PMID- 28485713
OWN - NLM
STAT- MEDLINE
DCOM- 20180212
LR  - 20181113
IS  - 2050-084X (Electronic)
IS  - 2050-084X (Linking)
VI  - 6
DP  - 2017 May 9
TI  - Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear 
      genome using molecular beacon probes.
LID - e21660 [pii]
LID - 10.7554/eLife.21660 [doi]
AB  - High-resolution visualization of short non-repetitive DNA in situ in the nuclear 
      genome is essential for studying looping interactions and chromatin organization 
      in single cells. Recent advances in fluorescence in situ hybridization (FISH) 
      using Oligopaint probes have enabled super-resolution imaging of genomic domains 
      with a resolution limit of 4.9 kb. To target shorter elements, we developed a 
      simple FISH method that uses molecular beacon (MB) probes to facilitate the 
      probe-target binding, while minimizing non-specific fluorescence. We used 
      three-dimensional stochastic optical reconstruction microscopy (3D-STORM) with 
      optimized imaging conditions to efficiently distinguish sparsely distributed 
      Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and only 
      29-34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb 
      integrated or endogenous unique DNA in situ in human or mouse genome, 
      respectively. We demonstrated our MB-based FISH method was capable of visualizing 
      the so far shortest non-repetitive genomic sequence in 3D at super-resolution.
FAU - Ni, Yanxiang
AU  - Ni Y
AD  - Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and 
      Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, 
      Shenzhen, China.
AD  - MOE Key laboratory of Bioinformatics; Bioinformatics Division and Center for 
      Synthetic and Systems Biology, TNLIST; School of Medicine, Tsinghua University, 
      Beijing, China.
AD  - School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China.
FAU - Cao, Bo
AU  - Cao B
AD  - Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and 
      Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, 
      Shenzhen, China.
FAU - Ma, Tszshan
AU  - Ma T
AD  - MOE Key laboratory of Bioinformatics; Bioinformatics Division and Center for 
      Synthetic and Systems Biology, TNLIST; School of Medicine, Tsinghua University, 
      Beijing, China.
FAU - Niu, Gang
AU  - Niu G
AD  - Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and 
      Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, 
      Shenzhen, China.
AD  - LemonData Biotech, Shenzhen, China.
AD  - Phil Rivers Technology, Beijing, China.
FAU - Huo, Yingdong
AU  - Huo Y
AD  - Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and 
      Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, 
      Shenzhen, China.
FAU - Huang, Jiandong
AU  - Huang J
AD  - School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China.
FAU - Chen, Danni
AU  - Chen D
AD  - Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and 
      Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, 
      Shenzhen, China.
FAU - Liu, Yi
AU  - Liu Y
AD  - Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and 
      Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, 
      Shenzhen, China.
FAU - Yu, Bin
AU  - Yu B
AD  - Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and 
      Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, 
      Shenzhen, China.
FAU - Zhang, Michael Q
AU  - Zhang MQ
AUID- ORCID: 0000-0002-7408-1830
AD  - MOE Key laboratory of Bioinformatics; Bioinformatics Division and Center for 
      Synthetic and Systems Biology, TNLIST; School of Medicine, Tsinghua University, 
      Beijing, China.
AD  - Department of Biological Sciences, Center for Systems Biology, The University of 
      Texas at Dallas, Dallas, United States.
FAU - Niu, Hanben
AU  - Niu H
AD  - Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and 
      Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, 
      Shenzhen, China.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20170509
PL  - England
TA  - Elife
JT  - eLife
JID - 101579614
RN  - 0 (Fluorescent Dyes)
RN  - 0 (Receptors, AMPA)
SB  - IM
MH  - Animals
MH  - Cells, Cultured
MH  - Fluorescent Dyes/metabolism
MH  - Neurons/chemistry
MH  - *Optical Imaging
MH  - Rats
MH  - Receptors, AMPA/*analysis
MH  - Staining and Labeling
MH  - Synapses/*chemistry
PMC - PMC5433842
OTO - NOTNLM
OT  - chromatin organization
OT  - chromosomes
OT  - fluorescence in situ hybridization
OT  - genes
OT  - molecular beacons
OT  - non-repetitive DNA
OT  - none
OT  - stochastic optical reconstruction microscopy
OT  - super-resolution imaging
COIS- The authors declare that no competing interests exist.
EDAT- 2017/05/10 06:00
MHDA- 2018/02/13 06:00
PMCR- 2017/05/10
CRDT- 2017/05/10 06:00
PHST- 2016/09/20 00:00 [received]
PHST- 2017/04/24 00:00 [accepted]
PHST- 2017/05/10 06:00 [pubmed]
PHST- 2018/02/13 06:00 [medline]
PHST- 2017/05/10 06:00 [entrez]
PHST- 2017/05/10 00:00 [pmc-release]
AID - e21660 [pii]
AID - 21660 [pii]
AID - 10.7554/eLife.21660 [doi]
PST - epublish
SO  - Elife. 2017 May 9;6:e21660. doi: 10.7554/eLife.21660.