CAFA is Capillary Automated Footprinting Analysis algorithms. The use of capillary electrophoresis with fluorescently labeled nucleic acids revolutionized DNA sequencing, effectively fueling the genomic revolution. We present an application of this technology for the high-throughput structural analysis of nucleic acids by chemical and enzymatic mapping (‘footprinting’). We achieve the throughput and data quality necessary for genomic-scale structural analysis by combining fluorophore labeling of nucleic acids with novel quantitation algorithms.The accuracy, throughput and reproducibility of CAFA analysis are demonstrated using hydroxyl radical footprinting of RNA. The versatility of CAFA is illustrated by dimethyl sulfate mapping of RNA secondary structure and DNase I mapping of a protein binding to a specific sequence of DNA. Our experimental and computational approach facilitates the acquisition of high-throughput chemical probing data for solution structural analysis of nucleic acids.
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Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, Laederach A,
High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis,
Nucleic Acids Res. 2008 Jun;36(11):e63. Epub 2008 May 13 (2008)