PMID- 30418432
OWN - NLM
STAT- Publisher
LR  - 20240227
IS  - 1546-1696 (Electronic)
IS  - 1087-0156 (Print)
IS  - 1087-0156 (Linking)
DP  - 2018 Nov 12
TI  - ClampFISH detects individual nucleic acid molecules using click chemistry-based 
      amplification.
LID - 10.1038/nbt.4286 [doi]
AB  - Methods for detecting single nucleic acids in cell and tissues, such as 
      fluorescence in situ hybridization (FISH), are limited by relatively low signal 
      intensity and nonspecific probe binding. Here we present click-amplifying FISH 
      (clampFISH), a method for fluorescence detection of nucleic acids that achieves 
      high specificity and high-gain (>400-fold) signal amplification. ClampFISH probes 
      form a 'C' configuration upon hybridization to the sequence of interest in a 
      double helical manner. The ends of the probes are ligated together using 
      bio-orthogonal click chemistry, effectively locking the probes around the target. 
      Iterative rounds of hybridization and click amplify the fluorescence intensity. 
      We show that clampFISH enables the detection of RNA species with 
      low-magnification microscopy and in RNA-based flow cytometry. Additionally, we 
      show that the modular design of clampFISH probes allows multiplexing of RNA and 
      DNA detection, that the locking mechanism prevents probe detachment in expansion 
      microscopy, and that clampFISH can be applied in tissue samples.
FAU - Rouhanifard, Sara H
AU  - Rouhanifard SH
AUID- ORCID: 0000-0002-6991-4877
AD  - Department of Bioengineering, University of Pennsylvania, Philadelphia 
      Pennsylvania, USA.
FAU - Mellis, Ian A
AU  - Mellis IA
AUID- ORCID: 0000-0002-6239-4821
AD  - Department of Bioengineering, University of Pennsylvania, Philadelphia 
      Pennsylvania, USA.
AD  - Genomics and Computational Biology Group, Perelman School of Medicine, University 
      of Pennsylvania, Philadelphia, Pennsylvania, USA.
FAU - Dunagin, Margaret
AU  - Dunagin M
AD  - Department of Bioengineering, University of Pennsylvania, Philadelphia 
      Pennsylvania, USA.
FAU - Bayatpour, Sareh
AU  - Bayatpour S
AD  - Department of Bioengineering, University of Pennsylvania, Philadelphia 
      Pennsylvania, USA.
FAU - Jiang, Connie L
AU  - Jiang CL
AD  - Department of Bioengineering, University of Pennsylvania, Philadelphia 
      Pennsylvania, USA.
AD  - Cell and Molecular Biology Group, Perelman School of Medicine, University of 
      Pennsylvania, Philadelphia, Pennsylvania, USA.
FAU - Dardani, Ian
AU  - Dardani I
AD  - Department of Bioengineering, University of Pennsylvania, Philadelphia 
      Pennsylvania, USA.
FAU - Symmons, Orsolya
AU  - Symmons O
AD  - Department of Bioengineering, University of Pennsylvania, Philadelphia 
      Pennsylvania, USA.
FAU - Emert, Benjamin
AU  - Emert B
AD  - Department of Bioengineering, University of Pennsylvania, Philadelphia 
      Pennsylvania, USA.
AD  - Genomics and Computational Biology Group, Perelman School of Medicine, University 
      of Pennsylvania, Philadelphia, Pennsylvania, USA.
FAU - Torre, Eduardo
AU  - Torre E
AD  - Department of Bioengineering, University of Pennsylvania, Philadelphia 
      Pennsylvania, USA.
AD  - Department of Biochemistry and Biophysics, Perelman School of Medicine, 
      University of Pennsylvania, Philadelphia, Pennsylvania, USA.
FAU - Cote, Allison
AU  - Cote A
AD  - Department of Bioengineering, University of Pennsylvania, Philadelphia 
      Pennsylvania, USA.
FAU - Sullivan, Alessandra
AU  - Sullivan A
AD  - Altius Institute for Biomedical Sciences, Seattle, Washington, USA.
FAU - Stamatoyannopoulos, John A
AU  - Stamatoyannopoulos JA
AD  - Altius Institute for Biomedical Sciences, Seattle, Washington, USA.
FAU - Raj, Arjun
AU  - Raj A
AUID- ORCID: 0000-0002-2915-6960
AD  - Department of Bioengineering, University of Pennsylvania, Philadelphia 
      Pennsylvania, USA.
AD  - Genomics and Computational Biology Group, Perelman School of Medicine, University 
      of Pennsylvania, Philadelphia, Pennsylvania, USA.
AD  - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 
      Philadelphia, Pennsylvania, USA.
LA  - eng
GR  - T32 DK007780/DK/NIDDK NIH HHS/United States
GR  - R01 HG009283/HG/NHGRI NIH HHS/United States
GR  - F32 GM120929/GM/NIGMS NIH HHS/United States
GR  - RM1 HG007743/HG/NHGRI NIH HHS/United States
GR  - F30 NS100595/NS/NINDS NIH HHS/United States
GR  - U01 HL129998/HL/NHLBI NIH HHS/United States
GR  - T32 HG000046/HG/NHGRI NIH HHS/United States
GR  - R33 EB019767/EB/NIBIB NIH HHS/United States
PT  - Journal Article
DEP - 20181112
PL  - United States
TA  - Nat Biotechnol
JT  - Nature biotechnology
JID - 9604648
PMC - PMC6511493
MID - NIHMS1507951
COIS- Competing interests: A.R. receives royalties related to Stellaris RNA FISH 
      probes.
EDAT- 2018/11/13 06:00
MHDA- 2018/11/13 06:00
PMCR- 2019/05/13
CRDT- 2018/11/13 06:00
PHST- 2018/05/07 00:00 [received]
PHST- 2018/09/24 00:00 [accepted]
PHST- 2018/11/13 06:00 [entrez]
PHST- 2018/11/13 06:00 [pubmed]
PHST- 2018/11/13 06:00 [medline]
PHST- 2019/05/13 00:00 [pmc-release]
AID - nbt.4286 [pii]
AID - 10.1038/nbt.4286 [doi]
PST - aheadofprint
SO  - Nat Biotechnol. 2018 Nov 12:10.1038/nbt.4286. doi: 10.1038/nbt.4286.