DNA binding fluorescent proteins for the direct visualization of large DNA molecules.
Fluorescent proteins that also bind DNA molecules are useful reagents for a broad range of biological applications because they can be optically localized and tracked within cells, or provide versatile labels for in vitro experiments. We report a novel design for a fluorescent, DNA-binding protein (FP-DBP) that completely 'paints' entire DNA molecules, whereby sequence-independent DNA binding is accomplished by linking a fluorescent protein to two small peptides (KWKWKKA) using lysine for binding to the DNA phosphates, and tryptophan for intercalating between DNA bases. Importantly, this ubiquitous binding motif enables fluorescent proteins (Kd = 14.7 μM) to confluently stain DNA molecules and such binding is reversible via pH shifts. These proteins offer useful robust advantages for single DNA molecule studies: lack of fluorophore mediated photocleavage and staining that does not perturb polymer contour lengths. Accordingly, we demonstrate confluent staining of naked DNA molecules presented within microfluidic devices, or localized within live bacterial cells.
Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea.
Seonghyun
S
Lee
Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea.
Yeeun
Y
Oh
Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea.
Jungyoon
J
Lee
Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea.
Sojeong
S
Choe
Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Korea.
Sangyong
S
Lim
Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea.
Hyun Soo
HS
Lee
Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea jokyubong@sogang.ac.kr.
Kyubong
K
Jo
Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53705, USA.
David C
DC
Schwartz
D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism*; D008856:Microscopy, Fluorescence; D057054:Molecular Imaging / Q000379:methods; D011993:Recombinant Fusion Proteins
D004268:DNA-Binding Proteins; D008164:Luminescent Proteins; D011993:Recombinant Fusion Proteins; D004247:DNA