Allele-Specific Holliday Junction Formation: A New Mechanism of Allelic Discrimination for SNP Scoring
Open accessAbstract
We report here a new mechanism for allelic discrimination—allele-specific Holliday Junction formation. The Holliday Junction (HJ) is a unique DNA structure that can be formed in a sequence-nonspecific manner by routine PCR. To cause the PCR-based HJ formation to occur in an allele-specific manner, the PCR primers are manipulated such that an extra mismatch next to a SNP of interest is introduced between a target and a reference amplicon and a GC-clamp is added. Based on this new mechanism, novel SNP genotyping methods were developed, including a homogeneous fluorescence polarization (FP) competition assay that requires neither labeled primers/probes nor expensive enzymes/substrates. Using this novel genotyping technology, we were able to convert >95% of SNP sequences into genotyping assays that work well under a universal set of assay conditions and achieved 100% accuracy in clinical samples.
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The flow of information from genes to proteins has not yet been investigated on a genome-wide scale.
“While it is now clear that regulation occurs at multiple levels, the flow of information from genes to proteins has not yet been investigated on a genome-wide scale 2,6 .”
From Global quantification of mammalian gene expression control (2011) · cites this paper as [6]
The SNP Assay Design and Discussion passages concern allele-specific genotyping and a possible application to detecting gene expression; they do not assess the flow of information from genes to proteins. Searches for the claim’s wording and for genome-wide gene-expression, protein and regulation terms found no passage addressing whether that flow had been investigated genome-wide. Page numbers were not available in our copy. (LLM, conf=0.77)
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Ferizi, M., Aneja, M. K., Balmayor, E. R., Badieyan, Z. S., Mykhaylyk, O., Rudolph, C., & Plank, C. (2016) · Scientific Reports · doi:10.1038/srep39149 · Cited by 46 · see citing works
- Authors
- Yang, Q., Lishanski, A., Yang, W., Hatcher, S., Seet, H., & Gregg, J. P.
- Affiliations
- University of California Davis Medical Center (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2003-07
- Volume
- 13
- Issue
- 7
- Pages
- 1754-1764
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC403749
- OpenAlex
- W2002203989
- Cited by
- 136
- References
- 0
- Citations by year
- 2022: 1 · 2021: 9 · 2020: 3 · 2019: 4 · 2018: 5 · 2017: 12 · 2016: 9 · 2015: 7 · 2014: 12 · 2013: 6 · 2012: 6
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- Holliday junction, SNP genotyping, PCR genotyping, mismatched primers, DNA secondary structure
- MeSH terms
- Alleles, DNA Helicases, DNA-Binding Proteins, Electrophoresis, Agar Gel, Electrophoresis, Polyacrylamide Gel, Endodeoxyribonucleases, Fluorescence Polarization, Genotype, Models, Genetic, Recombination, Genetic, Selection, Genetic, Polymerase Chain Reaction, Base Pair Mismatch, Polymorphism, Single Nucleotide, GC Rich Sequence, Nucleic Acid Amplification Techniques, Electrophoretic Mobility Shift Assay, Escherichia coli Proteins, Databases, Genetic
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