Improved allelic differentiation using sequence-specific oligonucleotide hybridization incorporating an additional base-analogue mismatch.
Sequence-specific oligonucleotide hybridization (SSOH, 'dot-blotting') is a widely employed method of typing single nucleotide polymorphisms (SNPs), but it is often compromised by lack of allelic differentiation. We describe a novel improvement to SSOH that incorporates an additional misma...
| Main Authors: | , , , |
|---|---|
| Format: | Journal article |
| Language: | English |
| Published: |
2004
|
| _version_ | 1797083517200367616 |
|---|---|
| author | Burgner, D D'Amato, M Kwiatkowski, D Loakes, D |
| author_facet | Burgner, D D'Amato, M Kwiatkowski, D Loakes, D |
| author_sort | Burgner, D |
| collection | OXFORD |
| description | Sequence-specific oligonucleotide hybridization (SSOH, 'dot-blotting') is a widely employed method of typing single nucleotide polymorphisms (SNPs), but it is often compromised by lack of allelic differentiation. We describe a novel improvement to SSOH that incorporates an additional mismatch into the oligonucleotide probe using the universal base analogue 3-nitropyrrole. This method greatly increases allelic differentiation compared to standard SSOH where oligonucleotides contain only SNP-defining base changes. Moreover, stringency of the hybridisation is predictably maintained over a wide range of temperatures, which can be calculated empirically, thus facilitating the genotyping of multiple SNPs using similar conditions. This improved method increases the usefulness of hybridisation-based methods of rapid genotyping of SNPs and may have implications for array methodologies. |
| first_indexed | 2024-03-07T01:42:43Z |
| format | Journal article |
| id | oxford-uuid:97684664-9fff-4c57-ac88-04da3815b588 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T01:42:43Z |
| publishDate | 2004 |
| record_format | dspace |
| spelling | oxford-uuid:97684664-9fff-4c57-ac88-04da3815b5882022-03-26T23:59:21ZImproved allelic differentiation using sequence-specific oligonucleotide hybridization incorporating an additional base-analogue mismatch.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:97684664-9fff-4c57-ac88-04da3815b588EnglishSymplectic Elements at Oxford2004Burgner, DD'Amato, MKwiatkowski, DLoakes, DSequence-specific oligonucleotide hybridization (SSOH, 'dot-blotting') is a widely employed method of typing single nucleotide polymorphisms (SNPs), but it is often compromised by lack of allelic differentiation. We describe a novel improvement to SSOH that incorporates an additional mismatch into the oligonucleotide probe using the universal base analogue 3-nitropyrrole. This method greatly increases allelic differentiation compared to standard SSOH where oligonucleotides contain only SNP-defining base changes. Moreover, stringency of the hybridisation is predictably maintained over a wide range of temperatures, which can be calculated empirically, thus facilitating the genotyping of multiple SNPs using similar conditions. This improved method increases the usefulness of hybridisation-based methods of rapid genotyping of SNPs and may have implications for array methodologies. |
| spellingShingle | Burgner, D D'Amato, M Kwiatkowski, D Loakes, D Improved allelic differentiation using sequence-specific oligonucleotide hybridization incorporating an additional base-analogue mismatch. |
| title | Improved allelic differentiation using sequence-specific oligonucleotide hybridization incorporating an additional base-analogue mismatch. |
| title_full | Improved allelic differentiation using sequence-specific oligonucleotide hybridization incorporating an additional base-analogue mismatch. |
| title_fullStr | Improved allelic differentiation using sequence-specific oligonucleotide hybridization incorporating an additional base-analogue mismatch. |
| title_full_unstemmed | Improved allelic differentiation using sequence-specific oligonucleotide hybridization incorporating an additional base-analogue mismatch. |
| title_short | Improved allelic differentiation using sequence-specific oligonucleotide hybridization incorporating an additional base-analogue mismatch. |
| title_sort | improved allelic differentiation using sequence specific oligonucleotide hybridization incorporating an additional base analogue mismatch |
| work_keys_str_mv | AT burgnerd improvedallelicdifferentiationusingsequencespecificoligonucleotidehybridizationincorporatinganadditionalbaseanaloguemismatch AT damatom improvedallelicdifferentiationusingsequencespecificoligonucleotidehybridizationincorporatinganadditionalbaseanaloguemismatch AT kwiatkowskid improvedallelicdifferentiationusingsequencespecificoligonucleotidehybridizationincorporatinganadditionalbaseanaloguemismatch AT loakesd improvedallelicdifferentiationusingsequencespecificoligonucleotidehybridizationincorporatinganadditionalbaseanaloguemismatch |