Surface enhanced Raman spectra of oligonucleotides induced by spermine

The label-free detection of oligonucleotides of 12–14 bases at a concentration of 10−7M (double helix) was achieved by using surface enhanced Raman scattering (SERS) and spermine as the aggregant of Ag sol. The wavenumbers of the produced SERS spectra of DNA are similar to those in the corresponding normal Raman spectra of free DNA, allowing the detailed assignment of the vibrational modes. The conformation of the adsorbed DNA, the adsorption geometry, and a molecular model of the interactions among DNA, spermine, and Ag nanoparticle are derived from the SERS spectra. The results show that the protonated amine groups of spermine interact with phosphodioxygens of DNA and N7s of dA and dG from the major groove. The protonated amines are also attracted to the negatively charged Ag surface and thus induce the adsorption of DNA on the metal surface. The DNA remains mostly in the B-conformation with a variation in the C5′O dihedral angle. DNA lies flat with the bases perpendicular to the metal surface. Copyright © 2006 John Wiley & Sons, Ltd.

[1]  L. Movileanu,et al.  Temperature dependence of the Raman spectrum of DNA. II. Raman signatures of premelting and melting transitions of poly(dA).poly(dT) and comparison with poly(dA-dT).poly(dA-dT). , 2002, Biopolymers.

[2]  A. H. Wang,et al.  Partial B-to-A DNA transition upon minor groove binding of protein Sac7d monitored by Raman spectroscopy. , 2004, Biochemistry.

[3]  Shuming Nie,et al.  Direct Observation of Size-Dependent Optical Enhancement in Single Metal Nanoparticles , 1998 .

[4]  Tuan Vo-Dinh,et al.  Surface-enhanced Raman scattering detection of the breast cancer susceptibility gene BRCA1 using a silver-coated microarray platform , 2002 .

[5]  R. Wartell,et al.  Characteristics and variations of B-type DNA conformations in solution: a quantitative analysis of Raman band intensities of eight DNAs. , 1986, Biochemistry.

[6]  S. Sánchez‐Cortés,et al.  Adsorption of polyethyleneimine on silver nanoparticles and its interaction with a plasmid DNA: a surface-enhanced Raman scattering study. , 2002, Biomacromolecules.

[7]  Bernhard Lendl,et al.  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 , 2003 .

[8]  G. A. Thomas,et al.  Flexibility of nucleic acid conformations. 1. Comparison of the intensities of the Raman-active backbone vibrations in double-helical nucleic acids and model double-helical dinucleotide crystals , 1983 .

[9]  J. C. Jones,et al.  Quantitative assessment of surface-enhanced resonance Raman scattering for the analysis of dyes on colloidal silver. , 1999, Analytical chemistry.

[10]  D. Fornasiero,et al.  Analysis of the visible absorption and SERS excitation spectra of silver sols , 1987 .

[11]  A. Rich,et al.  Raman spectra of single crystals of r(GCG)d(CGC) and d(CCCCGGGG) as models for A DNA, their structure transitions in aqueous solution, and comparison with double-helical poly(dG).poly(dC). , 1986, Biochemistry.

[12]  M. Albrecht,et al.  Plasma resonance enhancement of Raman scattering by pyridine adsorbed on silver or gold sol particles of size comparable to the excitation wavelength , 1979 .

[13]  H. Nürnberg,et al.  Surface-Enhanced Raman Scattering (SERS) Spectroscopy of Nucleic Acids , 1981 .

[14]  Catherine J. Murphy,et al.  Oligonucleotide Adsorption to Gold Nanoparticles: A Surface-Enhanced Raman Spectroscopy Study of Intrinsically Bent DNA , 2001 .

[15]  G. Thomas,et al.  Vibrational Analysis of Nucleic Acids. 2. Ab Initio Calculation of the Molecular Force Field and Normal Modes of Dimethyl Phosphate , 1995 .

[16]  W. Peticolas,et al.  Determination of the backbone structure of nucleic acids and nucleic acid oligomers by laser Raman scattering. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Duncan Graham,et al.  Selective detection of deoxyribonucleic acid at ultralow concentrations by SERRS , 1997 .

[18]  J. Benevides,et al.  Characterization of DNA structures by Raman spectroscopy: high-salt and low-salt forms of double helical poly(dG-dC) in H2O and D2O solutions and application to B, Z and A-DNA. , 1983, Nucleic acids research.

[19]  D. Meisel,et al.  Adsorption and surface-enhanced Raman of dyes on silver and gold sols , 1982 .

[20]  M. L. Nichols.  The Reduction of Silver Salts with Hydroxylamine , 1934 .

[21]  R. Clark,et al.  Spectroscopy of surfaces , 1988 .

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

[23]  Tuan Vo-Dinh,et al.  Cancer gene detection using surface-enhanced Raman scattering (SERS) , 2002 .

[24]  K. Ji,et al.  Surface-Enhanced Raman Spectra of Calf Thymus DNA Adsorbed on Concentrated Silver Colloid , 2005, Applied spectroscopy.

[25]  K. Kneipp,et al.  Surface enhanced Raman scattering (SERS) of nucleic acids adsrobed on colloidal silver particles , 1986 .

[26]  V. Bloomfield,et al.  Structural basis of polyamine-DNA recognition: spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy. , 2000, Nucleic acids research.

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

[28]  G. A. van der Marel,et al.  Crystal and solution structures of the B-DNA dodecamer d(CGCAAATTTGCG) probed by Raman spectroscopy: heterogeneity in the crystal structure does not persist in the solution structure. , 1988, Biochemistry.

[29]  Duncan Graham,et al.  Comparison of surface-enhanced resonance Raman scattering from unaggregated and aggregated nanoparticles. , 2004, Analytical chemistry.

[30]  G. Thomas,et al.  Characterization of DNA structures by laser Raman spectroscopy , 1984, Biopolymers.

[31]  Arieh Warshel,et al.  Extreme conformational flexibility of the furanose ring in DNA and RNA , 1978 .

[32]  孙世刚,et al.  Investigation of ordered ds-DNA monolayers on gold electrodes , 2002 .

[33]  I. Haworth,et al.  A molecular mechanics study of spermine complexation to DNA: a new model for sperm ine-poly(dG-dC) binding , 1991, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[34]  Guenter Schmid,et al.  Large clusters and colloids. Metals in the embryonic state , 1992 .

[35]  F. Sánchez-Jiménez,et al.  Fourier transform Raman study of the structural specificities on the interaction between DNA and biogenic polyamines. , 2001, Biophysical journal.

[36]  K. Kashiwagi,et al.  Polyamines: mysterious modulators of cellular functions. , 2000, Biochemical and biophysical research communications.

[37]  M. Moskovits.  Surface-enhanced spectroscopy , 1985 .

[38]  G. A. van der Marel,et al.  Effect of the G.T mismatch on backbone and sugar conformations of Z-DNA and B-DNA: analysis by Raman spectroscopy of crystal and solution structures of d(CGCGTG) and d(CGCGCG). , 1989, Biochemistry.

[39]  P. White,et al.  Characterization of the Surface of a Citrate-Reduced Colloid Optimized for Use as a Substrate for Surface-Enhanced Resonance Raman Scattering , 1995 .

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