Probing DNA hybridization efficiency and single base mismatch by X-ray photoelectron spectroscopy.

We demonstrated the use of X-ray photoelectron spectroscopy (XPS) to study DNA hybridization. Target DNA labeled with hexachloro-fluorescein (HEX) was hybridized to DNA arrays with four different probes. Each probe dot of the hybridized arrays was detected with XPS. The XPS Cl2p peak areas were found to decrease with an increase in mismatched bases in DNA probes. The Cl2p core-level peak area ratio of a probe perfectly matched to one, two and three base-mismatched probes accorded well with the results of conventional fluorescent imaging, which shows that XPS is a potential tool for analyzing DNA arrays. The DNA arrays' hybridization efficiency was assessed by the molar ratio of chlorine to phosphorus in a DNA strand, which was determined from the relevant XPS Cl2p and P2p core-level peak areas after hybridization. This could provide a new method to detect DNA hybridization efficiency.

Electrochemical detection of single a-g mismatch using biosensing surface based on gold nanoparticles.

The study of small drug molecules interacting with nucleic acids is an area of intense research that has particular relevance in our understanding of relative mechanism in chemotherapeutic applications and the association between genetics (including sequence variation) and drug response. In this contribution, we demonstrate how the sequence-specific binding of an anticancer drug Dacarbazine (DTIC) to single base (A-G) mismatch could be sensitively detected by combining electrochemical detection with biosensing surface based on gold nanoparticles.

Detection of p16 hypermethylation in gastric carcinomas using a seminested methylation-specific PCR.

Aberrant DNA methylation of a CpG site is among the earliest and most frequent alterations in various tumors including gastric carcinoma. The aim of this study is to detect tumor-associated aberrant hypermethylation of the p16 gene from 60 gastric tumor and corresponding normal tissues using a seminested methylation-specific PCR (MSP). The results indicated that hypermethylation of the p16 gene could be detected in 80% (48/60) of the gastric tumor samples from the first PCR. However, the frequency increased significantly to 86.7% (52/60) of the gastric tumor samples after the second PCR. These results show that this technique increases the sensitivity of detecting p16 hypermethylation from tumor samples. Furthermore, the aberrant methylation of p16 was observed in all of the stages, confirming that this epigenetic alteration is an early event during gastric carcinogenesis. Clinicopathologic parameters such as age, sex, and histological differentiation of GC were not significantly associated with the methylation status.

Microarray-based method for detecting methylation changes of p16(Ink4a) gene 5'-CpG islands in gastric carcinomas.

AIM: Aberrant DNA methylation of CpG site is among the earliest and most frequent alterations in cancer. Several studies suggest that aberrant methylation of the CpG sites of the tumor suppressor gene is closely associated with carcinogenesis. However, large-scale analysis of candidate genes has so far been hampered by the lack of high-throughput approach for analyzing DNA methylation. The aim of this study was to describe a microarray-based method for detecting changes of DNA methylation in cancer. METHODS: This method used bisulfite-modified DNA as a template for PCR amplification, resulting in conversion of unmethylated cytosine, but not methylated cytosine, into thymine within CpG islands of interest. Therefore, the amplified product might contain a pool of DNA fragments with altered nucleotide sequences due to differential methylation status. Nine sets of oligonucleotide probes were designed to fabricate a DNA microarray to detect the methylation changes of p16 gene CpG islands in gastric carcinomas. The results were further validated by methylation-specific PCR (MSP). RESULTS: The experimental results showed that the microarray assay could successfully detect methylation changes of p16 gene in 18 gastric tumor samples. Moreover, it could also potentially increase the frequency of detecting p16 methylation from tumor samples than MSP. CONCLUSION: Microarray assay could be applied as a useful tool for mapping methylation changes in multiple CpG loci and for generating epigenetic profiles in cancer.

Cell detection based on protein array using modified glass slides.

A protein array for cell detection was fabricated by spotting different antibodies on modified glass slides. Glass slides were modified to allow antibodies to be immobilized on it and to selectively bind antigens. Antibodies were specially selected with the cells to be detected as targets, which permitted target cells in samples to bind specifically to the array with little nonspecific binding. Results can be obtained by directly putting the samples onto the array for 1 h or a little longer to let the cells specifically interact with the antibodies. After washing the unbound samples away, images were observed with a microscope and captured with a CCD camera. The assessment of antibody-cell binding was evaluated by capturing red blood cells (RBCs) in human blood with blood group antibodies (anti-A and anti-B). Blood group antibodies were spotted on the modified glass slide and kept at 4<.deg> degrees C overnight for immobilization. Human blood samples diluted to different concentrations were used to examine the sensitivity and specificity of the method.