| Title: |
Optimization of Single-Base-Pair Mismatch Discrimination in |
| Authors: |
Oligonucleotide Microarrays; David A |
| Contributors: |
The Pennsylvania State University CiteSeerX Archives |
| Source: |
http://www.luc.edu/biology/kelly/aem_03.pdf. |
| Publication Year: |
2002 |
| Collection: |
CiteSeerX |
| Description: |
The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting pro-files). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphy-lococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray. DNA microarray technology provides parallel nucleic acid hybridizations for a large number of immobilized oligonucle-otides or larger DNA fragments on a small surface area (21). In clinical and environmental microbiology, this technology |
| Document Type: |
text |
| File Description: |
application/pdf |
| Language: |
English |
| Relation: |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.491.1776; http://www.luc.edu/biology/kelly/aem_03.pdf |
| Availability: |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.491.1776; http://www.luc.edu/biology/kelly/aem_03.pdf |
| Rights: |
Metadata may be used without restrictions as long as the oai identifier remains attached to it. |
| Accession Number: |
edsbas.6E1B3278 |
| Database: |
BASE |