Name: visualizing the interaction between the qdot-labeled protein and site-specifically modified &#955; dna at the single molecule level
Uploaded: 2018-07-17T14:30:00
Description: Watch this Scientific Journal Video about Visualizing the Interaction Between the Qdot-labeled Protein and Site-specifically Modified ÃŽÂ» DNA at the Single Molecule Level at JoVE.com

我们感谢哈桑 Yardimci 博士和弗朗克斯学院的穆罕默德·塞维姆 Yardimci 博士在单分子实验中的亲切帮助, 丹尼尔博士 Duzdevich 来自哥伦比亚大学格林的实验室, 北京大学宇杰太阳博士和春来牌博士。清华大学进行有益的讨论。这项研究得到了中国国家自然科学基金31371264、31401059、中国科学院跨学科创新小组和来自皇家学会的牛顿高级研究金 (NA140085) 的支持。

1. ARS317 DNA 基质的制备
<ol><li>DNA 基质结构与包装<ol>
<li>用Xho酶消化原生λ DNA;利用含有20个 bp 同源序列的XhoI. 酶在 lambda dna 上的 ARS317, 从萌芽酵母的基因组 dna 中放大543的 bp dna 片段。添加 100 Xho我消化了λ dna 和10的 dna 片段到10µL 同源重组反应系统, 并孵化的反应在37摄氏度为30分钟。</li>
		<li>要包装重组λ DNA, 添加25µL 的 lambda 包装提取物进入重组产品, 并孵化反应在30摄氏度90?...

<ol>
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S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanism+of+transcriptional+bursting+in+bacteria.">Mechanism of transcriptional bursting in bacteria.</a> Cell. 158 (2), 314-326 (2014).</li><li>Wegner, K. 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D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-time+single-molecule+imaging+reveals+a+direct+interaction+between+UvrC+and+UvrB+on+DNA+tightropes.">Real-time single-molecule imaging reveals a direct interaction between UvrC and UvrB on DNA tightropes.</a> Nucleic acids research. 41 (9), 4901-4912 (2013).</li><li>Kad, N. M., Wang, H., Kennedy, G. G., Warshaw, D. M., Van Houten, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Collaborative+dynamic+DNA+scanning+by+nucleotide+excision+repair+proteins+investigated+by+single-molecule+imaging+of+quantum-dot-labeled+proteins.">Collaborative dynamic DNA scanning by nucleotide excision repair proteins investigated by single-molecule imaging of quantum-dot-labeled proteins.</a> Molecular cell. 37 (5), 702-713 (2010).</li><li>Chandradoss, S. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Surface+Passivation+for+Single-molecule+Protein+Studies.">Surface Passivation for Single-molecule Protein Studies.</a> Jove-Journal of Visualized Experiments. (86), (2014).</li><li>Chen, X. Q., Zhao, E. S., Fu, Y. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Using+single-molecule+approach+to+visualize+the+nucleosome+assembly+in+yeast+nucleoplasmic+extracts.">Using single-molecule approach to visualize the nucleosome assembly in yeast nucleoplasmic extracts.</a> Science Bulletin. 62 (6), 399-404 (2017).</li><li>Yardimci, H., Loveland, A. B., van Oijen, A. M., Walter, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-molecule+analysis+of+DNA+replication+in+Xenopus+egg+extracts.">Single-molecule analysis of DNA replication in Xenopus egg extracts.</a> Methods. 57 (2), 179-186 (2012).</li><li>Tanner, N. A., Loparo, J. J., van Oijen, A. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visualizing+single-molecule+DNA+replication+with+fluorescence+microscopy.">Visualizing single-molecule DNA replication with fluorescence microscopy.</a> Journal of visualized experiments: JoVE. (32), (2009).</li><li>Lockett, T. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+bacteriophage+&#955;+DNA+purification+procedure+suitable+for+the+analysis+of+DNA+from+either+large+or+multiple+small+lysates.">A bacteriophage &#955; DNA purification procedure suitable for the analysis of DNA from either large or multiple small lysates.</a> Analytical biochemistry. 185 (2), 230-234 (1990).</li><li>Smith, E. A., Chen, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=How+to+prevent+the+loss+of+surface+functionality+derived+from+aminosilanes.">How to prevent the loss of surface functionality derived from aminosilanes.</a> Langmuir. 24 (21), 12405-12409 (2008).</li><li>Kim, Y., Torre, A., Leal, A. A., Finkelstein, I. 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在这里, 我们提出了一个协议, 以观察 Qdot 标记蛋白和现场特异修饰的λ DNA 的相互作用, 使用 TIRFM 在一个流动细胞。必要的步骤包括对 dna 基质进行特定地点的修饰、dna biotinylation、盖玻片清洁和功能化、流动细胞制备和单分子成像。有两个要点值得注意。首先, 所有与λ DNA 有关的步骤都应该轻轻地操纵, 以减少任何可能的伤害,例如避免反复吹打的混合。第二, 确保盖玻片的清洁程度, 以尽量...

蛋白质和 dna 之间的相互作用对许多复杂的生物过程至关重要, 例如 dna 复制、dna 修复和转录。虽然传统的方法已经揭示了这些过程的性质, 但许多关键机制仍然不清楚。最近, 随着快速发展的单一分子技术, 一些机制已经解决了1,2,3。
单分子荧光显微技术在实时可视化蛋白质-DNA 相互作用中的应用主要取决于荧光检测和荧光探针的发展。对于单个分子研究, 重要的是要用合适的荧光探针来标记感兴趣的蛋白质, 因为荧光检测系统大多是商用的。
荧光蛋白通常用于分子生物学。然而, 低荧光亮度和抗漂白稳定性限制了它在许多单分子检测中的应用。量子点 (Qdots) 是微小的发光纳米粒子4。由于其独特的光学特性, Qdots 的亮度为 10-20 倍, 比广泛使用的有机染料5倍更稳定。此外, Qdots 有一个大的斯托克斯转移 (励磁和发射峰的位置的区别)5。因此, Qdots 可用于长时间观察 (分钟到数小时) 和获取高信噪比的图像, 而不能用于定量测定。
到目前为止, 有两种方法来标记一个目标蛋白与 Qdots 网站-特别是: 标记与 Qdot 共轭的主要或次级抗体6,7,8;或者直接用 Qdots 标记靶蛋白, 这是基于生物素与链亲和素9、10、11、12、13之间的强相互作用。链亲和素涂层的 Qdots 在商业上是可利用的。在最近的研究中, 比拉和 Avi 标记蛋白在体内10的联合表达纯化了高效率的芽酵母中特异的生物素化蛋白。通过以下和优化单分子检测14,15,16,17, 我们观察了 Qdot 标记蛋白和 DNA 在单一分子水平上的相互作用, 使用TIRFM10。
在这里, 我们选择萌芽的酵母起源识别复合体 (兽人), 它可以专门识别和绑定到自主复制序列 (ARS), 作为我们的蛋白质的兴趣。下面的协议提出了一个逐步的过程, 以可视化的互动 Qdot 标记兽人与 ARS 使用 TIRFM。介绍了该部位的制备, 特别是修饰的 dna 基质、dna biotinylation、盖玻片清洗和功能化、流动细胞组装和单分子成像。

<table>
	<tbody>
		<tr>
			<td>Lambda DNA</td>
			<td>New England Biolabs</td>
			<td>N3011</td>
			<td>Store 25 &#956;L aliquots at -20 &#186;C.</td>
		</tr>
		<tr>
			<td>XhoI enzyme</td>
			<td>Thermo Fisher Scientific</td>
			<td>FD0694</td>
			<td></td>
		</tr>
		<tr>
			<td>Quick-fusion cloning kit</td>
			<td>Biotool</td>
			<td>B22611</td>
			<td></td>
		</tr>
		<tr>
			<td>MaxPlax Lambda 
			Packaging Extracts</td>
			<td>Epicentre</td>
			<td>MP5110</td>
			<td>Bacterial strain LE392MP 
			is included in this package.</td>
		</tr>
		<tr>
			<td>MgSO4</td>
			<td>Sinopharm Chemical Reagent Co.,Ltd</td>
			<td>10013092</td>
			<td>Any brand is acceptable.</td>
		</tr>
		<tr>
			<td>Tris</td>
			<td>Amresco</td>
			<td>0497-5KG</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Beijing Chemical works</td>
			<td>N/A</td>
			<td>Any brand is acceptable.</td>
		</tr>
		<tr>
			<td>MgCl2</td>
			<td>Sinopharm Chemical Reagent Co.,Ltd</td>
			<td>10012818</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Beijing Chemical works</td>
			<td>N/A</td>
			<td>Any brand is acceptable.</td>
		</tr>
		<tr>
			<td>NZ-amine</td>
			<td>Amresco</td>
			<td>J853-250G</td>
			<td></td>
		</tr>
		<tr>
			<td>Casamino acids</td>
			<td>Sigma-Aldrich</td>
			<td>22090-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>PEG8000</td>
			<td>Beyotime</td>
			<td>ST483</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnetic stirring apparatus</td>
			<td>IKA</td>
			<td>KMO2 basic</td>
			<td></td>
		</tr>
		<tr>
			<td>15 mL Eppendorf tube</td>
			<td>Eppendorf</td>
			<td>30122151</td>
			<td>15 mL, sterile, bulk, 500pcs</td>
		</tr>
		<tr>
			<td>Rnase</td>
			<td>SIGMA</td>
			<td>R4875-100MG</td>
			<td></td>
		</tr>
		<tr>
			<td>Dnase</td>
			<td>SIGMA</td>
			<td>D5319-500UG</td>
			<td></td>
		</tr>
		<tr>
			<td>Proteinase K</td>
			<td>Amresco</td>
			<td>0706-100MG</td>
			<td></td>
		</tr>
		<tr>
			<td>Biotinylated primers</td>
			<td>Thermo Fisher Scientific</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 DNA ligase, T4 DNA Ligase, Reaction Buffer (10x)</td>
			<td>New England Biolabs</td>
			<td>M0202</td>
			<td></td>
		</tr>
		<tr>
			<td>Coverslip</td>
			<td>Thermo Fisher Scientific</td>
			<td>22266882</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol</td>
			<td>Sinopharm Chemical Reagent Co.,Ltd</td>
			<td>10009259</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium hydroxide (KOH)</td>
			<td>Sigma-Aldrich</td>
			<td>306568-100G</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetone</td>
			<td>Thermo Fisher Scientific</td>
			<td>A949-4</td>
			<td></td>
		</tr>
		<tr>
			<td>H2SO4</td>
			<td>Sinopharm Chemical Reagent Co.,Ltd</td>
			<td>80120891</td>
			<td>sulfuric acid</td>
		</tr>
		<tr>
			<td>H2O2</td>
			<td>Sinopharm Chemical Reagent Co.,Ltd</td>
			<td>10011218</td>
			<td>30% Hydrogen peroxide</td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Sigma-Aldrich</td>
			<td>322415-2L</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetic acid</td>
			<td>Sigma-Aldrich</td>
			<td>V900798</td>
			<td></td>
		</tr>
		<tr>
			<td>APTES</td>
			<td>Sigma-Aldrich</td>
			<td>A3648</td>
			<td></td>
		</tr>
		<tr>
			<td>mPEG 
			(methoxy-polyethylene glycol)</td>
			<td>Lysan</td>
			<td>mPEG-SVA-5000</td>
			<td></td>
		</tr>
		<tr>
			<td>biotin-PEG 
			(biotin-polyethylene glycol)</td>
			<td>Lysan</td>
			<td>Biotin-PEG-SVA-5000</td>
			<td></td>
		</tr>
		<tr>
			<td>NaHCO3</td>
			<td>Sigma-Aldrich</td>
			<td>31437-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Vacuum desiccator</td>
			<td>Tianjin Branch Billion Lung Experimental Equipment Co., Ltd.</td>
			<td>IPC250-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Vacuum sealer</td>
			<td>MAGIC SEAL</td>
			<td>WP300</td>
			<td></td>
		</tr>
		<tr>
			<td>Diamond-tipped glass scribe</td>
			<td>ELECTRON MICROSCOPY SCIENCES</td>
			<td>70036</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass slide</td>
			<td>Sail Brand</td>
			<td>7101</td>
			<td></td>
		</tr>
		<tr>
			<td>Inlet tubing</td>
			<td>SCI (Scientific Commodties INC.)</td>
			<td>BB31695-PE/2</td>
			<td>inner diameter 0.38 mm; outer diameter 1.09 mm.</td>
		</tr>
		<tr>
			<td>Outlet tubing</td>
			<td>SCI (Scientific Commodties INC.)</td>
			<td>BB31695-PE/4</td>
			<td>inner diameter 0.76 mm; outer diameter 1.22 mm.</td>
		</tr>
		<tr>
			<td>Double-sided tape</td>
			<td>Sigma-Aldrich</td>
			<td>GBL620001-1EA</td>
			<td></td>
		</tr>
		<tr>
			<td>Epoxy</td>
			<td>LEAFTOP</td>
			<td>9005</td>
			<td>five minutes epoxy</td>
		</tr>
		<tr>
			<td>Streptavidin</td>
			<td>Sigma-Aldrich</td>
			<td>S4762</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorescence Microscope</td>
			<td>Olympus</td>
			<td>IX71</td>
			<td></td>
		</tr>
		<tr>
			<td>Infusion/withdrawal 
			programmable pump</td>
			<td>Harvard apparatus</td>
			<td>70-4504</td>
			<td></td>
		</tr>
		<tr>
			<td>532 nm laser</td>
			<td>Coherent</td>
			<td>Sapphire-532-50</td>
			<td></td>
		</tr>
		<tr>
			<td>640 nm laser</td>
			<td>Coherent</td>
			<td>OBIS-640-100</td>
			<td></td>
		</tr>
		<tr>
			<td>EMCCD Camera</td>
			<td>Andor</td>
			<td>DU-897E-CS0-BV</td>
			<td></td>
		</tr>
		<tr>
			<td>W-View Gemini Imaging 
			splitting optics</td>
			<td>Hamamatsu photonics K.K.</td>
			<td>A12801-01</td>
			<td></td>
		</tr>
		<tr>
			<td>TIRF illumination system</td>
			<td>Olympus</td>
			<td>IX2-RFAEVA2</td>
			<td></td>
		</tr>
		<tr>
			<td>60&#215;TIRF objective</td>
			<td>Olympus</td>
			<td>APON60XOTIRF</td>
			<td></td>
		</tr>
		<tr>
			<td>Quad-edge laser dichroic 
			beamsplitter</td>
			<td>Semrock</td>
			<td>Di01-R405/488/ 
			532/635-25x36</td>
			<td></td>
		</tr>
		<tr>
			<td>Quad-band bandpass filter</td>
			<td>Semrock</td>
			<td>FF01-446/510/ 
			581/703-25</td>
			<td></td>
		</tr>
		<tr>
			<td>Dichroic beamsplitter</td>
			<td>Semrock</td>
			<td>FF649-Di01-25x36</td>
			<td></td>
		</tr>
		<tr>
			<td>Emission filter</td>
			<td>Chroma Technology Corp</td>
			<td>ET585/65m</td>
			<td></td>
		</tr>
		<tr>
			<td>Emission filter</td>
			<td>Chroma Technology Corp</td>
			<td>ET665lp</td>
			<td></td>
		</tr>
		<tr>
			<td>FocalCheck fluorescence, microscope test slide #1</td>
			<td>Thermo Fisher Scientific</td>
			<td>F36909</td>
			<td></td>
		</tr>
		<tr>
			<td>SYTOX Orange</td>
			<td>Thermo Fisher Scientific</td>
			<td>S11368</td>
			<td></td>
		</tr>
		<tr>
			<td>Qdot705 Streptavidin Conjugate</td>
			<td>Thermo Fisher Scientific</td>
			<td>Q10163MP</td>
			<td>Store at 4 &#186;C, do not freeze.</td>
		</tr>
		<tr>
			<td>ATP</td>
			<td>Amresco</td>
			<td>0220-25G</td>
			<td>Prepare 200 mM ATP solution, using ddH2O, adjust pH to 7.0, and store 10 &#956;L aliquots at -20 &#186;C.</td>
		</tr>
		<tr>
			<td>DTT</td>
			<td>Amresco</td>
			<td>M109-5G</td>
			<td>Prepare 1 M solution using ddH2O, and store 10 &#956;l aliquots at -20 &#186;C.</td>
		</tr>
	</tbody>
</table>

visualizing the interaction between the qdot-labeled protein and site-specifically modified &#955; dna at the single molecule level

荧光显微镜在解剖单一分子水平复杂生物过程的机制方面做出了巨大贡献。在用于研究 DNA-蛋白质相互作用的单分子检测中, 有两个重要的因素需要考虑: 具有足够长度的 dna 基质, 便于观察和用合适的荧光探针对蛋白质进行标记。48.5 kb 的λ dna 是一个很好的候选 dna 基质。量子点 (Qdots) 作为一类荧光探针, 允许长时间观测 (分钟到数小时) 和高质量的图像采集。本文提出了一种在单分子水平上研究 DNA-蛋白质相互作用的协议, 包括制备一个特异修饰的λ dna, 并用链亲和素包覆 Qdots 标记靶蛋白。为了证明概念, 我们选择了在萌芽的酵母中的兽人 (原产地识别复合体) 作为一种感兴趣的蛋白质, 并可视化其与 TIRFM (自主复制序列) 的相互作用。与其他荧光探针相比, Qdots 在单分子研究中具有明显的优越性, 因为它对漂白具有较高的稳定性, 但应注意到该特性限制了其在定量测定中的应用。

为了可视化 Qdot 标记兽人与 ARS 之间的相互作用, 我们首先构造了λ-ARS317 DNA 基底。通过同源重组将含有 ARS317 的 dna 片段集成到XhoI. (33.5 kb) 的原生λ dna 中 (图 1A)。重组产物采用提取物包装, 在 LB 板上培养包装的噬菌体颗粒 (图 1B)。用 PCR 法筛选阳性噬菌体斑块, 并经测序证实 (图 1C)。ARS317 DNA 从液体?...

Watch this Scientific Journal Video about Visualizing the Interaction Between the Qdot-labeled Protein and Site-specifically Modified ÃŽÂ» DNA at the Single Molecule Level at JoVE.com

Visualizing the Interaction Between the Qdot-labeled Protein and Site-specifically Modified ÃƒÆ’Ã…Â½Ãƒâ€šÃ‚Â» DNA at the Single Molecule Level

在这里, 我们提出了一个协议, 研究 DNA 蛋白相互作用的全内反射荧光显微镜 (TIRFM) 使用一个网站专门修改的λ DNA 基底和量子点标记蛋白。

Qdot 标记蛋白与现场特异修饰的λ DNA 在单分子水平上的相互作用可视化

The fluorescence microscopy&#160;has made great contributions in dissecting the mechanisms of complex biological processes at the single molecule level. ...

Research

JoVE Journal

Biology

Visualizing the Interaction Between the Qdot-labeled Protein and Site-specifically Modified &#955; DNA at the Single Molecule Level

Method for Measurement of Viral Fusion Kinetics at the Single Particle Level

病毒融合动力学测量方法在单粒子能级

Membrane fusion is an essential step during entry of enveloped viruses into cells. Conventional fusion assays typically report on a large number of fusion ...

科研

生物学

Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

可视化的单分子荧光显微镜下的DNA复制

We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA ...

Studying Proteolysis of Cyclin B at the Single Cell Level in Whole Cell Populations

在整个细胞群在单细胞水平上研究细胞周期蛋白B的蛋白水解

Equal distribution of chromosomes between the two daughter cells during cell division is a prerequisite for guaranteeing genetic stability 1. Inaccuracies ...

The MultiBac Protein Complex Production Platform at the EMBL

在EMBL的MultiBac蛋白质复杂的生产平台

Proteomics  research revealed the impressive complexity of eukaryotic proteomes in  unprecedented detail. It is now a commonly accepted notion that ...

Analysis of Global RNA Synthesis at the Single Cell Level following Hypoxia

全球合成的RNA在单细胞水平以下的低氧分析

Hypoxia or lowering of the oxygen availability is involved in many physiological and pathological processes. At the molecular level, cells initiate a ...

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

结合单分子操纵和成像蛋白-DNA相互作用的研究

The paper describes the combination of optical tweezers and single molecule fluorescence detection for the study of protein-DNA interaction. The method ...

Quantitative Immunofluorescence Assay to Measure the Variation in Protein Levels at Centrosomes

定量免疫检测，以衡量在中心体的变异蛋白水平

Centrosomes are small but important organelles that serve as the poles of mitotic spindle to maintain genomic integrity or assemble primary cilia to ...

Identifying Protein-protein Interaction Sites Using Peptide Arrays

鉴定蛋白质相互作用的网站使用多肽阵列

Protein-protein interactions mediate most of the processes in the living cell and control homeostasis of the organism. Impaired protein interactions may ...

Analysis of LINE-1 Retrotransposition at the Single Nucleus Level

在单核级LINE-1逆转录转座子分析

Long interspersed nuclear element-1 (Line-1 or L1) accounts for approximately 17% of the DNA present in the human genome. While the majority of L1s are ...

CUBIC Protocol Visualizes Protein Expression at Single Cell Resolution in Whole Mount Skin Preparations

CUBIC协议可视化在全山皮肤配方单细胞分辨率蛋白表达

The skin is essential for our survival. The outer epidermal layer consists of the interfollicular epidermis, which is a stratified squamous epithelium ...