Agasti, S.S., Wang, Y., Schueder, F., Sukumar, A., Jungmann, R., and Yin, P. (2017). DNA-barcoded labeling probes for highly multiplexed exchange-PAINT imaging. Chem. Sci. 8, 3080–3091. https://doi.org/10.1039/c6sc05420j.
Al-Lazikani, B., Lesk, A.M., and Chothia, C. (1997). Standard conformations for the canonical structures of immunoglobulins. J. Mol. Biol. 273, 927–948. https://doi.org/10.1006/jmbi.1997.1354.
Andreska, T., Aufmkolk, S., Sauer, M., and Blum, R. (2014). High abundance of BDNF within glutamatergic presynapses of cultured hippocampal neurons. Front. Cell. Neurosci. 8, 107. https://doi.org/10.3389/fncel.2014.00107.
Andrews, N.P., Boeckman, J.X., Manning, C.F., Nguyen, J.T., Bechtold, H., Dumitras, C., Gong, B., Nguyen, K., van der List, D., Murray, K.D., et al. (2019). A toolbox of IgG subclass-switched recombinant monoclonal anti- bodies for enhanced multiplex immunolabeling of brain. Elife 8, e43322. https://doi.org/10.7554/eLife.43322.
Arimori, T., Kitago, Y., Umitsu, M., Fujii, Y., Asaki, R., Tamura-Kawakami, K., and Takagi, J. (2017). Fv-clasp: an artificially designed small antibody frag- ment with improved production compatibility, stability, and crystallizability. Structure 25, 1611–1622.e4. https://doi.org/10.1016/j.str.2017.08.011.
Betapudi, V. (2010). Myosin II motor proteins with different functions determine the fate of lamellipodia extension during cell spreading. PLoS One 5, e8560. https://doi.org/10.1371/journal.pone.0008560.
Blumhardt, P., Stein, J., Mu€cksch, J., Stehr, F., Bauer, J., Jungmann, R., and Schwille, P. (2018). Photo-induced depletion of binding sites in DNA-PAINT microscopy. Molecules 23, E3165. https://doi.org/10.3390/molecules2312 3165.
Burnette, D.T., Shao, L., Ott, C., Pasapera, A.M., Fischer, R.S., Baird, M.A., Der Loughian, C., Delanoe-Ayari, H., Paszek, M.J., Davidson, M.W., et al. (2014). A contractile and counterbalancing adhesion system controls the 3D shape of crawling cells. J. Cell Biol. 205, 83–96. https://doi.org/10.1083/jcb. 201311104.
Chan, K.Y., Jang, M.J., Yoo, B.B., Greenbaum, A., Ravi, N., Wu, W.L., Sa´ n- chez-Guardado, L., Lois, C., Mazmanian, S.K., Deverman, B.E., and Gradi- naru, V. (2017). Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems. Nat. Neurosci. 20, 1172–1179. https://doi.org/10.1038/nn.4593.
Chen, S., Weitemier, A.Z., Zeng, X., He, L., Wang, X., Tao, Y., Huang, A.J.Y., Hashimotodani, Y., Kano, M., Iwasaki, H., et al. (2018). Near-infrared deep brain stimulation via upconversion nanoparticle-mediated optogenetics. Sci- ence 359, 679–684. https://doi.org/10.1126/science.aaq1144.
Chothia, C., and Lesk, A.M. (1987). Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196, 901–917. https://doi.org/10. 1016/0022-2836(87)90412-8.
Clark, L.A., Boriack-Sjodin, P.A., Eldredge, J., Fitch, C., Friedman, B., Hanf, K.J.M., Jarpe, M., Liparoto, S.F., Li, Y., Lugovskoy, A., et al. (2006). Affinity enhancement of an in vivo matured therapeutic antibody using structure- based computational design. Protein Sci. 15, 949–960. https://doi.org/10. 1110/ps.052030506.
Dani, A., Huang, B., Bergan, J., Dulac, C., and Zhuang, X. (2010). Superreso- lution imaging of chemical synapses in the brain. Neuron 68, 843–856. https:// doi.org/10.1016/j.neuron.2010.11.021.
Descloux, A., Grußmayer, K.S., and Radenovic, A. (2019). Parameter-free im- age resolution estimation based on decorrelation analysis. Nat. Methods 16, 918–924. https://doi.org/10.1038/s41592-019-0515-7.
Dong, J.X., Lee, Y., Kirmiz, M., Palacio, S., Dumitras, C., Moreno, C.M., Sando, R., Santana, L.F., Su€dhof, T.C., Gong, B., et al. (2019). A toolbox of nanobodies developed and validated for use as intrabodies and nanoscale immunolabels in mammalian brain neurons. Elife 8, e48750. https://doi.org/10.7554/eLife. 48750.
Dunbar, J., and Deane, C.M. (2016). ANARCI: antigen receptor numbering and receptor classification. Bioinformatics 32, 298–300. https://doi.org/10.1093/ bioinformatics/btv552.
Dunbar, J., Krawczyk, K., Leem, J., Baker, T., Fuchs, A., Georges, G., Shi, J., and Deane, C.M. (2014). SAbDab: the structural antibody database. Nucleic Acids Res. 42, D1140–D1146. https://doi.org/10.1093/nar/gkt1043.
Eklund, A.S., Ganji, M., Gavins, G., Seitz, O., and Jungmann, R. (2020). Pep- tide-PAINT super-resolution imaging using transient coiled coil interactions. Nano Lett. 20, 6732–6737. https://doi.org/10.1021/acs.nanolett.0c02620.
Farrell, M.V., Nunez, A.C., Yang, Z., Pe´ rez-Ferreros, P., Gaus, K., and Goyette,
J. (2022). Protein-PAINT: superresolution microscopy with signaling proteins. Sci. Signal. 15, eabg9782. https://doi.org/10.1126/scisignal.abg9782.
Fujii, Y., Kaneko, M., Neyazaki, M., Nogi, T., Kato, Y., and Takagi, J. (2014). PA tag: a versatile protein tagging system using a super high affinity antibody against a dodecapeptide derived from human podoplanin. Protein Expr. Purif. 95, 240–247. https://doi.org/10.1016/j.pep.2014.01.009.
Glebov, O.O., Cox, S., Humphreys, L., and Burrone, J. (2016). Neuronal activity controls transsynaptic geometry. Sci. Rep. 6, 22703. https://doi.org/10.1038/ srep22703.
Gunasekara, H., Munaweera, R., and Hu, Y.S. (2021). Chaotropic perturbation of noncovalent interactions of the hemagglutinin tag monoclonal antibody fragment enables superresolution molecular census. ACS Nano 16, 129–139. https://doi.org/10.1021/acsnano.1c04237.
Guo, S.M., Veneziano, R., Gordonov, S., Li, L., Danielson, E., Perez de Arce, K., Park, D., Kulesa, A.B., Wamhoff, E.C., Blainey, P.C., et al. (2019). Multi- plexed and high-throughput neuronal fluorescence imaging with diffusible probes. Nat. Commun. 10, 4377. https://doi.org/10.1038/s41467-019-
12372-6.
Go¨ tzke, H., Kilisch, M., Martı´nez-Carranza, M., Sograte-Idrissi, S., Rajavel, A., Schlichthaerle, T., Engels, N., Jungmann, R., Stenmark, P., Opazo, F., and Frey, S. (2019). The ALFA-tag is a highly versatile tool for nanobody-based bioscience applications. Nat. Commun. 10, 4403. https://doi.org/10.1038/ s41467-019-12301-7.
Haidar, J.N., Yuan, Q.A., Zeng, L., Snavely, M., Luna, X., Zhang, H., Zhu, W., Ludwig, D.L., and Zhu, Z. (2012). A universal combinatorial design of antibody framework to graft distinct CDR sequences: a bioinformatics approach. Pro- teins 80, 896–912. https://doi.org/10.1002/prot.23246.
Harris, L.J., Skaletsky, E., and McPherson, A. (1998). Crystallographic struc- ture of an intact IgG1 monoclonal antibody. J. Mol. Biol. 275, 861–872. https://doi.org/10.1006/jmbi.1997.1508.
Houlihan, G., Gatti-Lafranconi, P., Lowe, D., and Hollfelder, F. (2015). Directed evolution of anti-HER2 DARPins by SNAP display reveals stability/function trade-offs in the selection process. Protein Eng. Des. Sel. 28, 269–279. https://doi.org/10.1093/protein/gzv029.
Huang, B., Bates, M., and Zhuang, X. (2009). Super-resolution fluorescence microscopy. Annu. Rev. Biochem. 78, 993–1016. https://doi.org/10.1146/an- nurev.biochem.77.061906.092014.
Ikeda, K., Koga, T., Sasaki, F., Ueno, A., Saeki, K., Okuno, T., and Yokomizo, T. (2017). Generation and characterization of a human-mouse chimeric high-af- finity antibody that detects the DYKDDDDK FLAG peptide. Biochem. Biophys. Res. Commun. 486, 1077–1082. https://doi.org/10.1016/j.bbrc.2017.03.165.
Ilardi, J.M., Mochida, S., and Sheng, Z.H. (1999). Snapin: a SNARE-associated protein implicated in synaptic transmission. Nat. Neurosci. 2, 119–124. https:// doi.org/10.1038/5673.
Jungmann, R., Avendan˜ o, M.S., Woehrstein, J.B., Dai, M., Shih, W.M., and Yin,
P. (2014). Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat. Methods 11, 313–318. https://doi.org/10.1038/ nmeth.2835.
Kang, T.H., and Seong, B.L. (2020). Solubility, stability, and avidity of recom- binant antibody fragments expressed in microorganisms. Front. Microbiol. 11, 1927. https://doi.org/10.3389/fmicb.2020.01927.
Kiuchi, T., Higuchi, M., Takamura, A., Maruoka, M., and Watanabe, N. (2015). Multitarget super-resolution microscopy with high-density labeling by exchangeable probes. Nat. Methods 12, 743–746. https://doi.org/10.1038/ nmeth.3466.
Klevanski, M., Herrmannsdoerfer, F., Sass, S., Venkataramani, V., Heilemann, M., and Kuner, T. (2020). Automated highly multiplexed super-resolution imag- ing of protein nano-architecture in cells and tissues. Nat. Commun. 11, 1552. https://doi.org/10.1038/s41467-020-15362-1.
Koide, S., and Sidhu, S.S. (2009). The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins. ACS Chem. Biol. 4, 325–334. https://doi.org/10.1021/cb800314v.
Lehmann, A., Wixted, J.H.F., Shapovalov, M.V., Roder, H., Dunbrack, R.L., and Robinson, M.K. (2015). Stability engineering of anti-EGFR scFv antibodies by rational design of a lambda-to-kappa swap of the VL framework using a structure-guided approach. mAbs 7, 1058–1071. https://doi.org/10.1080/
19420862.2015.1088618.
Li, L., Chen, S., Miao, Z., Liu, Y., Liu, X., Xiao, Z.X., and Cao, Y. (2019). AbRSA:a robust tool for antibody numbering. Protein Sci. 28, 1524–1531. https://doi. org/10.1002/pro.3633.
Lima, W.C., Gasteiger, E., Marcatili, P., Duek, P., Bairoch, A., and Cosson, P. (2020). The ABCD database: a repository for chemically defined antibodies. Nucleic Acids Res. 48, D261–D264. https://doi.org/10.1093/nar/gkz714.
Miyoshi, T., Zhang, Q., Miyake, T., Watanabe, S., Ohnishi, H., Chen, J., Vish- wasrao, H.D., Chakraborty, O., Belyantseva, I.A., Perrin, B.J., et al. (2021). Semi-automated single-molecule microscopy screening of fast-dissociating specific antibodies directly from hybridoma cultures. Cell Rep. 34, 108708. https://doi.org/10.1016/j.celrep.2021.108708.
Oi, C., Gidden, Z., Holyoake, L., Kantelberg, O., Mochrie, S., Horrocks, M.H., and Regan, L. (2020). LIVE-PAINT allows super-resolution microscopy inside living cells using reversible peptide-protein interactions. Commun. Biol. 3,
458. https://doi.org/10.1038/s42003-020-01188-6.
Olivier, N., Keller, D., Go¨ nczy, P., and Manley, S. (2013). Resolution doubling in 3D-STORM imaging through improved buffers. PLoS One 8, e69004. https:// doi.org/10.1371/journal.pone.0069004.
Pleiner, T., Bates, M., Trakhanov, S., Lee, C.T., Schliep, J.E., Chug, H., Bo¨ hn- ing, M., Stark, H., Urlaub, H., and Go¨ rlich, D. (2015). Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native pro- tein complex isolation. Elife 4, e11349. https://doi.org/10.7554/eLife.11349.
Popp, M.W., Antos, J.M., Grotenbreg, G.M., Spooner, E., and Ploegh, H.L. (2007). Sortagging: a versatile method for protein labeling. Nat. Chem. Biol. 3, 707–708. https://doi.org/10.1038/nchembio.2007.31.
Rabia, L.A., Desai, A.A., Jhajj, H.S., and Tessier, P.M. (2018). Understanding and overcoming trade-offs between antibody affinity, specificity, stability and solubility. Biochem. Eng. J. 137, 365–374. https://doi.org/10.1016/j.bej. 2018.06.003.
Ricci, M.A., Manzo, C., Garcı´a-Parajo, M.F., Lakadamyali, M., and Cosma,
M.P. (2015). Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. Cell 160, 1145–1158. https://doi.org/10.1016/j.cell. 2015.01.054.
Schenck, S., Kunz, L., Sahlender, D., Pardon, E., Geertsma, E.R., Savtchouk, I., Suzuki, T., Neldner, Y., Sˇtefanic´, S., Steyaert, J., et al. (2017). Generation and characterization of anti-VGLUT nanobodies acting as inhibitors of transport. Biochemistry 56, 3962–3971. https://doi.org/10.1021/acs.bio- chem.7b00436.
Schneider, C.A., Rasband, W.S., and Eliceiri, K.W. (2012). NIH Image to Im- ageJ: 25 years of image analysis. Nat. Methods 9, 671–675. https://doi.org/ 10.1038/nmeth.2089.
Sela-Culang, I., Kunik, V., and Ofran, Y. (2013). The structural basis of anti- body-antigen recognition. Front. Immunol. 4, 302. https://doi.org/10.3389/ fimmu.2013.00302.
Shi, X., Lim, J., and Ha, T. (2010). Acidification of the oxygen scavenging sys- tem in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe. Anal. Chem. 82, 6132–6138. https://doi.org/10.1021/ ac1008749.
Sidenstein, S.C., D’Este, E., Bo¨ hm, M.J., Danzl, J.G., Belov, V.N., and Hell,
S.W. (2016). Multicolour multilevel STED nanoscopy of actin/spectrin organi- zation at synapses. Sci. Rep. 6, 26725. https://doi.org/10.1038/srep26725.
Sircar, A., Sanni, K.A., Shi, J., and Gray, J.J. (2011). Analysis and modeling of the variable region of camelid single-domain antibodies. J. Immunol. 186, 6357–6367. https://doi.org/10.4049/jimmunol.1100116.
Sograte-Idrissi, S., Schlichthaerle, T., Duque-Afonso, C.J., Alevra, M., Strauss, S., Moser, T., Jungmann, R., Rizzoli, S.O., and Opazo, F. (2020). Circumven- tion of common labelling artefacts using secondary nanobodies. Nanoscale 12, 10226–10239. https://doi.org/10.1039/d0nr00227e.
Sugiyama, Y., Kawabata, I., Sobue, K., and Okabe, S. (2005). Determination of absolute protein numbers in single synapses by a GFP-based calibration tech- nique. Nat. Methods 2, 677–684. https://doi.org/10.1038/nmeth783.
Suzuki, J., Kanemaru, K., Ishii, K., Ohkura, M., Okubo, Y., and Iino, M. (2014). Imaging intraorganellar Ca2+ at subcellular resolution using CEPIA. Nat. Com- mun. 5, 4153. https://doi.org/10.1038/ncomms5153.
Tabata, S., Nampo, M., Mihara, E., Tamura-Kawakami, K., Fujii, I., and Takagi,
J. (2010). A rapid screening method for cell lines producing singly-tagged re- combinant proteins using the "TARGET tag" system. J. Proteomics 73, 1777–1785. https://doi.org/10.1016/j.jprot.2010.05.012.
Tanaka, T., Thomas, J., Van Montfort, R., Miller, A., and Rabbitts, T. (2021). Pan RAS-binding compounds selected from a chemical library by inhibiting interaction between RAS and a reduced affinity intracellular antibody. Sci. Rep. 11, 1712. https://doi.org/10.1038/s41598-021-81262-z.
Tao-Cheng, J.H., Azzam, R., Crocker, V., Winters, C.A., and Reese, T. (2015). Depolarization of hippocampal neurons induces formation of nonsynaptic NMDA receptor islands resembling nascent postsynaptic densities. eNeuro 2, ENEURO.0066-15.2015. https://doi.org/10.1523/ENEURO.0066-15.2015.
Tas, R.P., Albertazzi, L., and Voets, I.K. (2021). Small peptide-protein interac- tion pair for genetically encoded, fixation compatible peptide-PAINT. Nano Lett. 21, 9509–9516. https://doi.org/10.1021/acs.nanolett.1c02895.
Thul, P.J., A˚ kesson, L., Wiking, M., Mahdessian, D., Geladaki, A., Ait Blal, H., Alm, T., Asplund, A., Bjo¨ rk, L., Breckels, L.M., et al. (2017). A subcellular map of the human proteome. Science 356, eaal3321. https://doi.org/10.1126/sci- ence.aal3321.
Tiller, K.E., Li, L., Kumar, S., Julian, M.C., Garde, S., and Tessier, P.M. (2017). Arginine mutations in antibody complementarity-determining regions display context-dependent affinity/specificity trade-offs. J. Biol. Chem. 292, 16638– 16652. https://doi.org/10.1074/jbc.M117.783837.
Tojkander, S., Gateva, G., Schevzov, G., Hotulainen, P., Naumanen, P., Martin, C., Gunning, P.W., and Lappalainen, P. (2011). A molecular pathway for myosin II recruitment to stress fibers. Curr. Biol. 21, 539–550. https://doi. org/10.1016/j.cub.2011.03.007.
Tsumoto, K., Ogasahara, K., Ueda, Y., Watanabe, K., Yutani, K., and Kumagai,
I. (1995). Role of Tyr residues in the contact region of anti-lysozyme mono- clonal antibody HyHEL10 for antigen binding. J. Biol. Chem. 270, 18551– 18557. https://doi.org/10.1074/jbc.270.31.18551.
Vallet-Courbin, A., Larivie` re, M., Hocquellet, A., Hemadou, A., Parimala, S.N., Laroche-Traineau, J., Santarelli, X., Clofent-Sanchez, G., Jacobin-Valat, M.J., and Noubhani, A. (2017). A recombinant human anti-platelet scFv antibody produced in Pichia pastoris for atheroma targeting. PLoS One 12, e0170305. https://doi.org/10.1371/journal.pone.0170305.
van de Linde, S., Lo¨ schberger, A., Klein, T., Heidbreder, M., Wolter, S., Heile- mann, M., and Sauer, M. (2011). Direct stochastic optical reconstruction mi- croscopy with standard fluorescent probes. Nat. Protoc. 6, 991–1009. https://doi.org/10.1038/nprot.2011.336.
Watanabe, N., and Mitchison, T.J. (2002). Single-molecule speckle analysis of actin filament turnover in lamellipodia. Science 295, 1083–1086. https://doi. org/10.1126/science.1067470.
Watson, J.F., Pinggera, A., Ho, H., and Greger, I.H. (2021). AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP g8 interactions. Nat. Commun. 12, 5083. https://doi.org/10.1038/s41467- 021-25281-4.
Wilhelm, B.G., Mandad, S., Truckenbrodt, S., Kro¨ hnert, K., Scha¨ fer, C., Rammner, B., Koo, S.J., Claßen, G.A., Krauss, M., Haucke, V., et al. (2014). Composition of isolated synaptic boutons reveals the amounts of vesicle traf- ficking proteins. Science 344, 1023–1028. https://doi.org/10.1126/science.
1252884.
Xu, K., Zhong, G., and Zhuang, X. (2013). Actin, spectrin, and associated pro- teins form a periodic cytoskeletal structure in axons. Science 339, 452–456. https://doi.org/10.1126/science.1232251.
Yamashiro, S., Mizuno, H., Smith, M.B., Ryan, G.L., Kiuchi, T., Vavylonis, D., and Watanabe, N. (2014). New single-molecule speckle microscopy reveals modification of the retrograde actin flow by focal adhesions at nanometer scales. Mol. Biol. Cell 25, 1010–1024. https://doi.org/10.1091/mbc.E13-03- 0162.
Yamashita, T., Mizohata, E., Nagatoishi, S., Watanabe, T., Nakakido, M., Iwa- nari, H., Mochizuki, Y., Nakayama, T., Kado, Y., Yokota, Y., et al. (2019). Affinity improvement of a cancer-targeted antibody through alanine-induced adjust-ment of antigen-antibody interface. Structure 27, 519–527.e5. https://doi. org/10.1016/j.str.2018.11.002.
Ye, X., and Cai, Q. (2014). Snapin-mediated BACE1 retrograde transport is essential for its degradation in lysosomes and regulation of APP processing in neurons. Cell Rep. 6, 24–31. https://doi.org/10.1016/j.celrep.2013.12.008.
Zhou, H., Fisher, R.J., and Papas, T.S. (1994). Optimization of primer se- quences for mouse scFv repertoire display library construction. Nucleic Acids Res. 22, 888–889. https://doi.org/10.1093/nar/22.5.888.
Zhou, R., Han, B., Xia, C., and Zhuang, X. (2019). Membrane-associated peri- odic skeleton is a signaling platform for RTK transactivation in neurons. Sci- ence 365, 929–934. https://doi.org/10.1126/science.aaw5937.
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