Dongmao Zhang

Surface-Enhanced Raman Spectroscopy of DNA

We report a method for obtaining highly reproducible surface-enhanced Raman spectroscopy (SERS) of single and double-stranded thiolated DNA oligomers. Following a protocol that relaxes the DNA into an extended conformation, SERS spectra of DNA oligonucleotides are found to be extremely similar, strongly dominated by the Stokes modes of adenine. A spectral correlation function analysis useful for assessing reproducibility and for quantifying the highly complex changes corresponding to modifications in molecular conformation of the adsorbate molecules is introduced. This approach is used to monitor the interaction of DNA with cisplatin, a chemotherapy agent in widespread use.

Gold Nanoparticles Can Induce the Formation of Protein-based Aggregates at Physiological pH

Protein-nanoparticle interactions are of central importance in the biomedical applications of nanoparticles, as well as in the growing biosafety concerns of nanomaterials. We observe that gold nanoparticles initiate protein aggregation at physiological pH, resulting in the formation of extended, amorphous protein-nanoparticle assemblies, accompanied by large protein aggregates without embedded nanoparticles. Proteins at the Au nanoparticle surface are observed to be partially unfolded; these nanoparticle-induced misfolded proteins likely catalyze the observed aggregate formation and growth.

Removal of Molecular Adsorbates on Gold Nanoparticles Using Sodium Borohydride in Water

The mechanism of sodium borohydride removal of organothiols from gold nanoparticles (AuNPs) was studied using an experimental investigation and computational modeling. Organothiols and other AuNP surface adsorbates such as thiophene, adenine, rhodamine, small anions (Br(-) and I(-)), and a polymer (PVP, poly(N-vinylpyrrolidone)) can all be rapidly and completely removed from the AuNP surfaces. A computational study showed that hydride derived from sodium borohydride has a higher binding affinity to AuNPs than organothiols. Thus, it can displace organothiols and all the other adsorbates tested from AuNPs. Sodium borohydride may be used as a hazard-free, general-purpose detergent that should find utility in a variety of AuNP applications including catalysis, biosensing, surface enhanced Raman spectroscopy, and AuNP recycle and reuse.

Aromatic amino acids providing characteristic motifs in the Raman and SERS spectroscopy of peptides.

Raman and surface-enhanced Raman spectroscopies (SERS) are potentially important tools in the characterization of biomolecules such as proteins and DNA. In this work, SERS spectra of three cysteine-containing aromatic peptides: tryptophan-cysteine, tyrosine-cysteine, and phenylalanine-cysteine, bound to Au nanoshell substrates, were obtained, and compared to their respective normal Raman spectra. While the linewidths of the SERS peaks are significantly broadened (up to 70%), no significant spectral shifts (<6 cm (-1)) of the major Stokes modes were observed between the two modalities. We show that the Raman and SERS spectra of penetratin, a cell-penetrating peptide oligomer, can be comprised quite reliably from the spectra of its constituent aromatic amino acids except in the backbone regions where the spectral intensities are critically dependent on the length and conformations of the probed molecules. From this study we conclude that, together with protein backbone groups, aromatic amino acid residues provide the overwhelmingly dominant features in the Raman and SERS spectra of peptides and proteins when present. It follows that the Raman modes of these three small constructed peptides may likely apply to the assignment of Raman and SERS features in the spectra of other peptides and proteins.

Direct Optical Detection of Aptamer Conformational Changes Induced by Target Molecules

Aptamers are single-stranded DNA/RNA oligomers that fold into three-dimensional conformations in the presence of specific molecular targets. Surface-enhanced Raman spectroscopy (SERS) of thiol-bound DNA aptamer self-assembled monolayers on Au nanoshell surfaces provides a direct, label-free detection method for the interaction of DNA aptamers with target molecules. A spectral cross-correlation function, Gamma, is shown to be a useful metric to quantify complex changes in the SERS spectra resulting from conformational changes in the aptamer induced by target analytes. While the pristine, unexposed anti-PDGF (PDGF = platelet-derived growth factor) aptamer yields highly reproducible spectra with Gamma = 0.91 +/- 0.01, following incubation with PDGF, the reproducibility of the SERS spectra is dramatically reduced, yielding Gamma = 0.67 +/- 0.02. This approach also allows us to discriminate the response of a cocaine aptamer to its target from its weaker response to nonspecific analyte molecules.

Enhanced Chemical Classification of Raman Images in the Presence of Strong Fluorescence Interference

Raman spectra and spectral images containing severe fluorescence interference are analyzed by using a variety of correlation and classification algorithms, both before and after preprocessing with the use of the Savitzky-Golay second-derivative (SGSD) method (and other related methods). Spectral correlation coefficient, principal component, and minimum Euclidean distance analyses demonstrate superior suppression of background and noise interference in Raman spectra when using SGSD preprocessing. The tested spectra include fluorescence interference that is more intense than the Raman features of interest and also contains broad background peaks that vary in shape and intensity from sample to sample. The high chemical information content of the SGSD-processed Raman spectra is demonstrated by using quantitative comparisons of correlation coefficients in a series of synthetic Raman spectra with either different or identical large backgrounds. The practical utility of SGSD in chemical image classification is illustrated by using an experimental Raman image of sugar microcrystals on substrates with large interfering background signals. The functional equivalence of SGSD and other windowed preprocessing algorithms is discussed.

Enhanced Chemical Classification of Raman Images Using Multiresolution Wavelet Transformation

Multiresolution wavelet transformation (MWT) and block thresholding is used to effectively suppress both background and noise interference while minimally distorting Raman spectral features. The performance of MWT as a spectral pre-processing algorithm is demonstrated using both synthetic spectra and experimental hyper-spectral Raman images with large background and noise components. The results are quantified by comparing correlation coefficients of synthetic spectra with either the same or different backgrounds. The improved chemical imaging performance obtained using MWT is demonstrated by comparing principal component analysis (PCA) channel images and spectral angle mapping (SAM) classified images before and after MWT pre-processing.

Stripping of Cosmic Spike Spectral Artifacts Using a New Upper-Bound Spectrum Algorithm

A new upper-bound spectrum (UBS) method for removal of cosmic spike artifacts from spectra or images collected using a charge-coupled device (CCD) detector is proposed. This algorithm, which is shown to outperform previous methods, relies on an upper-bound spectrum, derived from scaled copies of consecutively collected spectra, which serves as a threshold for the detection of suspected cosmic spikes. Detected spikes are removed by replacement with the corresponding points in other spectra. Thus, unlike other commonly used methods, the UBS algorithm requires no smoothing or noise filtering and more reliably removes cosmic spikes of all magnitudes while introducing far less (if any) spectral distortion. The UBS method is tested using both synthetic and experimental (gypsum and gypsum/hematite mixture) spectra containing variable background (fluorescence), noise, and cosmic spike interference. The UBS method may in rare instances mistakenly identify spectral noise or photo-induced changes in band intensity (or shape) as cosmic spikes. However, as demonstrated through the use of both synthetic and experimental examples, such misidentifications produce little or no spectral distortion or artifacts in the resulting cosmic-spike-free output spectra.

Chemical Segregation and Reduction of Raman Background Interference Using Drop Coating Deposition

A new application of the recently described drop coating deposition Raman (DCDR) method facilitates the segregation and independent spectral characterization of mixture components. The quality of the normal (un-enhanced) Raman spectra are significantly improved as a result of reduced spectral interference from fluorescent impurities and buffer compounds. Fluorescence of commercial amino acid (O-phospho-L-serine) and protein (myoglobin) samples is reduced by over an order of magnitude using DCDR, more effectively than prolonged photo-bleaching. Furthermore, DCDR is used to obtain high-quality Raman spectra of proteins, lysozyme, and insulin, derived from solutions with up to 1000-fold excess buffer concentration. Possible thermodynamic and kinetic contributions to the observed segregation phenomena are discussed.

Ratiometric Surface Enhanced Raman Quantification of Ligand Adsorption onto a Gold Nanoparticle

Surface modification is essential in biomedical applications and nanotechnological developments. We report a novel method using surface-enhanced Raman spectroscopy (SERS) for quantifying ligand adsorption onto gold nanoparticles (AuNPs). After centrifugal or settlement removal of the AuNPs-ligand complex, the amount of unbound ligand in the supernatant was determined ratiometrically with an isotope-encoded SERS reference method where known amounts of isotope-substituted ligand were added to the supernatant as an internal reference. Not only is this ratiometric method robust and accurate but it is also very easy to perform. Using this technique, the binding constant and packing density of the model ligand mercaptobenzimidazole (MBI) on a AuNP was determined for the very first time.