Effect of Oligonucleotide Truncation on Single-nucleotide Distinction by Solid Phase Hybridization

Document identifier: oai:dalea.du.se:2297
Publication year: 2002
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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.

Authors

Magnus Jobs

Högskolan Dalarna; Medicinsk vetenskap
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    header: 
        identifier: oai:dalea.du.se:2297
        datestamp: 2021-04-15T12:55:16Z
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                recordContentSource: du
                recordCreationDate: 2006-09-19
            identifier: http://urn.kb.se/resolve?urn=urn:nbn:se:du-2297
            titleInfo: 
                @attributes: 
                    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
                part: 
                    detail: 
                            @attributes: 
                                type: volume
                            number: 74
                            @attributes: 
                                type: issue
                            number: 1
                    extent: 
                        start: 199
                        end: 202
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                form: print
            typeOfResource: text