Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich I V, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong S-C, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee T-H, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen T-O, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CA and Weiss S (2021) FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife, 10:e60416 Link


Celetti G*, Paci G*, Caria J, VanDelinder V#, Bachand G# and Lemke EA# (2020) The liquid state of FG-nucleoporins mimics permeability barrier properties of nuclear pore complexes. J Cell Biol, 219 (1): e201907157 (*indicates joint contribution, #indicates joint correspondence) Link

Koehler C, Estrada Girona G, Reinkemeier CD and Lemke EA (2020) Inducible genetic code expansion in eukaryotes. ChemBioChem, 21:3216–3219 Link

Paci G, Zheng T, Caria J, Zilman A# and Lemke EA# (2020) Molecular determinants of large cargo transport into the nucleus. Elife, 9:e55963 (#indicates joint correspondence) Link

Reinkemeier CD and Lemke EA (2020) Raising the ribosomal repertoire. Nat Chem, 12:503–504 Link


Chowdhury A, Kovalenko SA, Aramburu IV, Tan PS, Ernsting NP and Lemke EA (2019) Mechanism-dependent modulation of ultrafast interfacial water dynamics in intrinsically disordered protein complexes. Angew Chemie Int Ed, 58:4720–4724 Link

Chowdhury A, Yu M and Lemke EA (2019) Phase separation comes of age: From phenomenology to single molecules. Mol Cell, 74:413–415 Link

Lu M, Ma X, Castillo-Menendez LR, Gorman J, Alsahafi N, Ermel U, Terry DS, Chambers M, Peng D, Zhang B, Zhou T, Reichard N, Wang K, Grover JR, Carman BP, Gardner MR, Nikić-Spiegel I, Sugawara A, Arthos J, Lemke EA, Smith AB, Farzan M, Abrams C, Munro JB, McDermott AB, Finzi A, Kwong PD, Blanchard SC, Sodroski JG and Mothes W (2019) Associating HIV-1 envelope glycoprotein structures with states on the virus observed by smFRET. Nature, 568:415–419 Link

Reinkemeier CD, Girona GE and Lemke EA (2019) Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes. Science, 363:eaaw2644 Link


Brabham RL, Spears RJ, Walton J, Tyagi S, Lemke EA and Fascione MA (2018) Palladium-unleashed proteins: Gentle aldehyde decaging for site-selective protein modification. Chem Commun, 54:1501–1504 Link

Das DK, Govindan R, Nikić-Spiegel I, Krammer F, Lemke EA and Munro JB (2018) Direct visualization of the conformational dynamics of single influenza hemagglutinin trimers. Cell, 174:926–937.e12 Link

Fuertes G*, Banterle N*, Ruff KM*, Chowdhury A*, Pappu RV, Svergun DI# and Lemke EA# (2018) Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.” Science, 361:eaau8230 (*indicates joint contribution, #indicates joint correspondence) Link

Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Rezaei Adariani S, Ambrose B, Aznauryan M, Barth A, Birkedal V, Bowen ME, Chen H, Cordes T, Eilert T, Fijen C, Gebhardt C, Götz M, Gouridis G, Gratton E, Ha T, Hao P, Hanke CA, Hartmann A, Hendrix J, Hildebrandt LL, Hirschfeld V, Hohlbein J, Hua B, Hübner CG, Kallis E, Kapanidis AN, Kim J-Y, Krainer G, Lamb DC, Lee NK, Lemke EA, Levesque B, Levitus M, McCann JJ, Naredi-Rainer N, Nettels D, Ngo T, Qiu R, Robb NC, Röcker C, Sanabria H, Schlierf M, Schröder T, Schuler B, Seidel H, Streit L, Thurn J, Tinnefeld P, Tyagi S, Vandenberk N, Vera AM, Weninger KR, Wünsch B, Yanez-Orozco IS, Michaelis J, Seidel CAM, Craggs TD and Hugel T (2018) Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study. Nat Methods, 15:669–676 Link

Koehler C and Lemke EA (2018) MultiBacTAG-genetic code expansion using the baculovirus expression system in Sf21 cells. Pages 297–311 in: Noncanonical amino acids; Methods in molecular biology, vol. 1728 (ed. Lemke EA), Humana Press, New York Link

Kormos A, Koehler C, Fodor EA, Rutkai ZR, Martin ME, Mező G, Lemke EA and Kele P (2018) Bistetrazine-cyanines as double-clicking fluorogenic two-point binder or crosslinker probes. Chem Eur J, 24:8841–8847 Link

Kozma E, Paci G, Estrada Girona G, Lemke EA and Kele P (2018) Fluorogenic tetrazine-siliconrhodamine probe for the labeling of noncanonical amino acid tagged proteins. Pages 337–363 in: Noncanonical amino acids; Methods in molecular biology, vol. 1728 (ed. Lemke E), Humana Press, New York Link

Lemke EA (2018) Noncanonical amino acids: Methods and protocols. 408 pages, Humana Press, New York Link

Mikhaleva S and Lemke EA (2018) Beyond the transport function of import receptors: What’s all the FUS about? Cell, 173:549–553 Link

Tan PS, Aramburu IV, Mercadante D, Tyagi S, Chowdhury A, Spitz D, Shammas SL, Gräter F and Lemke EA (2018) Two differential binding mechanisms of FG-nucleoporins and nuclear transport receptors. Cell Rep, 22:3660–3671 Link

Tan PS and Lemke EA (2018) Probing differential binding mechanisms of phenylalanine-glycine-rich nucleoporins by single-molecule FRET. Pages 327–346 in: Intrinsically disordered proteins; Methods in Enzymology, vol. 611 (ed. Rhoades E), Academic Press, Cambridge Link

Wawryszyn M, Sauter PF, Nieger M, Koos MRM, Koehler C, Luy B, Lemke EA and Bräse S (2018) Synthesis of azido-glycans for chemical glycomodification of proteins. European J Org Chem, 2018:4296–4305 Link


Aramburu IV and Lemke EA (2017) Floppy but not sloppy: Interaction mechanism of FG-nucleoporins and nuclear transport receptors. Semin Cell Dev Biol, 68:34–41 Link

Demeter O*, Kormos A*, Koehler C, Mező G, Németh K, Kozma E, Takács LB, Lemke EA# and Kele P# (2017) Bisazide cyanine dyes as fluorogenic probes for bis-cyclooctynylated peptide tags and as fluorogenic cross-linkers of cyclooctynylated protein. Bioconjug Chem, 28:1552–1559 (*indicates joint contribution, #indicates joint correspondence) Link

Fuertes G, Banterle N, Ruff KM, Chowdhury A, Mercadante D, Koehler C, Kachala M, Estrada Girona G, Milles S, Mishra A, Onck PR, Gräter F, Esteban-Martín S, Pappu R V., Svergun DI and Lemke EA (2017) Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements. Proc Natl Acad Sci USA, 114:E6342–E6351 Link

Gupta K, Watson AA, Baptista T, Scheer E, Chambers AL, Koehler C, Zou J, Obong-Ebong I, Kandiah E, Temblador A, Round A, Forest E, Man P, Bieniossek C, Laue ED, Lemke EA, Rappsilber J, Robinson C V., Devys D, Tora L and Berger I (2017) Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID. eLife, 6:e30395 Link

Kipper K, Lundius EG, Ćurić V, Nikić I, Wiessler M, Lemke EA and Elf J (2017) Application of noncanonical amino acids for protein labeling in a genomically recoded Escherichia coli. ACS Synth Biol, 6:233–255 Link

Kozma E, Estrada Girona G, Paci G, Lemke EA and Kele P (2017) Bioorthogonal double-fluorogenic siliconrhodamine probes for intracellular super-resolution microscopy. Chem Commun, 53:6696–6699 Link

Kucher S, Korneev S, Tyagi S, Apfelbaum R, Grohmann D, Lemke EA, Klare JP, Steinhoff H-J and Klose D (2017) Orthogonal spin labeling using click chemistry for in vitro and in vivo applications. J Magn Reson, 275:38–45 Link

Mercadante D, Wagner JA, Aramburu I V., Lemke EA and Gräter F (2017) Sampling long- versus short-range interactions defines the ability of force fields to reproduce the dynamics of intrinsically disordered proteins. J Chem Theory Comput, 13:3964–3974 Link

Paci G and Lemke EA (2017) Shining a light on phase separation in the cell. Cell, 168:11–13 Link

Sakin V, Hanne J, Dunder J, Anders-Össwein M, Laketa V, Nikić I, Kräusslich H-G, Lemke EA and Müller B (2017) A versatile tool for live-cell imaging and super-resolution nanoscopy studies of HIV-1 Env distribution and mobility. Cell Chem Biol, 24:635–645.e5 Link

Warner JB*, Ruff KM*, Tan PS, Lemke EA, Pappu R V. and Lashuel HA (2017) Monomeric huntingtin exon 1 has similar overall structural features for wild-type and pathological polyglutamine lengths. J Am Chem Soc, 139:14456–14469 (*indicates joint contribution) Link


Banterle N and Lemke EA (2016) Nanoscale devices for linkerless long-term single-molecule observation. Curr Opin Biotechnol, 39:105–112 Link

Knorr G, Kozma E, Herner A, Lemke EA and Kele P (2016) New red-emitting tetrazine-phenoxazine fluorogenic labels for live-cell intracellular bioorthogonal labeling schemes. Chem Eur J, 22:8972–8979 Link

Koehler C, Sauter PF, Wawryszyn M, Girona GE, Gupta K, Landry JJM, Fritz MH-Y, Radic K, Hoffmann J-E, Chen ZA, Zou J, Tan PS, Galik B, Junttila S, Stolt-Bergner P, Pruneri G, Gyenesei A, Schultz C, Biskup MB, Besir H, Benes V, Rappsilber J, Jechlinger M, Korbel JO, Berger I, Braese S and Lemke EA (2016) Genetic code expansion for multiprotein complex engineering. Nat Methods, 13:997–1000 Link

Kozma E, Nikić I, Varga BR, Aramburu IV, Kang JH, Fackler OT, Lemke EA and Kele P (2016) Hydrophilic trans -cyclooctenylated noncanonical amino acids for fast intracellular protein labeling. ChemBioChem, 17:1518–1524 Link

Lemke EA (2016) The multiple faces of disordered nucleoporins. J Mol Biol, 428:2011–2024 Link

Nikić I, Estrada Girona G, Kang JH, Paci G, Mikhaleva S, Koehler C, Shymanska N V., Ventura Santos C, Spitz D and Lemke EA (2016) Debugging eukaryotic genetic code expansion for site-specific click-PAINT super-resolution microscopy. Angew Chemie Int Ed, 55:16172–16176 Link

Sakin V, Paci G, Lemke EA and Müller B (2016) Labeling of virus components for advanced, quantitative imaging analyses. FEBS Lett, 590:1896–1914 Link


Delaforge E, Milles S, Bouvignies G, Bouvier D, Boivin S, Salvi N, Maurin D, Martel A, Round A, Lemke EA, Ringkjøbing Jensen M, Hart DJ and Blackledge M (2015) Large-scale conformational dynamics control H5N1 Influenza Polymerase PB2 binding to Importin α. J Am Chem Soc, 137:15122–15134 Link

Hoffmann J-E, Plass T, Nikić I, Aramburu IV, Koehler C, Gillandt H, Lemke EA and Schultz C (2015) Highly stable trans -cyclooctene amino acids for live-cell labeling. Chem Eur J, 21:12266–12270 Link

Mercadante D, Milles S, Fuertes G, Svergun DI, Lemke EA and Gräter F (2015) Kirkwood–Buff approach rescues overcollapse of a disordered protein in canonical protein force fields. J Phys Chem B, 119:7975–7984 Link

Milles S, Mercadante D, Aramburu IV, Jensen MR, Banterle N, Koehler C, Tyagi S, Clarke J, Shammas SL, Blackledge M#, Gräter F# and Lemke EA# (2015) Plasticity of an ultrafast interaction between nucleoporins and nuclear transport receptors. Cell, 163:734–745 (# indicates joint correspondence) Link

Nikić I, Kang JH, Girona GE, Aramburu IV and Lemke EA (2015) Labeling proteins on live mammalian cells using click chemistry. Nat Protoc, 10:780–791 Link

Nikić I and Lemke EA (2015) Genetic code expansion enabled site-specific dual-color protein labeling: Superresolution microscopy and beyond. Curr Opin Chem Biol, 28:164–173 Link

Tyagi S and Lemke EA (2015) Single-molecule FRET and crosslinking studies in structural biology enabled by noncanonical amino acids. Curr Opin Struct Biol, 32:66–73 Link

von Appen A, Kosinski J, Sparks L, Ori A, DiGuilio AL, Vollmer B, Mackmull M-T, Banterle N, Parca L, Kastritis P, Buczak K, Mosalaganti S, Hagen W, Andres-Pons A, Lemke EA, Bork P, Antonin W, Glavy JS, Bui KH and Beck M (2015) In situ structural analysis of the human nuclear pore complex. Nature, 526:140–143 Link

Vreja IC, Nikić I, Göttfert F, Bates M, Kröhnert K, Outeiro TF, Hell SW, Lemke EA and Rizzoli SO (2015) Super-resolution microscopy of clickable amino acids reveals the effects of fluorescent protein tagging on protein assemblies. ACS Nano, 9:11034–11041 Link

Wagner JA, Mercadante D, Nikić I, Lemke EA and Gräter F (2015) Origin of orthogonality of strain-promoted click reactions. Chem Eur J, 21:12431–12435 Link


Dunne M, Mertens HDT, Garefalaki V, Jeffries CM, Thompson A, Lemke EA, Svergun DI, Mayer MJ, Narbad A and Meijers R (2014) The CD27L and CTP1L endolysins targeting Clostridia contain a built-in trigger and release factor. PLOS Pathog, 10:e1004228 Link

Herner A, Estrada Girona G, Nikić I, Kállay M, Lemke EA and Kele P (2014) New generation of bioorthogonally applicable fluorogenic dyes with visible excitations and large Stokes shifts. Bioconjug Chem, 25:1370–1374 Link

Lemke EA (2014) The exploding genetic code. ChemBioChem, 15:1691–1694 Link

Milles S and Lemke EA (2014) Mapping multivalency and differential affinities within large Intrinsically disordered protein complexes with segmental motion analysis. Angew Chemie Int Ed, 53:7364–7367 Link

Nikić I, Plass T, Schraidt O, Szymański J, Briggs JAG, Schultz C and Lemke EA (2014) Minimal tags for rapid dual-color live-cell labeling and super-resolution microscopy. Angew Chemie Int Ed, 53:2245–2249 Link

Pavic K, Rios P, Dzeyk K, Koehler C, Lemke EA and Köhn M (2014) Unnatural amino acid mutagenesis reveals dimerization as a negative regulatory mechanism of VHR’s phosphatase activity. ACS Chem Biol, 9:1451–1459 Link

Tyagi S, VanDelinder V, Banterle N, Fuertes G, Milles S, Agez M and Lemke EA (2014) Continuous throughput and long-term observation of single-molecule FRET without immobilization. Nat Methods, 11:297–300 Link


Banterle N, Bui KH, Lemke EA and Beck M (2013) Fourier ring correlation as a resolution criterion for super-resolution microscopy. J Struct Biol, 183:363–367 Link

Herner A, Nikić I, Kállay M, Lemke EA and Kele P (2013) A new family of bioorthogonally applicable fluorogenic labels. Org Biomol Chem, 11:3297 Link

Lukinavičius G, Umezawa K, Olivier N, Honigmann A, Yang G, Plass T, Mueller V, Reymond L, Corrêa Jr IR, Luo Z-G, Schultz C, Lemke EA, Heppenstall P, Eggeling C, Manley S and Johnsson K (2013) A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. Nat Chem, 5:132–139 Link

Milles S, Huy Bui K, Koehler C, Eltsov M, Beck M and Lemke EA (2013) Facilitated aggregation of FG nucleoporins under molecular crowding conditions. EMBO Rep, 14:178–183 Link

Milles S and Lemke EA (2013) What precision-protein-tuning and nano-resolved single molecule sciences can do for each other. BioEssays, 35:65–74 Link

Ori A, Banterle N, Iskar M, Andres-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P, Lemke EA and Beck M (2013) Cell type-specific nuclear pores: A case in point for context-dependent stoichiometry of molecular machines. Mol Syst Biol, 9:648 Link

Tyagi S and Lemke EA (2013) Genetically encoded click chemistry for single-molecule FRET of proteins. Pages 169–187 in: Laboratory Methods in Cell Biology, Imaging; Methods in Cell Biology, vol. 113 (ed. Conn MP), Academic Press, Cambridge Link


Borrmann A, Milles S, Plass T, Dommerholt J, Verkade JMM, Wießler M, Schultz C, van Hest JCM, van Delft FL and Lemke EA (2012) Genetic encoding of a bicyclo[6.1.0]nonyne-charged amino acid enables fast cellular protein imaging by metal-free ligation. ChemBioChem, 13:2094–2099 Link

Krishnan R, Goodman JL, Mukhopadhyay S, Pacheco CD, Lemke EA, Deniz AA and Lindquist S (2012) Conserved features of intermediates in amyloid assembly determine their benign or toxic states. Proc Natl Acad Sci USA, 109:11172–11177 Link

Milles S, Koehler C, Gambin Y, Deniz AA and Lemke EA (2012) Intramolecular three-colour single pair FRET of intrinsically disordered proteins with increased dynamic range. Mol Biosyst, 8:2531 Link

Milles S, Tyagi S, Banterle N, Koehler C, VanDelinder V, Plass T, Neal AP and Lemke EA (2012) Click strategies for single-molecule protein fluorescence. J Am Chem Soc, 134:5187–5195 Link

Plass T, Milles S, Koehler C, Szymański J, Mueller R, Wießler M, Schultz C and Lemke EA (2012) Amino acids for diels-alder reactions in living cells. Angew Chemie Int Ed, 51:4166–4170 Link


Gambin Y, VanDelinder V, Ferreon ACM, Lemke EA, Groisman A and Deniz AA (2011) Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing. Nat Methods, 8:239–241 Link

Lemke EA (2011) Site-specific labeling of proteins for single-molecule FRET measurements using genetically encoded ketone functionalities. Pages 3–15 in: Bioconjugation Protocols; Methods in Molecular Biology, vol. 751 (ed. Mark SS), Humana Press, New York Link

Lemke EA and Schultz C (2011) Principles for designing fluorescent sensors and reporters. Nat Chem Biol, 7:480–483 Link

Milles S and Lemke EA (2011) Single molecule study of the intrinsically disordered FG-repeat Nucleoporin 153. Biophys J, 101:1710–1719 Link

Plass T, Milles S, Koehler C, Schultz C and Lemke EA (2011) Genetically encoded copper-free click chemistry. Angew Chemie Int Ed, 50:3878–3881 Link


Lemke EA (2010) Precision control of cellular pathways with light. ChemBioChem, 11:1825–1827 Link


Ferreon ACM, Gambin Y, Lemke EA and Deniz AA (2009) Interplay of α-synuclein binding and conformational switching probed by single-molecule fluorescence. Proc Natl Acad Sci USA, 106:5645–5650 Link

Gambin Y, Schug A, Lemke EA, Lavinder JJ, Ferreon ACM, Magliery TJ, Onuchic JN and Deniz AA (2009) Direct single-molecule observation of a protein living in two opposed native structures. Proc Natl Acad Sci USA, 106:10153–10158 Link

Lee HS, Guo J, Lemke EA, Dimla RD and Schultz PG (2009) Genetic incorporation of a small, environmentally sensitive, fluorescent probe into proteins in Saccharomyces cerevisiae. J Am Chem Soc, 131:12921–12923 Link

Lemke EA, Gambin Y, Vandelinder V, Brustad EM, Liu H-W, Schultz PG, Groisman A and Deniz AA (2009) Microfluidic device for single-molecule experiments with enhanced photostability. J Am Chem Soc, 131:13610–13612 Link


Brustad EM, Lemke EA, Schultz PG and Deniz AA (2008) A general and efficient method for the site-specific dual-labeling of proteins for single molecule fluorescence resonance energy transfer. J Am Chem Soc, 130:17664–17665 Link

Deniz AA, Mukhopadhyay S and Lemke EA (2008) Single-molecule biophysics: At the interface of biology, physics and chemistry. J R Soc Interface, 5:15–45 Link


Henkel AW, Dittrich PS, Groemer TW, Lemke EA, Klingauf J, Klafki HW, Lewczuk P, Esselmann H, Schwille P, Kornhuber J and Wiltfang J (2007) Immune complexes of auto-antibodies against Aβ1-42 peptides patrol cerebrospinal fluid of non-Alzheimer’s patients. Mol Psychiatry, 12:601–610 Link

Lemke EA, Summerer D, Geierstanger BH, Brittain SM and Schultz PG (2007) Control of protein phosphorylation with a genetically encoded photocaged amino acid. Nat Chem Biol, 3:769–772 Link

Mukhopadhyay S, Krishnan R, Lemke EA, Lindquist S and Deniz AA (2007) A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures. Proc Natl Acad Sci USA, 104:2649–2654 Link


Takamori S, Holt M, Stenius K, Lemke EA, Grønborg M, Riedel D, Urlaub H, Schenck S, Brügger B, Ringler P, Müller SA, Rammner B, Gräter F, Hub JS, De Groot BL, Mieskes G, Moriyama Y, Klingauf J, Grubmüller H, Heuser J, Wieland F and Jahn R (2006) Molecular anatomy of a trafficking organelle. Cell, 127:831–846 Link


Jordan R, Lemke EA and Klingauf J (2005) Visualization of synaptic vesicle movement in intact synaptic boutons using fluorescence fluctuation spectroscopy. Biophys J, 89:2091–2102 Link

Lemke EA and Klingauf J (2005) Single synaptic vesicle tracking in individual hippocampal boutons at rest and during synaptic activity. J Neurosci, 25:11034–11044 Link


Chakraborty R, Lemke EA, Cao Z, Klebba PE and Van Der Helm D (2003) Identification and mutational studies of conserved amino acids in the outer membrane receptor protein, FepA, which affect transport but not binding of ferric-enterobactin in Escherichia coli. BioMetals, 4:507–518 Link