Abstract
Fluorescence microscopy is an essential tool for imaging tagged biological structures. Due to the wave nature of light, the resolution of a conventional fluorescence microscope is limited laterally to about 200 nm and axially to about 600 nm, which is often referred to as the Abbe limit. This hampers the observation of important biological structures and dynamics in the nano-scaled range ~10 nm to ~100 nm. Consequentially, various methods have been developed circumventing this limit of resolution. Super-resolution microscopy comprises several of those methods employing physical and/or chemical properties, such as optical/instrumental modifications and specific labeling of samples. In this article, we will give a brief insight into a variety of selected optical microscopy methods reaching super-resolution beyond the Abbe limit. We will survey three different concepts in connection to biological applications in radiation research without making a claim to be complete.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abbe E (1873) Beiträge zur Theorie des Mikroskops und der mikroskopischen Wahrnehmung. Arch Mikrosk Anat 9(1):413–418
Knoll M, Ruska E (1932) Das Elektronenmikroskop. Z Phys 78(5):318–339
Lorat Y, Brunner CU, Schanz S, Jakob B, Taucher-Scholz G, Rübe CE (2015) Nanoscale analysis of clustered DNA damage after high-LET irradiation by quantitative electron microscopy – the heavy burden to repair. DNA Repair 28:93–106
Betzig E, Trautman JK (1992) Near-field optics: microscopy, spectroscopy, and surface modification beyond the diffraction limit. Science 257(5067):189–195
Lewis A, Isaacson M, Harootunian A, Muray A (1984) Development of a 500 Å spatial resolution light microscope. Ultramicroscopy 13(3):227–231
Pohl DW, Denk W, Lanz M (1984) Optical stethoscopy: image recording with resolution λ/20. Appl Phys Lett 44(7):651–653
Perner B, Rapp A, Dressler C, Wollweber L, Beuthan J, Greulich KO, Hausmann M (2002) Variations in cell surfaces of estrogen treated breast cancer cells detected by a combined instrument for far-field and near-field microscopy. Anal Cell Pathol 24:89–100
Winkler R, Perner B, Rapp A, Durm M, Cremer C, Greulich KO, Hausmann M (2003) Labelling quality and chromosome morphology after low temperature FISH analysed by scanning far-field and near-field optical microscopy. J Microsc 209(1):23–33
Brakenhoff GJ, Blom P, Barends P (1979) Confocal scanning light microscopy with high aperture immersion lenses. J Microsc 117(2):219–232
Sheppard C, Choudhury A (1977) Image formation in the scanning microscope. Opt Acta 24(10):1051–1073
Hell SW, Lindek S, Cremer C, Stelzer EHK (1994) Measurement of the 4Pi‐confocal point spread function proves 75 nm axial resolution. Appl Phys Lett 64(11):1335–1337
Hell SW, Stelzer EHK (1992) Fundamental improvement of resolution with a 4Pi-confocal fluorescence microscope using two-photon excitation. Optic Commun 93(5):277–282
Gustafsson MGL, Agard DA, Sedat JW (1995) Sevenfold improvement of axial resolution in 3D wide-field microscopy using two objective lenses. Proc SPIE 2412:147–156
Gustafsson MGL, Agard DA, Sedat JW (1999) I5M: 3D widefield light microscopy with better than 100 nm axial resolution. J Microsc 195(1):10–16
Gustafsson MGL, Sedat JW, Agard DA (1997) Method and apparatus for three-dimensional microscopy with enhanced depth resolution. US 5671085 A
Bewersdorf J, Schmidt R, Hell SW (2006) Comparison of I5M and 4Pi-microscopy. J Microsc 222(2):105–117
Bailey B, Farkas DL, Taylor DL, Lanni F (1993) Enhancement of axial resolution in fluorescence microscopy by standing-wave excitation. Nature 366(6450):44–48
Schneider B, Upmann I, Kirsten I, Bradl J, Hausmann M, Cremer C (1999) A dual-laser, spatially modulated illumination fluorescence microscope. Eur. Microsc Anal 57:5–7
Albrecht B, Failla AV, Heintzmann R, Cremer C (2001) Spatially modulated illumination microscopy: online visualization of intensity distribution and prediction of nanometer precision of axial distance measurements by computer simulations. J Biomed Opt 6(3):292–299
Failla AV, Spoeri U, Albrecht B, Kroll A, Cremer C (2002) Nanosizing of fluorescent objects by spatially modulated illumination microscopy. Appl Optics 41(34):7275–7283
Grossmann C, Schwarz-Finsterle J, Schmitt E, Birk U, Hildenbrand G, Cremer C, Trakhtenbrot L, Hausmann M (2010) Variations of the spatial fluorescence distribution in ABL gene chromatin domains measured in blood cell nuclei by SMI microscopy after COMBO – FISH labelling. In: Microscopy: science, technology, applications and education, vol 1. Formatex, Badajoz, pp 688–695
Hildenbrand G, Rapp A, Spöri U, Wagner C, Cremer C, Hausmann M (2005) Nano-sizing of specific gene domains in intact human cell nuclei by spatially modulated illumination light microscopy. Biophys J 88(6):4312–4318
Wagner C, Hildenbrand G, Spöri U, Cremer C (2006) Beyond nanosizing: an approach to shape analysis of fluorescent nanostructures by SMI-microscopy. Optik 117(1):26–32
Gustafsson MGL (2000) Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J Microsc 198(2):82–87
Heintzmann R, Cremer CG (1999) Laterally modulated excitation microscopy: improvement of resolution by using a diffraction grating. Proc SPIE 3568:185–196
Neil MAA, Juškaitis R, Wilson T (1997) Method of obtaining optical sectioning by using structured light in a conventional microscope. Opt Lett 22(24):1905–1907
Neil MAA, Juškaitis R, Wilson T (1998) Real time 3D fluorescence microscopy by two beam interference illumination. Optic Commun 153(1-3):1–4
Shao L, Isaac B, Uzawa S, Agard DA, Sedat JW, Gustafsson MGL (2008) I5S: wide-field light microscopy with 100-nm-scale resolution in three dimensions. Biophys J 94(12):4971–4983
Gustafsson MGL (2005) Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc Natl Acad Sci U S A 102(37):13081–13086
Heintzmann R, Jovin TM, Cremer C (2002) Saturated patterned excitation microscopy---a concept for optical resolution improvement. J Opt Soc Am A 19(8):1599–1609
Chagin VO, Casas-Delucchi CS, Reinhart M, Schermelleh L, Markaki Y, Maiser A, Bolius JJ, Bensimon A, Fillies M, Domaing P, Rozanov YM, Leonhardt H, Cardoso MC (2016) 4D Visualization of replication foci in mammalian cells corresponding to individual replicons. Nat Commun 7:11231. doi:10.1038/ncomms11231
Schermelleh L, Carlton PM, Haase S, Shao L, Winoto L, Kner P, Burke B, Cardoso MC, Agard DA, Gustafsson MG, Leonhardt H, Sedat JW (2008) Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science 320(5881):1332–1336. doi:10.1126/science.1156947
Schermelleh L, Heintzmann R, Leonhardt H (2010) A guide to super-resolution fluorescence microscopy. J Cell Biol 190(2):165–175. doi:10.1083/jcb.201002018
Smeets D, Markaki Y, Schmid VJ, Kraus F, Tattermusch A, Cerase A, Sterr M, Fiedler S, Demmerle J, Popken J, Leonhardt H, Brockdorff N, Cremer T, Schermelleh L, Cremer M (2014) Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci. Epigenetics Chromatin 7:8. doi:10.1186/1756-8935-7-8
Baddeley D, Chagin VO, Schermelleh L, Martin S, Pombo A, Carlton PM, Gahl A, Domaing P, Birk U, Leonhardt H, Cremer C, Cardoso MC (2010) Measurement of replication structures at the nanometer scale using super-resolution light microscopy. Nucleic Acids Res 38(2):e8. doi:10.1093/nar/gkp901
Mitchell-Jordan S, Chen H, Franklin S, Stefani E, Bentolila LA, Vondriska TM (2012) Features of endogenous cardiomyocyte chromatin revealed by super-resolution STED microscopy. J Mol Cell Cardiol 53(4):552–558. doi:10.1016/j.yjmcc.2012.07.009
Markaki Y, Smeets D, Fiedler S, Schmid VJ, Schermelleh L, Cremer T, Cremer M (2012) The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture. Bioessays 34(5):412–426. doi:10.1002/bies.201100176
Fiolka R, Shao L, Rego EH, Davidson MW, Gustafsson MG (2012) Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination. Proc Natl Acad Sci U S A 109(14):5311–5315. doi:10.1073/pnas.1119262109
Shao L, Kner P, Rego EH, Gustafsson MG (2011) Super-resolution 3D microscopy of live whole cells using structured illumination. Nat Methods 8(12):1044–1046. doi:10.1038/nmeth.1734
Lopez Perez R, Best G, Nicolay NH, Greubel C, Rossberger S, Reindl J, Dollinger G, Weber KJ, Cremer C, Huber PE (2016) Superresolution light microscopy shows nanostructure of carbon ion radiation-induced DNA double-strand break repair foci. FASEB J 30(8):2767–2776. doi:10.1096/fj.201500106R
Natale F, Rapp A, Yu W, Maiser A, Harz H, Scholl A, Grulich S, Anton T, Hrl D, Chen W, Durante M, Taucher-Scholz G, Leonhardt H, Cristina Cardoso M (2017) Identification of the elementary structural units of the DNA damage response. Nat Commun 8:15760
Rossberger S, Ach T, Best G, Cremer C, Heintzmann R, Dithmar S (2013) High-resolution imaging of autofluorescent particles within drusen using structured illumination microscopy. Br J Ophthalmol 97(4):518–523. doi:10.1136/bjophthalmol-2012-302350
Bewersdorf J, Bennett BT, Knight KL (2006) H2AX chromatin structures and their response to DNA damage revealed by 4Pi microscopy. Proc Natl Acad Sci U S A 103(48):18137–18142. doi:10.1073/pnas.0608709103
Lorat Y, Schanz S, Schuler N, Wennemuth G, Rube C, Rube CE (2012) Beyond repair foci: DNA double-strand break repair in euchromatic and heterochromatic compartments analyzed by transmission electron microscopy. PLoS One 7(5):e38165. doi:10.1371/journal.pone.0038165
Hell SW, Wichmann J (1994) Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt Lett 19(11):780–782
Klar TA, Hell SW (1999) Subdiffraction resolution in far-field fluorescence microscopy. Opt Lett 24(14):954–956
Göttfert F, Wurm CA, Mueller V, Berning S, Cordes VC, Honigmann A, Hell SW (2013) Coaligned dual-channel STED nanoscopy and molecular diffusion analysis at 20 nm resolution. Biophys J 105(1):L01–L03
Wildanger D, Medda R, Kastrup L, Hell SW (2009) A compact STED microscope providing 3D nanoscale resolution. J Microsc 236(1):35–43
Bretschneider S, Eggeling C, Hell SW (2007) Breaking the diffraction barrier in fluorescence microscopy by optical shelving. Phys Rev Lett 98:218103
Hell SW, Kroug M (1995) Ground-state-depletion fluorscence microscopy: a concept for breaking the diffraction resolution limit. Appl Phys B 60(5):495–497
Finkenstaedt-Quinn SA, Qiu TA, Shin K, Haynes CL (2016) Super-resolution imaging for monitoring cytoskeleton dynamics. Analyst 141(20):5674–5688. doi:10.1039/c6an00731g
Miller SE, Mathiasen S, Bright NA, Pierre F, Kelly BT, Kladt N, Schauss A, Merrifield CJ, Stamou D, Honing S, Owen DJ (2015) CALM regulates clathrin-coated vesicle size and maturation by directly sensing and driving membrane curvature. Dev Cell 33(2):163–175. doi:10.1016/j.devcel.2015.03.002
Lau L, Lee YL, Sahl SJ, Stearns T, Moerner WE (2012) STED microscopy with optimized labeling density reveals 9-fold arrangement of a centriole protein. Biophys J 102(12):2926–2935. doi:10.1016/j.bpj.2012.05.015
Cseresnyes Z, Schwarz U, Green CM (2009) Analysis of replication factories in human cells by super-resolution light microscopy. BMC Cell Biol 10:88. doi:10.1186/1471-2121-10-88
Reindl J, Drexler GA, Girst S, Greubel C, Siebenwirth C, Drexler SE, Dollinger G, Friedl AA (2015) Nanoscopic exclusion between Rad51 and 53BP1 after ion irradiation in human HeLa cells. Phys Biol 12(6):066005. doi:10.1088/1478-3975/12/6/066005
Cremer C, Masters BR (2013) Resolution enhancement techniques in microscopy. Eur Phys J H 38(3):281–344. doi:10.1140/epjh/e2012-20060-1
Moerner WE, Kador L (1989) Optical detection and spectroscopy of single molecules in a solid. Phys Rev Lett 62:2535–2538
Orrit M, Bernard J (1990) Single pentacene molecules detected by fluorescence excitation in a p-terphenyl crystal. Phys Rev Lett 65:2716–2719
Betzig E (1995) Proposed method for molecular optical imaging. Opt Lett 20(3):237–239
Patterson GH, Lippincott-Schwartz J (2002) A photoactivatable GFP for selective photolabeling of proteins and cells. Science 297(5588):1873–1877
Bates M, Blosser TR, Zhuang X (2005) Short-range spectroscopic ruler based on a single-molecule optical switch. Phys Rev Lett 94:108101–108101
Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, Davidson MW, Lippincott-Schwartz J, Hess HF (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313(5793):1642–1645
Hess ST, Girirajan TPK, Mason MD (2006) Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91(11):4258–4272. doi:10.1529/biophysj.106.091116
Rust MJ, Bates M, Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3(10):793–796
Dickson RM, Cubitt AB, Tsien RY, Moerner WE (1997) On/off blinking and switching behaviour of single molecules of green fluorescent protein. Nature 388(6640):355–358
Geisler C, Schönle A, von Middendorff C, Bock H, Eggeling C, Egner A, Hell SW (2007) Resolution of λ/10 in fluorescence microscopy using fast single molecule photo-switching. Appl Phys A 88(2):223–226
Fölling J, Bossi M, Bock H, Medda R, Wurm CA, Hein B, Jakobs S, Eggeling C, Hell SW (2008) Fluorescence nanoscopy by ground-state depletion and single-molecule return. Nat Methods 5(11):943–945
Heilemann M, van de Linde S, Schüttpelz M, Kasper R, Seefeldt B, Mukherjee A, Tinnefeld P, Sauer M (2008) Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angew Chem Int Ed 47(33):6172–6176
Lemmer P, Gunkel M, Baddeley D, Kaufmann R, Urich A, Weiland Y, Reymann J, Müller P, Hausmann M, Cremer C (2008) SPDM: light microscopy with single-molecule resolution at the nanoscale. Appl Phys B 93(1):1–1
Dempsey GT, Bates M, Kowtoniuk WE, Liu DR, Tsien RY, Zhuang X (2009) Photoswitching mechanism of cyanine dyes. J Am Chem Soc 131(51):18192–18193. doi:10.1021/ja904588g
Huang B, Wang W, Bates M, Zhuang X (2008) Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319(5864):810–813
Juette MF, Gould TJ, Lessard MD, Mlodzianoski MJ, Nagpure BS, Bennett BT, Hess ST, Bewersdorf J (2008) Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples. Nat Methods 5(6):527–529
Pavani SRP, Thompson MA, Biteen JS, Lord SJ, Liu N, Twieg RJ, Piestun R, Moerner WE (2009) Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function. Proc Natl Acad Sci 106(9):2995–2999
Tang J, Akerboom J, Vaziri A, Looger LL, Shank CV (2010) Near-isotropic 3D optical nanoscopy with photon-limited chromophores. Proc Natl Acad Sci 107(22):10068–10073
Shtengel G, Galbraith JA, Galbraith CG, Lippincott-Schwartz J, Gillette JM, Manley S, Sougrat R, Waterman CM, Kanchanawong P, Davidson MW, Fetter RD, Hess HF (2009) Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. Proc Natl Acad Sci 106(9):3125–3130
Jia S, Vaughan JC, Zhuang X (2014) Isotropic three-dimensional super-resolution imaging with a self-bending point spread function. Nat Photon 8(4):302–306
Deschamps J, Mund M, Ries J (2014) 3D superresolution microscopy by supercritical angle detection. Opt Express 22(23):29081–29091
Kaufmann R, Müller P, Hildenbrand G, Hausmann M, Cremer C (2011) Analysis of Her2/neu membrane protein clusters in different types of breast cancer cells using localization microscopy. J Microsc 242(1):46–54
Boyd PS, Struve N, Bach M, Eberle JP, Gote M, Schock F, Cremer C, Kriegs M, Hausmann M (2016) Clustered localization of EGFRvIII in glioblastoma cells as detected by high precision localization microscopy. Nanoscale 8:20037–20047
Müller P, Lemmermann NA, Kaufmann R, Gunkel M, Paech D, Hildenbrand G, Holtappels R, Cremer C, Hausmann M (2014) Spatial distribution and structural arrangement of a murine cytomegalovirus glycoprotein detected by SPDM localization microscopy. Histochem Cell Biol 142(1):61–67
Bohn M, Diesinger P, Kaufmann R, Weiland Y, Müller P, Gunkel M, von Ketteler A, Lemmer P, Hausmann M, Heermann DW, Cremer C (2010) Localization microscopy reveals expression-dependent parameters of chromatin nanostructure. Biophys J 99(5):1358–1367
Zhang Y, Máté G, Müller P, Hillebrandt S, Krufczik M, Bach M, Kaufmann R, Hausmann M, Heermann DW (2015) Radiation induced chromatin conformation changes analysed by fluorescent localization microscopy, statistical physics, and graph theory. PLoS One 10(6):1–23
Stuhlmüller M, Schwarz-Finsterle J, Fey E, Lux J, Bach M, Cremer C, Hinderhofer K, Hausmann M, Hildenbrand G (2015) In situ optical sequencing and nano-structure analysis of a trinucleotide expansion region by localization microscopy after specific COMBO-FISH labelling. Nanoscale 7:17938–17946
Falk M, Hausmann M, Lukasova E, Biswas A, Hildenbrand G, Davidkova M, Krasavin E, Kleibl Z, Falkova I, Jezkova L, Stefancikova L, Sevcik J, Hofer M, Bacikova A, Matula P, Boreyko A, Vachelova J, Michaelidesova A, Kozubek S (2014) Determining omics spatiotemporal dimensions using exciting new nanoscopy techniques to assess complex cell responses to DNA damage: Part B structuromics. Crit Rev Eukaryot Gene Expr 24(3):225–247
Ceccaldi R, Rondinelli B, D’Andrea AD (2016) Repair pathway choices and consequences at the double-strand break. Trends Cell Biol 26(1):52–64
Mladenov E, Magin S, Soni A, Iliakis G (2016) DNA double-strand-break repair in higher eukaryotes and its role in genomic instability and cancer: cell cycle and proliferation-dependent regulation. Semin Cancer Biol 37-38:51–64
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Eberle, J.P. et al. (2017). Super-Resolution Microscopy Techniques and Their Potential for Applications in Radiation Biophysics. In: Erfle, H. (eds) Super-Resolution Microscopy. Methods in Molecular Biology, vol 1663. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7265-4_1
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7265-4_1
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7264-7
Online ISBN: 978-1-4939-7265-4
eBook Packages: Springer Protocols