (2021). Genomic Instability and Replicative Stress in Multiple Myeloma: The Final Curtain?. Cancers, 14.","DOI":"10.3390\/cancers14010025"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Baylin, S.B., and Jones, P.A. (2016). Epigenetic Determinants of Cancer. Cold Spring Harb. Perspect. Biol., 8.","DOI":"10.1101\/cshperspect.a019505"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"397","DOI":"10.2217\/bmm.09.26","article-title":"Epigenetic Mechanisms in Cancer","volume":"3","author":"Banerjee","year":"2009","journal-title":"Biomark. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"4","DOI":"10.21037\/lcm-21-59","article-title":"Epigenetic Mechanisms in Cancer","volume":"5","author":"Sendemir","year":"2022","journal-title":"Longhua Chin. Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/0027-5107(93)90052-H","article-title":"DNA Methylation and Mutation","volume":"285","author":"Holliday","year":"1993","journal-title":"Mutat. Res. Fundam. Mol. Mech. Mutagen."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"4632","DOI":"10.1200\/JCO.2004.07.151","article-title":"DNA Methylation and Cancer","volume":"22","author":"Das","year":"2004","journal-title":"J. Clin. Oncol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1093\/hmg\/10.7.687","article-title":"Aberrant Patterns of DNA Methylation, Chromatin Formation and Gene Expression in Cancer","volume":"10","author":"Baylin","year":"2001","journal-title":"Hum. Mol. Genet."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/301089a0","article-title":"Hypomethylation Distinguishes Genes of Some Human Cancers from Their Normal Counterparts","volume":"301","author":"Feinberg","year":"1983","journal-title":"Nature"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/nrc1799","article-title":"Epigenetic Gene Silencing in Cancer\u2014A Mechanism for Early Oncogenic Pathway Addiction?","volume":"6","author":"Baylin","year":"2006","journal-title":"Nat. Rev. Cancer"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"3940","DOI":"10.1073\/pnas.96.7.3940","article-title":"Transient Excess of MYC Activity Can Elicit Genomic Instability and Tumorigenesis","volume":"96","author":"Felsher","year":"1999","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"5124","DOI":"10.1073\/pnas.91.11.5124","article-title":"The Human Ha-Ras Oncogene Induces Genomic Instability in Murine Fibroblasts within One Cell Cycle","volume":"91","author":"Denko","year":"1994","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_15","unstructured":"Jin, B., and Robertson, K.D. (2013). Epigenetic Alterations in Oncogenesis, Springer."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Saitoh, T., and Oda, T. (2021). DNA Damage Response in Multiple Myeloma: The Role of the Tumor Microenvironment. Cancers, 13.","DOI":"10.3390\/cancers13030504"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Petrilla, C., Galloway, J., Kudalkar, R., Ismael, A., and Cottini, F. (2023). Understanding DNA Damage Response and DNA Repair in Multiple Myeloma. Cancers, 15.","DOI":"10.3390\/cancers15164155"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Mereu, E., Abbo, D., Paradzik, T., Cumerlato, M., Bandini, C., Labrador, M., Maccagno, M., Ronchetti, D., Manicardi, V., and Neri, A. (2023). Euchromatic Histone Lysine Methyltransferase 2 Inhibition Enhances Carfilzomib Sensitivity and Overcomes Drug Resistance in Multiple Myeloma Cell Lines. Cancers, 15.","DOI":"10.3390\/cancers15082199"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/1556-276X-8-47","article-title":"SERS-Active Silver Colloids Prepared by Reduction of Silver Nitrate with Short-Chain Polyethylene Glycol","volume":"8","author":"Stiufiuc","year":"2013","journal-title":"Nanoscale Res. Lett."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1126\/science.275.5303.1102","article-title":"Probing Single Molecules and Single Nanoparticles by Surface-Enhanced Raman Scattering","volume":"275","author":"Nie","year":"1997","journal-title":"Science"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1103\/PhysRevLett.78.1667","article-title":"Single Molecule Detection Using Surface-Enhanced Raman Scattering (SERS)","volume":"78","author":"Kneipp","year":"1997","journal-title":"Phys. Rev. Lett."},{"key":"ref_22","first-page":"557","article-title":"Surface-Enhanced Raman Spectroscopy Using Metallic Nanostructures","volume":"17","year":"1998","journal-title":"TrAC Trends Anal. Chem."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Bor\u0219a, R.-M., Toma, V., Onaciu, A., Moldovan, C.-S., M\u0103rginean, R., Cenariu, D., \u0218tiufiuc, G.-F., Dinu, C.-M., Bran, S., and Opri\u0219, H.-O. (2023). Developing New Diagnostic Tools Based on SERS Analysis of Filtered Salivary Samples for Oral Cancer Detection. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms241512125"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Faur, C.I., Dinu, C., Toma, V., Jurj, A., M\u0103rginean, R., Onaciu, A., Roman, R.C., Culic, C., Chiril\u0103, M., and Rotar, H. (2023). A New Detection Method of Oral and Oropharyngeal Squamous Cell Carcinoma Based on Multivariate Analysis of Surface Enhanced Raman Spectra of Salivary Exosomes. J. Pers. Med., 13.","DOI":"10.3390\/jpm13050762"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Munteanu, V.C., Munteanu, R.A., Gulei, D., M\u0103rginean, R., Schi\u021bcu, V.H., Onaciu, A., Toma, V., \u0218tiufiuc, G.F., Coman, I., and \u0218tiufiuc, R.I. (2022). New Insights into the Multivariate Analysis of SER Spectra Collected on Blood Samples for Prostate Cancer Detection: Towards a Better Understanding of the Role Played by Different Biomolecules on Cancer Screening: A Preliminary Study. Cancers, 14.","DOI":"10.3390\/cancers14133227"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"5723","DOI":"10.1021\/jp027460u","article-title":"A New Method for Fast Preparation of Highly Surface-Enhanced Raman Scattering (SERS) Active Silver Colloids at Room Temperature by Reduction of Silver Nitrate with Hydroxylamine Hydrochloride","volume":"107","author":"Leopold","year":"2003","journal-title":"J. Phys. Chem. B"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Moisoiu, V., Socaciu, A., Stefancu, A., Iancu, S., Boros, I., Alecsa, C., Rachieriu, C., Chiorean, A., Eniu, D., and Leopold, N. (2019). Breast Cancer Diagnosis by Surface-Enhanced Raman Scattering (SERS) of Urine. Appl. Sci., 9.","DOI":"10.3390\/app9040806"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"\u0218tiufiuc, G.F., Toma, V., Buse, M., M\u0103rginean, R., Morar-Bolba, G., Culic, B., Tetean, R., Leopold, N., Pavel, I., and Lucaciu, C.M. (2020). Solid Plasmonic Substrates for Breast Cancer Detection by Means of SERS Analysis of Blood Plasma. Nanomaterials, 10.","DOI":"10.3390\/nano10061212"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Safar, W., Azziz, A., Edely, M., and Lamy de la Chapelle, M. (2023). Conventional Raman, SERS and TERS Studies of DNA Compounds. Chemosensors, 11.","DOI":"10.3390\/chemosensors11070399"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1002\/jrs.1734","article-title":"Reference Database of Raman Spectra of Biological Molecules","volume":"38","author":"Vandenabeele","year":"2007","journal-title":"J. Raman Spectrosc."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/S0924-2031(99)00003-X","article-title":"Surface Enhanced Vibrational Spectra of Thymine","volume":"19","author":"Aroca","year":"1999","journal-title":"Vib. Spectrosc."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1002\/jrs.1250170311","article-title":"Surface-enhanced Raman Spectroscopy of DNA Bases","volume":"17","author":"Otto","year":"1986","journal-title":"J. Raman Spectrosc."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1002\/bip.360230206","article-title":"Characterization of DNA Structures by Laser Raman Spectroscopy","volume":"23","author":"Prescott","year":"1984","journal-title":"Biopolymers"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"4909","DOI":"10.1039\/C7CS00809K","article-title":"Direct Surface-Enhanced Raman Scattering (SERS) Spectroscopy of Nucleic Acids: From Fundamental Studies to Real-Life Applications","volume":"47","author":"Guerrini","year":"2018","journal-title":"Chem. Soc. Rev."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"5523","DOI":"10.1021\/ja800023j","article-title":"Surface-Enhanced Raman Spectroscopy of DNA","volume":"130","author":"Barhoumi","year":"2008","journal-title":"J. Am. Chem. Soc."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"7907","DOI":"10.1007\/s00216-019-02213-2","article-title":"SERS Assessment of the Cancer-Specific Methylation Pattern of Genomic DNA: Towards the Detection of Acute Myeloid Leukemia in Patients Undergoing Hematopoietic Stem Cell Transplantation","volume":"411","author":"Moisoiu","year":"2019","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1038\/ng.3291","article-title":"Whole-Genome Fingerprint of the DNA Methylome during Human B Cell Differentiation","volume":"47","author":"Kulis","year":"2015","journal-title":"Nat. Genet."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1182\/blood-2010-04-279539","article-title":"Aberrant Global Methylation Patterns Affect the Molecular Pathogenesis and Prognosis of Multiple Myeloma","volume":"117","author":"Walker","year":"2011","journal-title":"Blood"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Pyrak, E., Krajczewski, J., Kowalik, A., Kudelski, A., and Jaworska, A. (2019). Surface Enhanced Raman Spectroscopy for DNA Biosensors\u2014How Far Are We?. Molecules, 24.","DOI":"10.3390\/molecules24244423"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Chen, C., Liu, W., Tian, S., and Hong, T. (2019). Novel Surface-Enhanced Raman Spectroscopy Techniques for DNA, Protein and Drug Detection. Sensors, 19.","DOI":"10.3390\/s19071712"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Onaciu, A., Toma, V., Moldovan, C., \u021aigu, A.B., Cenariu, D., Culic, C., Bor\u0219a, R.M., David, L., \u0218tiufiuc, G.F., and Tetean, R. (2022). Nanoscale Investigation of DNA Demethylation in Leukemia Cells by Means of Ultrasensitive Vibrational Spectroscopy. Sensors, 23.","DOI":"10.3390\/s23010346"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1158\/1940-6207.CAPR-15-0349","article-title":"DNA Hypomethylation Contributes to Genomic Instability and Intestinal Cancer Initiation","volume":"9","author":"Sheaffer","year":"2016","journal-title":"Cancer Prev. Res."},{"key":"ref_43","unstructured":"Zhou, D., and Robertson, K.D. (2016). Genome Stability, Elsevier."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"76","DOI":"10.3389\/fgene.2017.00076","article-title":"DNA Methylation, Nuclear Organization, and Cancer","volume":"8","author":"Madakashira","year":"2017","journal-title":"Front. Genet."}],"container-title":["Biosensors"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6374\/14\/1\/41\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T13:45:51Z","timestamp":1760103951000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6374\/14\/1\/41"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,12]]},"references-count":44,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,1]]}},"alternative-id":["bios14010041"],"URL":"https:\/\/doi.org\/10.3390\/bios14010041","relation":{},"ISSN":["2079-6374"],"issn-type":[{"value":"2079-6374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,1,12]]}}}