Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes

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Abstract

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 Oligopaints probes 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 only 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) and optimized the imaging conditions to efficiently distinguish sparsely distributed Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and 29-34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in the human or mouse genome, respectively, demonstrating the capability of MB-based FISH in visualizing a so far shortest and non-repetitive genomic sequence in 3D at super-resolution.

Data availability

The following data sets were generated

1. Ni Y
2. Cao B
3. Ma T
4. Niu G
5. Huo Y
6. Huang J
7. Chen D
8. Liu Y
9. Yu B
10. Zhang M
11. Niu H.
(2017) Data from: Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes
Available at Dryad Digital Repository under a CC0 Public Domain Dedication.

http://dx.doi.org/10.5061/dryad.126k9

Article and author information

Author details

Yanxiang Ni

Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China

For correspondence
niyanxiang0000@gmail.com

Competing interests
The authors declare that no competing interests exist.
Bo Cao

Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China

Competing interests
The authors declare that no competing interests exist.
Tszshan Ma

MOE Key laboratory of Bioinformatics, Tsinghua University, Beijing, China

Competing interests
The authors declare that no competing interests exist.
Gang Niu

Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China

Competing interests
The authors declare that no competing interests exist.
Yingdong Huo

Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China

Competing interests
The authors declare that no competing interests exist.
Jiandong Huang

School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China

Competing interests
The authors declare that no competing interests exist.
Danni Chen

Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China

Competing interests
The authors declare that no competing interests exist.
Yi Liu

Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China

Competing interests
The authors declare that no competing interests exist.
Bin Yu

Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China

Competing interests
The authors declare that no competing interests exist.
Michael Qiwei Zhang

MOE Key laboratory of Bioinformatics, Tsinghua University, Beijing, China

For correspondence
michaelzhang@tsinghua.edu.cn

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-7408-1830
Hanben Niu

Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China

For correspondence
hbniu@szu.edu.cn

Competing interests
The authors declare that no competing interests exist.

Funding

National Natural Science Foundation of China (61235012)

Hanben Niu

National Natural Science Foundation of China (61335001)

Michael Qiwei Zhang

Shenzhen Science and Technology Planning Project (JCYJ20150324141711698)

Michael Qiwei Zhang

National Natural Science Foundation of China (31401146)

Yanxiang Ni

National Natural Science Foundation of China (31361163004)

Michael Qiwei Zhang

National Natural Science Foundation of China (91019016)

Michael Qiwei Zhang

the National Basic Research Program of China (2012CB825802)

Hanben Niu

the Special-Funded Program on National Key Scientific Instruments and Equipment Development (2012YQ150092)

Hanben Niu

the National Key Basic Research Project (2012CB316503)

Michael Qiwei Zhang

the National Key Basic Research Program of China (2015CB352005)

Hanben Niu

National Natural Science Foundation of China (61178080)

Michael Qiwei Zhang

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.