利用寡核苷酸随机光学重建显微镜（OligoSTORM）和寡核苷酸DNA点积累成像纳米技术（OligoDNA-PAINT）对基因组DNA进行原位超分辨率成像
In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT.
作者信息
Beliveau Brian J, Boettiger Alistair N, Nir Guy, Bintu Bogdan, Yin Peng, Zhuang Xiaowei, Wu C-Ting
机构信息
Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
出版信息
Methods Mol Biol. 2017;1663:231-252. doi: 10.1007/978-1-4939-7265-4_19.
Abstract
OligoSTORM and OligoDNA-PAINT meld the Oligopaint technology for fluorescent in situ hybridization (FISH) with, respectively, Stochastic Optical Reconstruction Microscopy (STORM) and DNA-based Point Accumulation for Imaging in Nanoscale Topography (DNA-PAINT) to enable in situ single-molecule super-resolution imaging of nucleic acids. Both strategies enable ≤20 nm resolution and are appropriate for imaging nanoscale features of the genomes of a wide range of species, including human, mouse, and fruit fly (Drosophila).
摘要
寡核苷酸随机光学重建显微镜（OligoSTORM）和寡核苷酸DNA点积累纳米形貌成像技术（OligoDNA-PAINT）分别将用于荧光原位杂交（FISH）的寡核苷酸技术与随机光学重建显微镜（STORM）和基于DNA的纳米尺度形貌成像点积累技术（DNA-PAINT）相结合，以实现核酸的原位单分子超分辨率成像。这两种策略都能实现≤20纳米的分辨率，适用于对包括人类、小鼠和果蝇（果蝇属）在内的多种物种基因组的纳米尺度特征进行成像。
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本文引用的文献
1
Spatial organization of chromatin domains and compartments in single chromosomes.
Science. 2016 Aug 5;353(6299):598-602. doi: 10.1126/science.aaf8084. Epub 2016 Jul 21.
2
Optical imaging of individual biomolecules in densely packed clusters.
Nat Nanotechnol. 2016 Sep;11(9):798-807. doi: 10.1038/nnano.2016.95. Epub 2016 Jul 4.
3
RNA Imaging with Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH).
Methods Enzymol. 2016;572:1-49. doi: 10.1016/bs.mie.2016.03.020. Epub 2016 Apr 27.
4
Quantitative super-resolution imaging with qPAINT.
Nat Methods. 2016 May;13(5):439-42. doi: 10.1038/nmeth.3804. Epub 2016 Mar 28.
5
Super-resolution imaging reveals distinct chromatin folding for different epigenetic states.
Nature. 2016 Jan 21;529(7586):418-22. doi: 10.1038/nature16496. Epub 2016 Jan 13.
6
Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries.
Nat Commun. 2015 Nov 16;6:8634. doi: 10.1038/ncomms9634.
7
Combined in vitro transcription and reverse transcription to amplify and label complex synthetic oligonucleotide probe libraries.
Biotechniques. 2015 Jun 1;58(6):301-7. doi: 10.2144/000114298. eCollection 2015 Jun.
8
Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes.
Nat Commun. 2015 May 12;6:7147. doi: 10.1038/ncomms8147.
9
RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.
Science. 2015 Apr 24;348(6233):aaa6090. doi: 10.1126/science.aaa6090. Epub 2015 Apr 9.
10
Super-resolution microscopy approaches for live cell imaging.
Biophys J. 2014 Oct 21;107(8):1777-1784. doi: 10.1016/j.bpj.2014.08.028.
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