Label-free surface-enhanced Raman spectroscopy detection of DNA with single-base sensitivity.

Direct, label-free detection of unmodified DNA is a great challenge for DNA analyses. Surface-enhanced Raman spectroscopy (SERS) is a promising tool for DNA analyses by providing intrinsic chemical information with a high sensitivity. To address the irreproducibility in SERS analysis that hampers reliable DNA detection, we used iodide-modified Ag nanoparticles to obtain highly reproducible SERS signals of single- and double-strand DNA in aqueous solutions close to physiological conditions. The phosphate backbone signal was used as an internal standard to calibrate the absolute signal of each base for a more reliable determination of the DNA structure, which has not been achieved before. Clear identification of DNA with single-base sensitivity and the observation of a hybridization event have been demonstrated.

[1]  Ling-ling Wu,et al.  SERS studies of self-assembled DNA monolayer - characterization of adsorption orientation of oligonucleotide probes and their hybridized helices on gold substrate , 2002 .

[2]  Marie Allen,et al.  A DNA microarray system for forensic SNP analysis. , 2005, Forensic science international.

[3]  W. Xie,et al.  Medical applications of surface-enhanced Raman scattering. , 2013, Physical chemistry chemical physics : PCCP.

[4]  Volker Deckert,et al.  Tip-enhanced Raman spectroscopy of single RNA strands: towards a novel direct-sequencing method. , 2008, Angewandte Chemie.

[5]  V. Bloomfield,et al.  Dependence of the Raman signature of genomic B-DNA on nucleotide base sequence. , 1999, Biopolymers.

[6]  A. Kalkan,et al.  Surface-enhanced Raman scattering captures conformational changes of single photoactive yellow protein molecules under photoexcitation. , 2010, Journal of the American Chemical Society.

[7]  Victor Guallar,et al.  Direct observation of single DNA structural alterations at low forces with surface-enhanced Raman scattering. , 2013, Biophysical journal.

[8]  P. Bartlett,et al.  A label-free, electrochemical SERS-based assay for detection of DNA hybridization and discrimination of mutations. , 2012, Journal of the American Chemical Society.

[9]  R. Dluhy,et al.  Removal of Surface Contamination and Self-Assembled Monolayers (SAMs) from Silver (Ag) Nanorod Substrates by Plasma Cleaning with Argon , 2011, Applied spectroscopy.

[10]  M. Diem,et al.  Spectroscopy , 2007, Acta Neuropsychiatrica.

[11]  Kishan Dholakia,et al.  Early detection of cervical neoplasia by Raman spectroscopy , 2007, International journal of cancer.

[12]  Evanthia Papadopoulou,et al.  Label-free detection of nanomolar unmodified single- and double-stranded DNA by using surface-enhanced Raman spectroscopy on Ag and Au colloids. , 2012, Chemistry.

[13]  Martin Moskovits,et al.  Surface-enhanced Raman spectroscopy for DNA detection by nanoparticle assembly onto smooth metal films. , 2007, Journal of the American Chemical Society.

[14]  Ai-hui Liang,et al.  Functional Nucleic Acid Nanoparticle-Based Resonance Scattering Spectral Probe , 2013, Plasmonics.

[15]  Zhuyuan Wang,et al.  Colorimetry and SERS dual-mode detection of telomerase activity: combining rapid screening with high sensitivity. , 2014, Nanoscale.

[16]  P. Bartlett,et al.  SERS-melting: a new method for discriminating mutations in DNA sequences. , 2008, Journal of the American Chemical Society.

[17]  W. Smith,et al.  Quantitative simultaneous multianalyte detection of DNA by dual-wavelength surface-enhanced resonance Raman scattering. , 2007, Angewandte Chemie.

[18]  Cheng Zong,et al.  Label-free detection of native proteins by surface-enhanced Raman spectroscopy using iodide-modified nanoparticles. , 2014, Analytical chemistry.

[19]  C. Mirkin,et al.  Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. , 2002, Science.

[20]  Jian-Feng Li,et al.  Electrochemical surface-enhanced Raman spectroscopy of nanostructures. , 2008, Chemical Society reviews.

[21]  M. Recanatini,et al.  Revealing DNA interactions with exogenous agents by surface-enhanced Raman scattering. , 2015, Journal of the American Chemical Society.

[22]  Duncan Graham,et al.  Surface‐Enhanced Resonance Raman Scattering as a Novel Method of DNA Discrimination , 2000 .

[23]  Evanthia Papadopoulou,et al.  Label-Free Detection of Single-Base Mismatches in DNA by Surface-Enhanced Raman Spectroscopy , 2011, Angewandte Chemie.

[24]  Yiping Zhao,et al.  Label-free detection of micro-RNA hybridization using surface-enhanced Raman spectroscopy and least-squares analysis. , 2012, Journal of the American Chemical Society.

[25]  H. P. Lu,et al.  Probing ground-state single-electron self-exchange across a molecule-metal interface. , 2011, Journal of the American Chemical Society.

[26]  Duncan Graham,et al.  Evaluation of surface-enhanced resonance Raman scattering for quantitative DNA analysis. , 2004, Analytical chemistry.

[27]  Max Diem,et al.  Raman and Infrared Microspectral Imaging of Mitotic Cells , 2006, Applied spectroscopy.

[28]  Sajanlal R. Panikkanvalappil,et al.  Surface-enhanced Raman spectroscopy for real-time monitoring of reactive oxygen species-induced DNA damage and its prevention by platinum nanoparticles. , 2013, ACS nano.

[29]  Janina Kneipp,et al.  In vivo molecular probing of cellular compartments with gold nanoparticles and nanoaggregates. , 2006, Nano letters.

[30]  S. Bell,et al.  Surface-enhanced Raman spectroscopy (SERS) for sub-micromolar detection of DNA/RNA mononucleotides. , 2006, Journal of the American Chemical Society.

[31]  Richard P Van Duyne,et al.  Transcutaneous glucose sensing by surface-enhanced spatially offset Raman spectroscopy in a rat model. , 2010, Analytical chemistry.

[32]  R. Álvarez-Puebla,et al.  Direct surface-enhanced Raman scattering analysis of DNA duplexes. , 2015, Angewandte Chemie.

[33]  Tuan Vo-Dinh,et al.  Label-free DNA biosensor based on SERS Molecular Sentinel on Nanowave chip. , 2013, Analytical chemistry.

[34]  S. Bell,et al.  DNA reorientation on Au nanoparticles: label-free detection of hybridization by surface enhanced Raman spectroscopy. , 2011, Chemical communications.

[35]  Mostafa A. El-Sayed,et al.  Probing the unique dehydration-induced structural modifications in cancer cell DNA using surface enhanced Raman spectroscopy. , 2013, Journal of the American Chemical Society.

[36]  A. Kasarskis,et al.  A window into third-generation sequencing. , 2010, Human molecular genetics.

[37]  Chun-yang Zhang,et al.  Single base extension reaction-based surface enhanced Raman spectroscopy for DNA methylation assay. , 2012, Biosensors & bioelectronics.

[38]  A. Haes,et al.  Purification implications on SERS activity of silica coated gold nanospheres. , 2012, Analytical chemistry.

[39]  Duncan Graham,et al.  Separation free DNA detection using surface enhanced Raman scattering. , 2011, Analytical chemistry.

[40]  Zachary D. Schultz,et al.  Advances in biomedical Raman microscopy. , 2014, Analytical chemistry.

[41]  J. Duguid,et al.  DNA melting investigated by differential scanning calorimetry and Raman spectroscopy. , 1996, Biophysical journal.

[42]  D. A. Stuart,et al.  In vivo glucose measurement by surface-enhanced Raman spectroscopy. , 2006, Analytical chemistry.

[43]  J. Nam,et al.  Single-molecule and single-particle-based correlation studies between localized surface plasmons of dimeric nanostructures with ~1 nm gap and surface-enhanced Raman scattering. , 2013, Nano letters.

[44]  Naomi J. Halas,et al.  Label-free detection of DNA hybridization using surface enhanced Raman spectroscopy. , 2010, Journal of the American Chemical Society.

[45]  H. Ju,et al.  Label-free surface-enhanced Raman spectroscopy for sensitive DNA detection by DNA-mediated silver nanoparticle growth. , 2013, Analytical chemistry.

[46]  N. Halas,et al.  Surface-enhanced Raman spectroscopy of DNA. , 2008, Journal of the American Chemical Society.