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Biomedical subjects

N R Isola

Publications and source records attributed to N R Isola.

17 recordsLinked to original sources

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.

Breast Neoplasms↗

Matrix-assisted laser desorption/ionization detection of polymerase chain reaction products by utilizing the 5'-3' exonuclease activity of Thermus aquaticus DNA polymerase.

The 5'-3' exonuclease activity of DNA polymerase was utilized in the polymerase chain reaction system to generate a specific signal concomitant with amplification. These signals were detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). This method obviates the need to perform extensive DNA purification of reaction products that is often necessary for detecting larger DNA molecules by mass spectrometry. Oligonucleotides complementary to the internal region of the amplicon are degraded by the 5'-3' exonuclease activity and the degradation products are analyzed by MALDI mass spectrometry. We refer to this assay as the Exo-taq assay or probe degradation assay. This method should be amenable to automation.

DNA↗

Biotin-enhanced fragmentation for direct deoxyribonucleic 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 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.

Base Sequence↗

Laser desorption mass spectrometry for microbial DNA analysis.

Recently, we demonstrated that a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF MS) can be used to determine the molecular weight of polymerase chain reaction (PCR) products of intact 16S rRNA regions and to profile their restriction digests. This is the first time that MALDI-TOF MS with ultraviolet (UV) photoionization has been used to analyze a PCR product of approximately 1600 nucleotides in length.

DNA, Bacterial↗

MALDI-TOF mass spectrometric method for detection of hybridized DNA oligomers.

Two new approaches for nucleic acid hybridizations by MALDI-TOF mass spectrometry are described. Hybridization using genomic DNA without polymerase chain reaction was demonstrated. Total genomic DNA of bacteriophages bound to charge-modified nylon membranes was identified by the hybridization of species-specific oligonucleotide probes. lambda-Phage DNA and M13 were used for the test with good success. Since MALDI-TOF mass spectrometry can be used to measure the molecular weights of different probes, mass spectrometry can be used for the detection of hybridizations with multiple probes. We demonstrate that multiple-probe hybridization can be resolved by mass spectrometry. Six probes with different mass tag were used for hybridization on a single spot. MALDI-TOF mass spectrometry was successfully used to measure these probes simultaneously. This provides a simple nonradioactive method for multiplex hybridization analysis. It has the potential to drastically increase the speed for microarray hybridization analysis in the future.

Bacteriophage M13↗

Nonresonant MALDI of oligonucleotides: mechanism of ion desorption.

Oligonucleotide ions have been detected using matrix-assisted laser desorption/ionization (MALDI) under nonresonant laser irradiation of the sample. When mass resolution was not limited by adduct attachment to the analyte ions, the nonresonant MALDI spectra demonstrated better resolution than the spectra acquired with resonant ultraviolet irradiation. We found that preparation of thin-film samples on absorbing substrate surfaces was critical for the success of NR-MALDI. The possible acoustic mechanisms of ion formation and desorption are discussed.

Oligonucleotides↗

Chemical cleavage sequencing of DNA using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

In this paper, we report for the first time use of laser desorption mass spectrometry for measurement of chemical cleavage sequencing products of DNA. In this method, the target DNA was labeled with biotin and subjected to chemical modification and cleavage according to the Maxam-Gilbert sequencing protocol. The biotin-containing fragments were captured by streptavidin-coated magnetic beads and separated from the other fragments. The captured fragments were released by hot ammonia treatment, and the released fragments were analyzed by mass spectrometry. Potential applications of this method in resolving sequence ambiguities and sequencing repeat sequences as well as in the analysis of DNA-protein interactions are discussed.

Amino Acid Sequence↗

Sequencing DNA using mass spectrometry for ladder detection.

Sequencing of DNA fragments of 130 and 200 bp using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for DNA ladder detection was demonstrated. With further improvement in mass resolution and detection sensitivity, mass spectrometry shows great promise for routine DNA sequencing in the future.

Bacteriophage lambda↗

Surface-enhanced Raman gene probe for HIV detection.

We report, for the first time, the use of surface-enhanced Raman (SERS)-active labels for primers used in polymerase chain reaction amplification of specific target DNA sequences. This method has the potential for combining the spectral selectivity and high sensitivity of the SERS technique with the inherent molecular specificity offered by DNA sequence hybridization. The effectiveness of the detection scheme is demonstrated using the gag gene sequence of the human immunodeficiency virus. The potential use of multiple probes for simultaneous detection of multiple biological targets is discussed.

Base 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.

Base Sequence↗

The variant mRNA isoform of human metastasis gene (CD44V) detected in the cell lines of human hepatocellular carcinoma.

The interaction of the cell surface receptor CD44 molecular with its ligands (addressin, extracellular matrix etc.,) plays an important role in fulfilling the lymphocyte homing and immune reaction. Recently alternatively spliced products of CD44 gene are found to be involved in tumor metastasis as well. Our report found that CD44 prototype RNA (CD44S) was present in all five tumor cell lines. Isoform CD44 RNA (CD44V) was recognized in three metastasized hepatocellular carcinoma cell lines, J5, HCC36, HEP3B. In addition, the J5 CD44 RNA isoform expressed two distinct transcripts which are of the same size as MDA-231 breast tumor cell line. The MDA-231 CD44 RNA variant (CD44V) has been confirmed to contain metastasis domain 4 and 5. It is implicated that the alternative RNA splicing may also play a major role in hepatocellular carcinoma metastasis.

Base Sequence↗

Members of the ALDH gene family are lens and corneal crystallins.

Many of the major lens proteins, known as crystallins, responsible for the structural integrity and functional utility of this visual tissue have been previously shown to be recruited proteins. This phenomena of a protein that is expressed and functions elsewhere acquiring a new function in another tissue has been termed 'gene sharing'. It is now becoming obvious that the cornea of vertebrates has similarly acquired proteins, and that at least one corneal protein, ALDH3 belongs to a gene family that has been previously identified as a lens crystallin. The recognition that both lens and corneal crystallins exist is a novel concept that has implications that involve the process by which multifunctional gene products have evolved. Members of the ALDH gene family function in both the cornea and lens as crystallins and the acquisition of multifunctionality by this gene family is unique. Based on our analysis we have deduced a supragene family relationship between the thiol protein esterases, aldehyde dehydrogenases, and the taxon-specific crystallins. Evolution of a complex organ such as the vertebrate eye is not a sequential and gradual process such as the Darwinian Giraffe's neck, since the eye can provide selective advantage only as a complete organ. Catastrophic theory proposes that the complex vertebrate eye with its lens, and focussing mechanism arose from the primitive eye spot which contained originally only the photoreceptor system by a one step event. In the evolution of the vertebrate eye it is evolutionarily plausible that several pre-existing proteins have been recruited to perform a structural role for this complex organ. It is also incumbent in evolutionary thought that any inherent enzymatic activity associated with this protein would be purely an incidental addition to the organ. However, the fact that most of these have pyridine nucleotide binding capacity, which is presumed important in giving protection from UV exposure, is noteworthy. Finally, to construct the vertebrate eye in one step from the existing visual pigment system such as the eyespot of unicellular organisms the following criteria would apparently be advantageous: (1) high water solubility; (2) transparency; and (3) common genetic regulatory elements (e.g. promoters/enhancers). Although it is an important observation that certain members of the aldehyde dehydrogenase gene family are present as structural proteins in the cornea and lens, it is not surprising that the phenomenon of gene sharing extends to another ocular tissue such as the cornea. In this context, it will be interesting to note if similar multifunctional gene products will be found as frequently in organs other than the eye.

Aldehyde Dehydrogenase↗

The complex CD44 transcriptional unit; alternative splicing of three internal exons generates the epithelial form of CD44.

We have utilized the polymerase chain reaction (PCR) to isolate a 3.5 kilobase pair (kb) genomic fragment that encodes the additional extracellular domain unique to the epithelial isoform of CD44 (CD44E). Nucleotide sequence was determined for this complete region and sequence comparison to our previously determined CD44R1 and CD44R2 cDNA sequences revealed the R region to be comprised of three exons of 102 bp, 90 bp, and 204 bp. Northern blot analysis of CD44 expressing cell lines confirmed the presence of CD44R1 transcripts and indicates that the epithelial domain may be inserted through alternative splicing into all CD44 transcript classes. Southern blot analysis of the CD44E genomic fragments is consistent with a single copy per human haploid genome. The data presented here further supports our model of the human CD44 transcriptional unit as a single gene complex that utilizes an invariant 5' initiation site, alternative internal and 3' end splicing, and multiple poly (A) sites to generate through RNA processing a diverse number of human CD44 isoforms.

Amino Acid Sequence↗

Bovine corneal protein 54K (BCP54) is a homologue of the tumor-associated (class 3) rat aldehyde dehydrogenase (RATALD).

Amino acid (aa) sequence data from Staphylococcus areas V8 protease-digested bovine corneal 54-kDa protein (BCP54) fragments were utilized to derive mixed oligodeoxyribonucleotide (oligo) primers complementary to the reverse translation products of these sequences. These degenerate oligo primers were used to prime the amplification of BCP54 sequence from bovine corneal epithelial cell cDNA. The cDNA probe generated by this mixed oligo-primed amplification of cDNA was cloned and dideoxy-sequenced. A search of the GenBank database (version 63.0) revealed extensive sequence similarity to the cDNA encoding tumor-associated rat liver (class 3) aldehyde dehydrogenase (RATALD). Nucleotide (nt) and aa sequence alignment of the BCP54 translation product reveals it is 78% and 84% homologous with RATALD at the nt and aa levels, respectively. Conservation of aa sequence elements common to the aldehyde dehydrogenase family thought to be of structural/functional significance is further substantiated by this analysis. Included in the discussion is the likelihood that gene sharing (genes encoding metabolic enzymes and other stable proteins) may extend to the cornea.

Aldehyde Dehydrogenase↗

Screening recombinant DNA libraries: a rapid and efficient method for isolating cDNA clones utilizing the PCR.

We describe an expeditious method for the isolation of cDNA clones utilizing PCR-based amplification of target sequences from cDNA libraries. This method is rapid, less labor-intensive and inexpensive when compared with screening libraries with radiolabeled probes. This method can be applied to isolate multiple members of a protein family as well as homologous genes in different species by designing appropriate primers to amplify the most conserved regions. Utilizing this method, a novel reticulocyte CD44 transcript was isolated.

Bacteriophage lambda↗

Banded polytene chromosomes in developing endosperm of pearl millet.

The occurrence of polyteny in the endosperm of field-grown plants as well as cultured endosperms of variety Vg272 of pearl millet (Pennisetum glaucum (L.) R.Br.) is recorded. There is a pronounced banded structure of these chromosomes similar to the ones observed in Dipteran salivary glands. Polyteny under physiologically controlled conditions also seems feasible in pearl millet.

Chromosome Banding↗

Discrimination between tumour and normal cells by staining with 3,4,5,6,16,17-hexadehydro-16-(methoxycarbonyl)-19 alpha-methyl-20 alpha-oxayohimbanium: the uracil ring as a target for the specific interaction between RNA(s) and the fluorescent probe.

3,4,5,6,16,17-Hexadehydro-16-(methoxycarbonyl)-19 alpha-methyl-20 alpha-oxayohimbanium (Alstonine) is a fluorescent alcaloid which has been known to stain tumour cells more efficiently than normal ones. In this paper the spectral properties of Alstonine were first investigated and its capability for preferential staining of tumour cells verified in culture using SK-OV-3 cells as tumour cells and Mouse 3T3 fibroblasts as controls. Then interactions between Alstonine and biological macromolecules were investigated to provide the rationale for preferential labelling. Molecular filtration techniques have demonstrated that binding occurs only with RNA molecules. Similar experiments were performed with different isopolynucleotides to find an explanation for that specificity. They provide evidence that binding occurs only in the presence of a uridyl ring. This is consistent with the specificity of the linkage to RNA. As the linkage of Alstonine with RNA did not induce any shift or obvious change in the intensity of its fluorescence spectrum, it is concluded that the binding might involve the side chain of the fluorescent compound.

3T3 Cells↗