Donnelly Nucleic Acid Binding Specificity Core
The Donnelly Nucleic Acid Binding Specificity Core (nabsCORE) offers services for characterizing the target specificities of nucleic acid binding proteins (DNA- and RNA-binding proteins) in vitro.
For DNA-binding proteins such as transcription factors, we perform either randomized DNA (HT-SELEX) or fragmented human genomic DNA (GHT-SELEX) based in vitro selection assays. For RNA-binding proteins, we perform RNAcompete, a microarray-based method. The nabsCORE facility primarily serves academic labs, operating on a cost-recovery basis.
Our systems are flexible and can be applied to any species. For proteins of interest, we design and generate expression constructs and perform DNA or RNA specificity determination experiments using epitope tagged recombinant proteins. We work closely with the Donnelly Sequencing Centre, which provides high-quality sequencing services. Our primary deliverable is raw data produced from DNA- or RNA-binding experiments. If required, nabsCORE can also provide motif analysis, and, in case of GHT-SELEX, genomic target site enrichment.
Our operations can accommodate large- and small-scale orders. Additionally, customized/diverse protein subsets can be analyzed; for example, for comparing wild-type and disease variants. If you are interested in our services, please contact donnelly.nabscore@utoronto.ca.
Services are modular, but typically include:
- Design of expression constructs
- Protein production
- DNA- or RNA-binding assays
- Next generation sequencing (for DNA-binding proteins) or microarray analysis (for RNA-binding proteins)
- Basic data processing (demultiplexing), quality measures and motif/enrichment analysis
Method references and previous projects:
HT-SELEX
GHT-SELEX
RNAcompete
- https://pubmed.ncbi.nlm.nih.gov/19561594/
- https://pubmed.ncbi.nlm.nih.gov/23846655/
- https://pubmed.ncbi.nlm.nih.gov/27956239/
- https://pubmed.ncbi.nlm.nih.gov/39464061/