Narayana R. Isola

Synthesis and characterization of SERS gene probe for BRCA-1 (breast cancer)

A protocol for binding cresyl fast violet (CFV), a SERS-active dye (label) containing an aromatic amino group with a modified oligomer having a carboxy derivatized thymidine moiety using carbodiimide coupling has been achieved for the first time. Covalent coupling between CFV and the oligomer has been confirmed by mass spectral analysis of the labeled oligomer. The fluorescence, SERS and absorption characteristics of the labeled product have been evaluated. The chosen oligomer contains a BRCA-1 (breast cancer) sequence, and hence has the potential for being used as a gene probe to identify BRCA-1 gene. It has high potential for being used in polymerase chain reaction (PCR) amplification, as has been performed with labeled oligonucleotide for the HIV sequence.

Matrix-assisted Laser Desorption/Ionization for Sequencing Single-stranded and Double-stranded DNA

The DNA sequence of a single-stranded and double-stranded template was determined. The templates were sequenced using the chain termination method and cycle sequencing method and detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The sequencing products were analyzed successfully without the laborious and expensive methods for removal of the template. Direct sequencing of the double-stranded template was achieved with minimal post-reaction purifications, which could be extremely important for mutation analysis and clinical diagnosis. A systematic study of the mechanisms and kinetics of sequencing reactions was also performed. The details of this analysis and directions for future improvements of the quality of sequencing are presented.

Differentiation of Normal and Neoplastic Cells by Synchronous Fluorescence: Rat Liver Epithelial and Rat Hepatoma Cell Models

In the present study, conventional and synchronous luminescence (SL) were utilized to investigate spectral differences in normal and neoplastic cells. The synchronous fluorescence (SF) method involves scanning simultaneously both emission and excitation wavelengths while keeping a constant wavelength interval between them. This SF procedure simplifies the emission spectrum and provides for greater selectivity and is used to detect subtle differences in the fluorescence emission of the biochemical species of cells from rat tissues. A difference between the fluorescent spectra of the normal rat liver epithelial (RLE) and hepatoma cell lines were detected using synchronous fluorescence. The potential use of SF as a screening tool for cancer diagnosis is discussed.

Development of a multiarray biosensor for DNA diagnostics

Abstract This work involves the development and evaluation of a multiarray biosensor for DNA diagnostics. The evaluation of various system components developed for the biosensor is discussed. The DNA probes labeled with visible and near infrared (NIR) dyes are evaluated. The detection system uses a two-dimensional charge-coupled device (CCD). Examples of application of gene probes in DNA hybridization experiments and in biomedical diagnosis (detection of the p53 cancer gene) are presented to illustrate the usefulness and potential of the biosensor device.

Development of a DNA biochip for gene diagnosis

We describe a biochip based on an integrated circuit photodiode array for use in medical diagnostics. The biochip is a self-contained device which has photosensors, amplifiers, discriminators and logic circuitry on board. The development and evaluation of various microchip system components of the genosensor are discussed. The performance of the DNA biochip device is illustrated with fluorescence detection of DNA probes specific to gene fragments of the human immuno-deficiency virus 1 system. The usefulness and potential to the DNA biochip technology for rapid and cost- effective medical diagnostics is discussed.

Biotin-enhanced fragmentation for direct deoxyribo nucleic acid sequencing using matrix-assisted laser desorption/ionization mass spectrometry

Fragmentation of synthetic oligonucleotides under the influence of biotin was investigated using 3-hydroxypicolinic acid (3-HPA) as a matrix-assisted laser desorption/ionization (MALDI) matrix. Addition of biotin into the sample enhanced fragmentation of the oligonucleotide between bases. However, when the biotin was tagged to the 5′-terminus of the oligonucleotide, enhancements were observed not only in desorption/ionization efficiency but also in the fragmentation of molecular ions. The fact that the protonation/deprotonation process occurs on the tagged biotin is a possible reason for the enhancement in desorption/ionization. Site-specific backbone cleavage fragmentation patterns were observed. The sequences of oligonucleotides can be obtained from their fragment ions. The direct sequencing of a 5′-biotin-tagged 25-mer is demonstrated.

SERS gene probe for DNA diagnostics

We describe the development of a surface-enhanced Raman scattering gene (SERGen) probe technology for rapid screening for diseases and pathogens through DNA hybridization assays. The technology combines the use of gene probes labeled with SERS-active markers, and nanostructured metallic platforms for inducing the SERS effect. As a result, SERGen-based methods can offer the spectral selectivity and sensitivity of SERS as well as the molecular specificity of DNA sequence hybridization. Furthermore, these new probe s preclude the use of radioactive labels. As illustrated herein, SERGen probes have been used as primers in polymerase chain reaction (PCR) amplifications of specific DNA sequences, hence further boosting the sensitivity of the technology. We also describe several approaches to developing SERS-active DNA assay platforms, addressing the challenges of making the SERGen technology accessible and practical for clinical settings. The usefulness of the SERGen approach has been demonstrated in the detection of HIV, BRCA1 breast cancer, and BAX genes. There is great potential for the use of numerous SERGen probes for multiplexed detection of multiple biological targets.

Alstonine as a potential fluorescent marker for tiny tumor detection and imaging

3,4,5,6,16,17-Hexadehydro-16-(methoxycarbolyl)-19(alpha) - methyl-20(alpha) -oxyohimbanium (alstonine) is a fluorescent alcaloid which is known to stain tumor cells more efficiently than normal. The interactions between alstonine and biological macromolecules were first investigated to provide the rationale for preferential labelling. Molecular filtration and spectrosfluorometric techniques with different macromolecules and isopolynucleotides have demonstrated that binding occurs only in the presence of uridyl rings. For the binding affect only the fluorescence intensity of alstonine it can be assumed that it involves only the side chain of the fluorescent compound. The capability for preferential staining was verified in culture using SK-OV-3 cells and rat hepatocarcinoma cells as tumor cells and Mouse fibroblasts or rat liver cells as controls. Techniques of image analysis have demonstrated the efficiency of cellular labelling even in aggregates of rat hepatocarcinoma. These experiments lead the way to the detection of tiny tumors developed on thin visceral walls, using a fiber optic device.

Development of gene-probe-based biosensors for environmental analysis

This work involves the design and development of species specific gene (DNA) probes designed to detect Pseudomonas species. A non radioactive detection system for DNA was designed to detect the presence of these microbes in environmental samples for biomonitoring applications. The details of the methodology and their applicability for various environmental analyses is discussed below.