Coordinate-based Colocalization Analysis of Single-molecule Localization Microscopy Data

Overview

Journal Histochem Cell Biol

Publisher Springer

Specialties Biochemistry
Cell Biology

Date 2011 Nov 17

PMID 22086768

Citations 88

Authors

Sebastian Malkusch

Ulrike Endesfelder

Justine Mondry

Marton Gelleri

Peter J Verveer

Mike Heilemann

Affiliations

Soon will be listed here.

Abstract

Colocalization of differently labeled biomolecules is a valuable tool in fluorescence microscopy and can provide information on biomolecular interactions. With the advent of super-resolution microscopy, colocalization analysis is getting closer to molecular resolution, bridging the gap to other technologies such as fluorescence resonance energy transfer. Among these novel microscopic techniques, single-molecule localization-based super-resolution methods offer the advantage of providing single-molecule coordinates that, rather than intensity information, can be used for colocalization analysis. This requires adapting the existing mathematical algorithms for localization microscopy data. Here, we introduce an algorithm for coordinate-based colocalization analysis which is suited for single-molecule super-resolution data. In addition, we present an experimental configuration for simultaneous dual-color imaging together with a robust approach to correct for optical aberrations with an accuracy of a few nanometers. We demonstrate the potential of our approach for cellular structures and for two proteins binding actin filaments.

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References

Smith C, Joseph N, Rieger B, Lidke K . Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat Methods. 2010; 7(5):373-5. PMC: 2862147. DOI: 10.1038/nmeth.1449. View

Heilemann M . Fluorescence microscopy beyond the diffraction limit. J Biotechnol. 2010; 149(4):243-51. DOI: 10.1016/j.jbiotec.2010.03.012. View

McKinney S, Murphy C, Hazelwood K, Davidson M, Looger L . A bright and photostable photoconvertible fluorescent protein. Nat Methods. 2009; 6(2):131-3. PMC: 2745648. DOI: 10.1038/nmeth.1296. View

Koyama-Honda I, Ritchie K, Fujiwara T, Iino R, Murakoshi H, Kasai R . Fluorescence imaging for monitoring the colocalization of two single molecules in living cells. Biophys J. 2004; 88(3):2126-36. PMC: 1305264. DOI: 10.1529/biophysj.104.048967. View

Ronneberger O, Baddeley D, Scheipl F, Verveer P, Burkhardt H, Cremer C . Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, methods, pitfalls. Chromosome Res. 2008; 16(3):523-62. DOI: 10.1007/s10577-008-1236-4. View

Heilemann M, van de Linde S, Schuttpelz M, Kasper R, Seefeldt B, Mukherjee A . Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angew Chem Int Ed Engl. 2008; 47(33):6172-6. DOI: 10.1002/anie.200802376. View

Fehon R, McClatchey A, Bretscher A . Organizing the cell cortex: the role of ERM proteins. Nat Rev Mol Cell Biol. 2010; 11(4):276-87. PMC: 2871950. DOI: 10.1038/nrm2866. View

Li Q, Lau A, Morris T, Guo L, Fordyce C, Stanley E . A syntaxin 1, Galpha(o), and N-type calcium channel complex at a presynaptic nerve terminal: analysis by quantitative immunocolocalization. J Neurosci. 2004; 24(16):4070-81. PMC: 6729428. DOI: 10.1523/JNEUROSCI.0346-04.2004. View

Schermelleh L, Carlton P, Haase S, Shao L, Winoto L, Kner P . Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science. 2008; 320(5881):1332-6. PMC: 2916659. DOI: 10.1126/science.1156947. View

10.

Churchman L, Okten Z, Rock R, Dawson J, Spudich J . Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. Proc Natl Acad Sci U S A. 2005; 102(5):1419-23. PMC: 545495. DOI: 10.1073/pnas.0409487102. View

11.

Rust M, Bates M, Zhuang X . Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods. 2006; 3(10):793-5. PMC: 2700296. DOI: 10.1038/nmeth929. View

12.

Pertsinidis A, Zhang Y, Chu S . Subnanometre single-molecule localization, registration and distance measurements. Nature. 2010; 466(7306):647-51. DOI: 10.1038/nature09163. View

13.

French A, Mills S, Swarup R, Bennett M, Pridmore T . Colocalization of fluorescent markers in confocal microscope images of plant cells. Nat Protoc. 2008; 3(4):619-28. DOI: 10.1038/nprot.2008.31. View

14.

Zinchuk V, Zinchuk O . Quantitative colocalization analysis of confocal fluorescence microscopy images. Curr Protoc Cell Biol. 2008; Chapter 4:Unit 4.19. DOI: 10.1002/0471143030.cb0419s39. View

15.

McClatchey A, Fehon R . Merlin and the ERM proteins--regulators of receptor distribution and signaling at the cell cortex. Trends Cell Biol. 2009; 19(5):198-206. PMC: 2796113. DOI: 10.1016/j.tcb.2009.02.006. View

16.

Wombacher R, Heidbreder M, van de Linde S, Sheetz M, Heilemann M, Cornish V . Live-cell super-resolution imaging with trimethoprim conjugates. Nat Methods. 2010; 7(9):717-9. DOI: 10.1038/nmeth.1489. View

17.

Endesfelder U, Malkusch S, Flottmann B, Mondry J, Liguzinski P, Verveer P . Chemically induced photoswitching of fluorescent probes--a general concept for super-resolution microscopy. Molecules. 2011; 16(4):3106-18. PMC: 6260607. DOI: 10.3390/molecules16043106. View

18.

Grecco H, Verveer P . FRET in cell biology: still shining in the age of super-resolution?. Chemphyschem. 2011; 12(3):484-90. DOI: 10.1002/cphc.201000795. View

19.

Wolter S, Endesfelder U, van de Linde S, Heilemann M, Sauer M . Measuring localization performance of super-resolution algorithms on very active samples. Opt Express. 2011; 19(8):7020-33. DOI: 10.1364/OE.19.007020. View

20.

Bolte S, Cordelieres F . A guided tour into subcellular colocalization analysis in light microscopy. J Microsc. 2007; 224(Pt 3):213-32. DOI: 10.1111/j.1365-2818.2006.01706.x. View