In-gel fluorescence probing of RNA-RNA interactions

Analytical Biochemistry

Volumn 362, Issue 2, 2007, Pages 278-280

  Dayie, Kwaku T ^a   Gumbs, Orlando H ^a   Eldho, Nadukkudy V ^a   Seetharaman, Mahadevan ^a   Thompson, Michalynn ^a  

^a LERNER RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CHEMISTRY;

FLUORESCENCE PROBING; RNA-RNA INTERACTION;

RNA;

RIBOZYME; RNA;

ARTICLE; ELECTROPHORETIC MOBILITY; GEL ELECTROPHORESIS; GEL MOBILITY SHIFT ASSAY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; RNA ANALYSIS; RNA BINDING;

EID: 33846883760     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2006.12.020     Document Type: Article

References (16)

1. Caprara M.G., and Nilsen T.W. RNA: versatility in form and function. Nat. Struct. Biol. 7 (2000) 831-833
2. Mattick J.S., and Makunin I.V. Small regulatory RNAs in mammals. Hum. Mol. Genet. 14 (2005) R121-R132
3. Doudna J.A., and Lorsch J.R. Ribozyme catalysis: not different just worse. Nat. Struct. Mol. Biol. 12 (2005) 395-402
4. Zamore P.D., and Haley B. Ribo-gnome: the big world of small RNAs. Science 309 (2005) 1519-1524
5. Revzin A. Gel electrophoresis assays for DNA-protein interactions. Biotechniques 7 (1989) 346-355
6. Ruscher K., Reuter M., Kupper D., Trendelenburg G., Dirnagl U., and Meisel A. A fluorescence based non-radioactive electrophoretic mobility shift assay. J. Biotechnol. 78 (2000) 163-170
7. McNamara P., Lew W., and Han L. Fluorescent imaging and analysis with Typhoon 8600. Electrophoresis 22 (2001) 837-842
8. Jing D., Agnew J., Patton W.F., Hendrickson J., and Beechem J.M. A sensitive two-color electrophoretic mobility shift assay for detecting both nucleic acids and protein in gels. Proteomics 3 (2003) 1172-1180
9. Costa M., Fontaine J.M., Loiseaux-de Goer S., and Michel F. A group II self-splicing intron from the brown alga Pylaiella littoralis is active at unusually low magnesium concentrations and forms populations of molecules with a uniform conformation. J. Mol. Biol. 274 (1997) 353-364
10. Gumbs O.H., Padgett R.A., and Dayie K.T. Fluorescence and solution NMR study of the active site of a 160-kDa group II intron ribozyme. RNA 12 (2006) 1693-1707
11. Brennecke J., Hipfner D.R., Stark A., Russell R.B., and Cohen S.M. Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113 (2003) 25-36
12. Jarrell K.A., Peebles C.L., Dietrich R.C., Romiti S.L., and Perlman P.S. Group II intron self-splicing. Alternative reaction conditions yield novel products. J. Biol. Chem. 263 (1988) 3432-3439
13. Panchuk-Voloshina N., P Haugland R., Bishop-Stewart J., Bhalgat M.K., Millard P.J., Mao F., Leung W.Y., and Haugland R.P. Alexa dyes, a series of new fluorescent dyes that yield exceptionally bright, photostable conjugates. J. Histochem. Cytochem. 47 (1999) 1179-1188
14. Berlier J.E., Rothe A., Buller G., Bradford J., Gray D.R., Filanoski B.J., Telford W.G., Yue S., Liu J., Cheung C.Y., Chang W., Hirsch J.D., Beechem J.M., and Haugland R.P. Quantitative comparison of long-wavelength Alexa Fluor dyes to Cy dyes: fluorescence of the dyes and their bioconjugates. J. Histochem. Cytochem. 51 (2003) 1699-1712
15. Ha I., Wightman B., and Ruvkun G. A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation. Genes Dev. 10 (1996) 3041-3050
16. Vella M.C., Choi E.-Y., Lin S.-Y., Reinert K., and Slack F.J. The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3′UTR. Genes Dev. 18 (2004) 132-137