The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.
Bright monomeric near-infrared fluorescent proteins as tags and biosensors for multiscale imaging
Open accessAbstract
Monomeric near-infrared (NIR) fluorescent proteins (FPs) are in high demand as protein tags and components of biosensors for deep-tissue imaging and multicolour microscopy. We report three bright and spectrally distinct monomeric NIR FPs, termed miRFPs, engineered from bacterial phytochrome, which can be used as easily as GFP-like FPs. miRFPs are 2–5-fold brighter in mammalian cells than other monomeric NIR FPs and perform well in protein fusions, allowing multicolour structured illumination microscopy. miRFPs enable development of several types of NIR biosensors, such as for protein–protein interactions, RNA detection, signalling cascades and cell fate. We demonstrate this by engineering the monomeric fluorescence complementation reporters, the IκBα reporter for NF-κB pathway and the cell cycle biosensor for detection of proliferation status of cells in culture and in animals. miRFPs allow non-invasive visualization and detection of biological processes at different scales, from super-resolution microscopy to in vivo imaging, using the same probes.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
NF-κB regulation in the immune system
Li, Q., & Verma, I. M. (2002) · Nature Reviews Immunology · doi:10.1038/nri910 · Cited by 4,007
A clearer vision for in vivo imaging
Weissleder, R. (2001) · Nature Biotechnology · doi:10.1038/86684 · Cited by 3,839
The NF- B Family of Transcription Factors and Its Regulation
Oeckinghaus, A., & Ghosh, S. (2009) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000034 · Cited by 2,842
A guide to choosing fluorescent proteins
Shaner, N. C., Steinbach, P. A., & Tsien, R. Y. (2005) · Nature Methods · doi:10.1038/nmeth819 · Cited by 2,840
Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression
Sakaue-Sawano, A., Kurokawa, H., Morimura, T., Hanyu, A., Hama, H., Osawa, H., Kashiwagi, S., Fukami, K., Miyata, T., Miyoshi, H., et al. (2008) · Cell · doi:10.1016/j.cell.2007.12.033 · Cited by 2,173
Hydrodynamics-based transfection in animals by systemic administration of plasmid DNA
Liu, F., Song, Y. K., & Liu, D. (1999) · Gene Therapy · doi:10.1038/sj.gt.3300947 · Cited by 1,727
The IKK NF-κB system: a treasure trove for drug development
Karin, M., Yamamoto, Y., & Wang, Q. M. (2004) · Nature Reviews Drug Discovery · doi:10.1038/nrd1279 · Cited by 1,364
Development of a self-inactivating lentivirus vector
Miyoshi, H., Blömer, U., Takahashi, M., Gage, F. H., & Verma, I. M. (1998) · Journal of Virology · doi:10.1128/jvi.72.10.8150-8157.1998 · Cited by 1,196
NF-κB functions in synaptic signaling and behavior
Meffert, M. K., Chang, J. M., Wiltgen, B. J., Fanselow, M. S., & Baltimore, D. (2003) · Nature Neuroscience · doi:10.1038/nn1110 · Cited by 690
Bright and stable near-infrared fluorescent protein for in vivo imaging
Filonov, G. S., Piatkevich, K. D., Ting, L.-M., Zhang, J., Kim, K., & Verkhusha, V. V. (2011) · Nature Biotechnology · doi:10.1038/nbt.1918 · Cited by 688
Self-citationMammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome
Shu, X., Royant, A., Lin, M. Z., Aguilera, T. A., Lev-Ram, V., Steinbach, P. A., & Tsien, R. Y. (2009) · Science · doi:10.1126/science.1168683 · Cited by 675
Far-red fluorescent tags for protein imaging in living tissues
Shcherbo, D., Murphy, C. S., Ermakova, G. V., Solovieva, E. A., Chepurnykh, T. V., Shcheglov, A. S., Verkhusha, V. V., Pletnev, V. Z., Hazelwood, K. L., Roche, P. M., et al. (2009) · Biochemical Journal · doi:10.1042/bj20081949 · Cited by 563
Self-citationNear-infrared fluorescent proteins for multicolor in vivo imaging
Shcherbakova, D. M., & Verkhusha, V. V. (2013) · Nature Methods · doi:10.1038/nmeth.2521 · Cited by 541
Self-citationStafford, W. F. (1992) · Analytical Biochemistry · doi:10.1016/0003-2697(92)90316-y · Cited by 515
A Brief History of Phytochromes
Rockwell, N. C., & Lagarias, J. C. (2010) · ChemPhysChem · doi:10.1002/cphc.200900894 · Cited by 360
An Enhanced Monomeric Blue Fluorescent Protein with the High Chemical Stability of the Chromophore
Subach, O. M., Cranfill, P. J., Davidson, M. W., & Verkhusha, V. V. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028674 · Cited by 352
Self-citationIdentifying off-target effects and hidden phenotypes of drugs in human cells
MacDonald, M. L., Lamerdin, J., Owens, S., Keon, B. H., Bilter, G. K., Shang, Z., Huang, Z., Yu, H., Dias, J., Minami, T., et al. (2006) · Nature Chemical Biology · doi:10.1038/nchembio790 · Cited by 293
Imaging dynamics of endogenous mitochondrial RNA in single living cells
Ozawa, T., Natori, Y., Sato, M., & Umezawa, Y. (2007) · Nature Methods · doi:10.1038/nmeth1030 · Cited by 282
Single β-Actin mRNA Detection in Neurons Reveals a Mechanism for Regulating Its Translatability
Buxbaum, A. R., Wu, B., & Singer, R. H. (2014) · Science · doi:10.1126/science.1242939 · Cited by 280
Fluorescence quantum yield of oxazine and carbazine laser dyes
Sens, R., & Drexhage, K. H. (1981) · Journal of Luminescence · doi:10.1016/0022-2313(81)90075-2 · Cited by 265
Miller, K. E., Kim, Y., Huh, W.-K., & Park, H.-O. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.03.005 · Cited by 250
Whitfield, M. L., Zheng, L.-X., Baldwin, A., Ohta, T., Hurt, M. M., & Marzluff, W. F. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.12.4188-4198.2000 · Cited by 248
Chu, J., Haynes, R. D., Corbel, S. Y., Li, P., González-González, E., Burg, J. S., Ataie, N. J., Lam, A. J., Cranfill, P. J., Baird, M. A., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2888 · Cited by 230
Philo, J. S. (2006) · Analytical Biochemistry · doi:10.1016/j.ab.2006.04.053 · Cited by 216
Wagner, J. R., Zhang, J., von Stetten, D., Günther, M., Murgida, D. H., Mroginski, M. A., Walker, J. M., Forest, K. T., Hildebrandt, P., & Vierstra, R. D. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m709355200 · Cited by 207
A noncytotoxic DsRed variant for whole-cell labeling
Strack, R. L., Strongin, D. E., Bhattacharyya, D., Tao, W., Berman, A., Broxmeyer, H. E., Keenan, R. J., & Glick, B. S. (2008) · Nature Methods · doi:10.1038/nmeth.1264 · Cited by 193
Natural Photoreceptors as a Source of Fluorescent Proteins, Biosensors, and Optogenetic Tools
Shcherbakova, D. M., Shemetov, A. A., Kaberniuk, A. A., & Verkhusha, V. V. (2015) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060614-034411 · Cited by 189
Self-citationA Rapidly Maturing Far-Red Derivative of DsRed-Express2 for Whole-Cell Labeling
Strack, R. L., Hein, B., Bhattacharyya, D., Hell, S. W., Keenan, R. J., & Glick, B. S. (2009) · Biochemistry · doi:10.1021/bi900870u · Cited by 187
A naturally monomeric infrared fluorescent protein for protein labeling in vivo
Yu, D., Baird, M. A., Allen, J. R., Howe, E. S., Klassen, M. P., Reade, A., Makhijani, K., Song, Y., Liu, S., Murthy, Z., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3447 · Cited by 168
An improved monomeric infrared fluorescent protein for neuronal and tumour brain imaging
Yu, D., Gustafson, W. C., Han, C., Lafaye, C., Noirclerc-Savoye, M., Ge, W.-P., Thayer, D. A., Huang, H., Kornberg, T. B., Royant, A., et al. (2014) · Nature Communications · doi:10.1038/ncomms4626 · Cited by 165
FUCCI sensors: powerful new tools for analysis of cell proliferation
Zielke, N., & Edgar, B. A. (2015) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.189 · Cited by 162
Morozova, K. S., Piatkevich, K. D., Gould, T. J., Zhang, J., Bewersdorf, J., & Verkhusha, V. V. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.04.025 · Cited by 159
Self-citationReal-time imaging of ligand-induced IKK activation in intact cells and in living mice
Gross, S., & Piwnica-Worms, D. R. (2005) · Nature Methods · doi:10.1038/nmeth779 · Cited by 153
Background free imaging of single mRNAs in live cells using split fluorescent proteins
Wu, B., Chen, J., & Singer, R. H. (2014) · Scientific Reports · doi:10.1038/srep03615 · Cited by 132
Near-infrared fluorescent proteins engineered from bacterial phytochromes
Shcherbakova, D. M., Baloban, M., & Verkhusha, V. V. (2015) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2015.06.005 · Cited by 129
Self-citationSynchronization of Cell Populations in G1/S and G2/M Phases of the Cell Cycle
Harper, J. V. (2004) · Humana Press eBooks · doi:10.1385/1-59259-857-9:157 · Cited by 117
Structure of a Bacteriophytochrome and Light-Stimulated Protomer Swapping with a Gene Repressor
Bellini, D., & Papiz, M. Z. (2012) · Structure · doi:10.1016/j.str.2012.06.002 · Cited by 97
Morell, M., Espargaró, A., Avilés, F. X., & Ventura, S. (2007) · PROTEOMICS · doi:10.1002/pmic.200600966 · Cited by 96
An infrared reporter to detect spatiotemporal dynamics of protein-protein interactions
Tchekanda, E., Sivanesan, D., & Michnick, S. W. (2014) · Nature Methods · doi:10.1038/nmeth.2934 · Cited by 92
Tracing the Silhouette of Individual Cells in S/G2/M Phases with Fluorescence
Sakaue-Sawano, A., Ohtawa, K., Hama, H., Kawano, M., Ogawa, M., & Miyawaki, A. (2008) · Chemistry & Biology · doi:10.1016/j.chembiol.2008.10.015 · Cited by 70
Split protein biosensor assays in molecular pharmacological studies
Wehr, M. C., & Rossner, M. J. (2015) · Drug Discovery Today · doi:10.1016/j.drudis.2015.11.004 · Cited by 65
Tao, W., Evans, B.-G., Yao, J., Cooper, S. H., Cornetta, K. G., Ballas, C. B., Hangoc, G., & Broxmeyer, H. E. (2006) · Stem Cells · doi:10.1634/stemcells.2006-0553 · Cited by 57
In Vivo image Analysis Using iRFP Transgenic Mice
Tran, M. T., Tanaka, J., Hamada, M., Sugiyama, Y., Sakaguchi, S., Nakamura, M., Takahashi, S., & Miwa, Y. (2014) · EXPERIMENTAL ANIMALS · doi:10.1538/expanim.63.311 · Cited by 50
Chen, M., Li, W., Zhang, Z., Liu, S., Zhang, X., Zhang, X., & Cui, Z. (2015) · Biomaterials · doi:10.1016/j.biomaterials.2015.01.038 · Cited by 39
Optimization of a genome-wide disordered lentivector-based short hairpin RNA library
Guryanova, O. A., Makhanov, M., Chenchik, A. A., Chumakov, P. M., & Frolova, E. I. (2006) · Molecular Biology · doi:10.1134/s002689330603006x · Cited by 11
Cited by
Human GBP1 binds LPS to initiate assembly of a caspase-4 activating platform on cytosolic bacteria
Santos, J. C., Boucher, D., Schneider, L. K., Demarco, B., Dilucca, M., Shkarina, K., Heilig, R., Chen, K. W., Lim, R. Y. H., & Broz, P. (2020) · Nature Communications · doi:10.1038/s41467-020-16889-z · Cited by 292
Near-Infrared Fluorescent Proteins, Biosensors, and Optogenetic Tools Engineered from Phytochromes
Chernov, K. G., Redchuk, T. A., Omelina, E. S., & Verkhusha, V. V. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00700 · Cited by 264
Self-citationNuclear F-Actin Counteracts Nuclear Deformation and Promotes Fork Repair during Replication Stress
Lamm, N., Read, M. N., Nobis, M., Van Ly, D., Page, S. G., Masamsetti, V. P., Timpson, P., Biro, M., & Cesare, A. J. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-00605-6 · Cited by 156
Socodato, R., Portugal, C. C., Canedo, T., Rodrigues, A., Almeida, T. O., Henriques, J. F., Vaz, S. H., Magalhães, J., Silva, C. M., Baptista, F. I., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107796 · Cited by 94
Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics
Dessauges, C., Mikelson, J., Dobrzyński, M., Jacques, M., Frismantiene, A., Gagliardi, P. A., Khammash, M., & Pertz, O. (2022) · Molecular Systems Biology · doi:10.15252/msb.202110670 · Cited by 48
Metadata
- Authors
- Shcherbakova, D. M., Baloban, M., Emelyanov, A. V., Brenowitz, M., Guo, P., & Verkhusha, V. V.
- Venue
- Nature Communications
- Published
- 2016-08-19
- Volume
- 7
- Issue
- 1
- Pages
- 12405-12405
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2516071618
- Cited by
- 312
- References
- 45
- FWCI
- 16.67
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
