Dana Carroll

Professor of Biochemistry

Carroll Photo

B.A. Swarthmore College

Ph.D. University of California, Berkeley




Dana Carroll's Lab Page

Dana Carroll's PubMed Literature Search


We work on gene targeting. The basis of genetic analysis is the isolation and characterization of altered genomic sequences. Traditionally mutations have been isolated based on observed phenotypes, but with many whole genome sequences now available, investigators often want to generate designed mutations in specific genes of interest.

We have developed methods that allow the creation of highly specific localized mutations and targeted gene replacements. The basis for our approach is the use of zinc-finger nucleases (ZFNs). These hybrid proteins have a DNA-binding domain that can direct cleavage activity to a wide range of genomic sequences. Cleavage induces mutations via repair by nonhomologous end joining and gene replacement by homologous recombination with a manipulated donor DNA. ZFNs have been used successfully in many organisms and cell types from plants to humans.

In our lab we apply ZFNs to direct genome alterations in model organisms, particularly flies and worms. In Drosophila we have achieved very high frequencies of both mutagenesis and gene replacement — in the vicinity of 10% of all target alleles. Such efficiencies have allowed us to produce novel mutations in specific genes without reliance on a known phenotype. Our work with C. elegans is less advanced, but we have shown that ZFNs work well in this organism and promise to provide the tools for an effective gene targeting procedure. Since breaks in DNA stimulate both local mutagenesis and recombination in essentially all organisms, the ZFN approach is very broadly applicable.

Carroll Figure One

Diagram of two ZFNs bound to a target sequence in the Drosophila yellow gene. Each zinc finger contacts three consecutive base pairs. The cleavage domains are green.

Example of a rosy mutation induced with ZFNs. The fly on the left has wild-type eye color; the one on the right is a rosy mutant.


  1. Carroll, D. (2011). Genome Engineering with Zinc-Finger Nucleases. Genetics, 188: 773-782
  2. Carroll D (2011) Zinc-finger nucleases: a panoramic view. Curr Gene Ther, 11:2-10
  3. Kim JS, Lee HJ, and Carroll D (2010) Genome editing with modularly assembled zinc-finger nucleases. Nat Methods, 7:91
  4. Takasu Y, Kobayashi I, Beumer K, Uchino K, Sezutsu H, Carroll D, Tamura T, and Zurovec M (2010) Targeted mutagenesis in the silkworm Bombyx mori using zinc-finger nuclease mRNA injections. Insect Biochem Mol Biol, 40:759-765
  5. Bozas A, Beumer KJ, Trautman JK, Carroll D (2009) Genetic analysis of zinc-finger nuclease-induced gene targeting in Drosophila. Genetics, 182:641-652
  6. Mittelman D, Moye C, Morton J, Sykoudis K, Lin Y, Carroll D, Wilson JH (2009) Zinc-finger directed double-strand breaks within CAG repeat tracts promote repeat instability in human cells. Proc Natl Acad Sci USA, 106:9607-9612
  7. Beumer KJ, Trautman JK, Bozas A, Liu J-L, Rutter J, Gall JG, Carroll D (2008) Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases. Proc Natl Acad Sci USA, 105:19821-19826
  8. Carroll D (2008) Progress and prospects: Zinc-finger nucleases as gene therapy agents. Gene Therapy, 15:1463-1468
  9. Morton J, Davis MW, Jorgensen EM, Carroll D (2006) Induction and repair of zinc-finger nuclease-targeted double-strand breaks in C. elegans somatic cells. Proc Natl Acad Sci USA, 103:16370-16375
  10. Carroll D, Morton JJ, Beumer KJ, Segal DJ (2006). Design, Construction and in vitro testing of zinc finger nucleases. Nature Protocols, 1:1329-1341
  11. Beumer K, Bhattacharrya G, Bibikova M, Trautman JK, Carroll D (2006) Efficient gene targeting in Drosophila with zinc finger nucleases. Genetics, 172:2391-2403

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