High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis

Somdeb Mitra, Inna V. Shcherbakova, Russ B. Altman, Michael Brenowitz, Alain Laederach

Research output: Contribution to journalArticlepeer-review

77 Scopus citations


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. We implemented these algorithms in the CAFA (capillary automated footprinting analysis) open-source software that is downloadable gratis from https://simtk.org/home/cafa. 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.

Original languageEnglish (US)
Article numbere63
JournalNucleic acids research
Issue number11
StatePublished - Jun 2008

ASJC Scopus subject areas

  • Genetics


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