Jump to ContentJump to Main Navigation
Show Summary Details
More options …

Biological Chemistry

Editor-in-Chief: Brüne, Bernhard

Editorial Board: Buchner, Johannes / Lei, Ming / Ludwig, Stephan / Thomas, Douglas D. / Turk, Boris / Wittinghofer, Alfred


IMPACT FACTOR 2017: 3.022

CiteScore 2018: 3.09

SCImago Journal Rank (SJR) 2018: 1.482
Source Normalized Impact per Paper (SNIP) 2018: 0.820

Online
ISSN
1437-4315
See all formats and pricing
More options …
Volume 393, Issue 1-2

Issues

Dye selection for live cell imaging of intact siRNA

Markus Hirsch
  • Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
  • Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Staudingerweg 5, D-55128 Mainz, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Dennis Strand
  • Department of Medicine I, Johannes Gutenberg-University Mainz, Obere Zahlbacher Strasse 63, D-55131 Mainz, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Mark Helm
  • Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
  • Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Staudingerweg 5, D-55128 Mainz, Germany
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2012-01-04 | DOI: https://doi.org/10.1515/BC-2011-256

Abstract

Investigations into the fate of small interfering RNA (siRNA) after transfection may unravel new ways to improve RNA interference (RNAi) efficiency. Because intracellular degradation of RNA may prevent reliable observation of fluorescence-labeled siRNA, new tools for fluorescence microscopy are warranted to cover the considerable duration of the RNAi effect. Here, the characterization and application of new fluorescence resonance energy transfer (FRET) dye pairs for sensing the integrity of duplex siRNA is reported, which allows an assessment of the degradation status of an siRNA cell population by live cell imaging. A panel of high-yield fluorescent dyes has been investigated for their suitability as FRET pairs for the investigation of RNA inside the cell. Nine dyes in 13 FRET pairs were evaluated based on the performance in assays of photostability, cross-excitation, bleed-through, as well as on quantified changes of fluorescence as a consequence of, e.g., RNA strand hybridization and pH variation. The Atto488/Atto590 FRET pair has been applied to live cell imaging, and has revealed first aspects of unusual trafficking of intact siRNA. A time-lapse study showed highly dynamic movement of siRNA in large perinuclear structures. These and the resulting optimized FRET labeled siRNA are expected to have significant impact on future observations of labeled RNAs in living cells.

Keywords: confocal fluorescence microscopy; fluorescence resonance energy transfer (FRET); RNA interference (RNAi); siRNA degradation; siRNA integrity; small interfering RNA (siRNA)

About the article

Corresponding author


Received: 2011-11-09

Accepted: 2011-12-05

Published Online: 2012-01-04

Published in Print: 2012-01-01


Citation Information: Biological Chemistry, Volume 393, Issue 1-2, Pages 23–35, ISSN (Online) 1437-4315, ISSN (Print) 1431-6730, DOI: https://doi.org/10.1515/BC-2011-256.

Export Citation

©2012 by Walter de Gruyter Berlin Boston.Get Permission

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

[1]
Ilaria Furlan, Ivana Domljanovic, Jesper Uhd, and Kira Astakhova
ChemBioChem, 2018
[2]
Socheata Ly, Deanna M. Navaroli, Marie-Cécile Didiot, James Cardia, Lakshmipathi Pandarinathan, Julia F. Alterman, Kevin Fogarty, Clive Standley, Lawrence M. Lifshitz, Karl D. Bellve, Matthieu Prot, Dimas Echeverria, Silvia Corvera, and Anastasia Khvorova
Nucleic Acids Research, 2017, Volume 45, Number 1, Page 15
[3]
M. Hirsch and M. Helm
Nucleic Acids Research, 2015, Volume 43, Number 9, Page 4650
[4]
Robert Silvers, Heiko Keller, Harald Schwalbe, and Martin Hengesbach
ChemBioChem, 2015, Volume 16, Number 7, Page 1109
[5]
Bo Yu, Xinmei Wang, Chenguang Zhou, Lesheng Teng, Wei Ren, Zhaogang Yang, Chih-Hsin Shih, Tianyou Wang, Robert J. Lee, Suoqin Tang, and L. James Lee
Pharmaceutical Research, 2014, Volume 31, Number 10, Page 2685
[6]
Ilja Tabujew, Christoph Freidel, Bettina Krieg, Mark Helm, Kaloian Koynov, Klaus Müllen, and Kalina Peneva
Macromolecular Rapid Communications, 2014, Volume 35, Number 13, Page 1191
[7]
Salifu Seidu-Larry, Bettina Krieg, Markus Hirsch, Mark Helm, and Olwen Domingo
Chemical Communications, 2012, Volume 48, Number 89, Page 11014

Comments (0)

Please log in or register to comment.
Log in