Effect of Oligonucleotide Truncation on Single-nucleotide Distinction by Solid Phase Hybridization
Document identifier: oai:dalea.du.se:2297
Publication year: 2002Abstract: Oligonucleotide microarrays are used to analyze target sequences on the basis of differences in hybridization stability between matched and mismatched probe-target duplexes. DNA microarray manufacture via photolithographic synthesis generates a minority of full-length oligonucleotide probes along with a series of 5'-truncated contaminants. In a model experiment, we now investigate the effect of truncated oligonucleotides on the ability to distinguish target sequence variants that differ in a single nucleotide position. A series of oligonucleotides, mixed in proportions simulating stepwise synthetic yields of between 82 and 100%, were bound to a solid support and allowed to hybridize to a target molecule. The extent of hybridization was monitored over a range of temperatures via the fluorescence of a double-strand-specific dye. The discriminatory power of pure oligonucleotide probes was found to be significantly greater than that of a population of truncated probes, but only over a limited temperature interval. We conclude that at optimal temperatures greater oligonucleotide quality can improve the performance of oligonucleotide hybridization microarrays.
Authors
Magnus Jobs
Högskolan Dalarna; Medicinsk vetenskap
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identifier: oai:dalea.du.se:2297
datestamp: 2021-04-15T12:55:16Z
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recordCreationDate: 2006-09-19
identifier: http://urn.kb.se/resolve?urn=urn:nbn:se:du-2297
titleInfo:
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lang: eng
title: Effect of Oligonucleotide Truncation on Single-nucleotide Distinction by Solid Phase Hybridization
abstract: Oligonucleotide microarrays are used to analyze target sequences on the basis of differences in hybridization stability between matched and mismatched probe-target duplexes. DNA microarray manufacture via photolithographic synthesis generates a minority of full-length oligonucleotide probes along with a series of 5'-truncated contaminants. In a model experiment we now investigate the effect of truncated oligonucleotides on the ability to distinguish target sequence variants that differ in a single nucleotide position. A series of oligonucleotides mixed in proportions simulating stepwise synthetic yields of between 82 and 100% were bound to a solid support and allowed to hybridize to a target molecule. The extent of hybridization was monitored over a range of temperatures via the fluorescence of a double-strand-specific dye. The discriminatory power of pure oligonucleotide probes was found to be significantly greater than that of a population of truncated probes but only over a limited temperature interval. We conclude that at optimal temperatures greater oligonucleotide quality can improve the performance of oligonucleotide hybridization microarrays.
language:
languageTerm: eng
genre:
publication/journal-article
ref
note:
Published
1
name:
@attributes:
type: personal
authority: du
namePart:
Jobs
Magnus
role:
roleTerm: aut
affiliation:
Högskolan Dalarna
Medicinsk vetenskap
nameIdentifier: mjb
originInfo:
dateIssued: 2002
relatedItem:
@attributes:
type: host
titleInfo:
title: Analytical Chemistry
identifier:
0003-2700
1520-6882
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detail:
@attributes:
type: volume
number: 74
@attributes:
type: issue
number: 1
extent:
start: 199
end: 202
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form: print
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