PMID- 32946120
OWN - NLM
STAT- MEDLINE
DCOM- 20210809
LR  - 20210809
IS  - 1097-0290 (Electronic)
IS  - 0006-3592 (Linking)
VI  - 117
IP  - 10
DP  - 2020 Oct
TI  - A comprehensive model for the diffusion and hybridization processes of nucleic 
      acid probes in fluorescence in situ hybridization.
PG  - 3212-3223
LID - 10.1002/bit.27462 [doi]
AB  - Fluorescence in situ hybridization (FISH) has been extensively used in the past 
      decades for the detection and localization of microorganisms. However, a 
      mechanistic approach of the whole FISH process is still missing, and the main 
      limiting steps for the hybridization to occur remain unclear. In here, FISH is 
      approached as a particular case of a diffusion-reaction kinetics, where molecular 
      probes (MPs) move from the hybridization solution to the target RNA site within 
      the cells. Based on literature models, the characteristic times taken by 
      different MPs to diffuse across multiple cellular barriers, as well as the 
      reaction time associated with the formation of the duplex molecular probe-RNA, 
      were estimated. Structural and size differences at the membrane level of 
      bacterial and animal cells were considered. For bacterial cells, the limiting 
      step for diffusion is likely to be the peptidoglycan layer (characteristic time 
      of 7.94 x 10(2) - 4.39 x 10(3) s), whereas for animal cells, the limiting step 
      should be the diffusion of the probe through the bulk (1.8-5.0 s) followed by the 
      diffusion through the lipid membrane (1 s). The information provided here may 
      serve as a basis for a more rational development of FISH protocols in the future.
CI  - (c) 2020 Wiley Periodicals LLC.
FAU - Lima, Joana F
AU  - Lima JF
AUID- ORCID: 0000-0003-2459-6729
AD  - LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and 
      Energy, Faculty of Engineering, University of Porto, Porto, Portugal.
AD  - Biomode, S.A., Braga, Portugal.
AD  - i3S, Instituto de Investigacao e Inovacao em Saude, Universidade do Porto, Porto, 
      Portugal.
AD  - Institute of Molecular Pathology and Immunology of the University of Porto, 
      Porto, Portugal.
FAU - Maia, Paulo
AU  - Maia P
AD  - LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and 
      Energy, Faculty of Engineering, University of Porto, Porto, Portugal.
FAU - T Magalhaes, Beatriz
AU  - T Magalhaes B
AUID- ORCID: 0000-0003-4434-6989
AD  - LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and 
      Energy, Faculty of Engineering, University of Porto, Porto, Portugal.
FAU - Cerqueira, Laura
AU  - Cerqueira L
AUID- ORCID: 0000-0001-8452-4749
AD  - LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and 
      Energy, Faculty of Engineering, University of Porto, Porto, Portugal.
AD  - Biomode, S.A., Braga, Portugal.
FAU - Azevedo, Nuno F
AU  - Azevedo NF
AUID- ORCID: 0000-0001-5864-3250
AD  - LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and 
      Energy, Faculty of Engineering, University of Porto, Porto, Portugal.
LA  - eng
GR  - POCI-01-0145-FEDER-029961/Fundacao para a Ciencia e a Tecnologia/International
GR  - POCI-01-0145-FEDER-031011/Fundacao para a Ciencia e a Tecnologia/International
GR  - SFRH/BD/143491/2019/Fundacao para a Ciencia e a Tecnologia/International
GR  - SFRH/BDE/51909/2012/Fundacao para a Ciencia e a Tecnologia/International
GR  - UIDB/00511/2020/Fundacao para a Ciencia e a Tecnologia/International
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Review
DEP - 20200702
PL  - United States
TA  - Biotechnol Bioeng
JT  - Biotechnology and bioengineering
JID - 7502021
RN  - 0 (Fluorescent Dyes)
RN  - 0 (Nucleic Acid Probes)
SB  - IM
MH  - Animals
MH  - Bacteria
MH  - Cells, Cultured
MH  - Diffusion
MH  - Fluorescent Dyes/*chemistry
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Nucleic Acid Probes/*chemistry
OTO - NOTNLM
OT  - FISH
OT  - cellular barriers
OT  - diffusion
OT  - molecular probes
OT  - nucleic acid mimics
EDAT- 2020/09/19 06:00
MHDA- 2021/08/10 06:00
CRDT- 2020/09/18 12:14
PHST- 2020/03/04 00:00 [received]
PHST- 2020/06/02 00:00 [revised]
PHST- 2020/06/05 00:00 [accepted]
PHST- 2020/09/18 12:14 [entrez]
PHST- 2020/09/19 06:00 [pubmed]
PHST- 2021/08/10 06:00 [medline]
AID - 10.1002/bit.27462 [doi]
PST - ppublish
SO  - Biotechnol Bioeng. 2020 Oct;117(10):3212-3223. doi: 10.1002/bit.27462. Epub 2020 
      Jul 2.