Name: real-time tracking of dna fragment separation by smartphone
Uploaded: 2017-06-01T15:00:00.000+00:00
Duration: 6 min 58 s
Description: Watch this Scientific Journal Video about Real-time Tracking of DNA Fragment Separation by Smartphone at JoVE.com

Wir bedanken uns herzlich bei der Unterstützung der Nationalen Naturwissenschaftlichen Stiftung von China (Nr. 21205078) und des Forschungsfonds für das Doktoratsstudium für Hochschulbildung in China (No.20123120110002). Diese Arbeit wurde teilweise durch das nationale Schlüsselforschungs- und Entwicklungsprogramm von China (2016YFB1102303), das nationale grundlegende Forschungsprogramm von China (973Programm 2015CB352001) und die nationale natürliche Wissenschafts-Grundlage von China (61378060) unterstützt.

1. Grunddesign des SGE-Chips <ol><li> Verwenden Sie jeden transparenten Kunststoff, wie Polymethylmethacrylat (PMMA) oder Polycarbonat. Hinweis: Der SGE-Chip ist in Abbildung 1B dargestellt. Der SGE-Chip besteht aus zylindrischen Löchern für den TBE-Puffer, Kanäle für die DNA-Trennung und zwei Bahnen, die entlang der Löcher für die Elektrode eingebettet sind. </li><li> Fertigungsarrays von SGE-Kanälen im PMMA-Block mit einer Lasergravurmaschine. Anmerkung: Die geometrischen Parameter des Chips hängen von der Größe der zu trennenden DNA ab. Zum Beispiel sind die optimalen Kanalparameter für den SGE-Chip 2,5 mm x 4,0 mm x 90 mm (Breite x Tiefe x Länge), wenn das DNA-Fragment kleiner als 1000 bp ist. </li><li> Basierend auf dem SGE-Design, fertigen Kämme, um die Brunnen im Chip zum Laden der DNA-Probe zu erstellen. </li></ol> 2. Vorbereitung des Agarosegels <ol><li> Vorbereiten von 0,5 × TBE durch Mischen von 10 × TBE (1 × TBE =89 mM Tris, 89 mM Borsäure und 2 mM EDTA; PH 8,4) und destilliertem Wasser im Verhältnis 1:19 </li><li> Vorbereitung 1,0% Agarose Gel für die Trennung von 100-bp DNA-Leitern. Anmerkung: Die Konzentration der Agarose in 0,5x TBE-Puffer hängt von den Größen der zu trennenden DNA-Fragmente ab. </li><li> Setzen Sie 0,1 g Agarose in einen Kolben und fügen Sie 10 ml 0,5x TBE-Puffer hinzu. Hinweis: Das Volumen der vorbereiteten Lösung sollte weniger als 1/3 der Kapazität des Kolbens betragen. </li><li> Den Kolben mit Konservierungsfilm abdichten und dann die Agarose / Puffermischung in einer Mikrowelle (Medium, 1,0 min) erhitzen. Vor dem Einsetzen der Flasche in die Mikrowelle, machen einige Löcher in der Konservierungsfolie im Falle einer Explosion. </li><li> Gießen Sie 2,7 ml geschmolzene Agarose-Lösung in 4 Kanäle des SGE-Chips. Legen Sie den Kamm in die Agarose-Lösung, um die Brunnen zu schaffen. Hinweis: Die geschmolzene Agarose-Lösung wird bei Raumtemperatur 3 min später auf den Gelzustand abkühlen gelassen. </li><li> Den Kamm aus der G entfernenEls und füge 0,9 ml 0,5x TBE-Puffer hinzu, um das Gel zu bedecken. </li></ol> 3. Die Elektrophorese im SGE-Chip durchführen <ol><li> Schalten Sie die LED-Lichtquelle ein und legen Sie einen 425 bis 505 nm Bandpassfilter über die Lichtquelle. </li><li> Mischen Sie 14,4 μl einer 100 bp DNA-Leiter und 1,6 μl SYBR Green mit einem Vortexer. </li><li> 4 μl Mischung in jede Vertiefung des Agarosegels im SGE-Chip geben ( Abbildung 2 ). </li><li> Setzen Sie die Elektrode in die beiden Bahnen des SGE-Chips. </li><li> Legen Sie einen 550 bis 700 nm Bandpassfilter über den SGE-Chip. </li><li> Schalten Sie die Stromquelle ein. Stellen Sie die elektrische Spannung auf 180 V (20 V / cm) ein. Schalte das Smartphone ein, um den DNA-Fragment-Trennprozess aufzuzeichnen (Abbildung 3 ). </li><li> Wenn die Elektrophorese 10 min später beendet ist, schalten Sie die Stromquelle und das LED-Licht aus. </li><li> Reinigen Sie den SGE-Chip. </li></ol>

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Agarose-Gelelektrophorese wird weithin für die Trennung von DNA, RNA und Protein eingesetzt. Diese Arbeit schlägt eine neue Methode vor, um das traditionelle Gelelektrophoreseprotokoll zu ersetzen. Die Ergebnisse zeigen, dass 50, 100 und 1000 bp DNA-Leitern in einer so kleinen zusammengebauten Vorrichtung gut getrennt werden können. Der große Vorteil dieser Methode ist, dass man nicht nur die Nukleinsäuren mit wenig chemischem Verbrauch trennen kann, sondern auch den Trennprozess aufzeichnen kann. Obwohl die DNA-Fr...

<html> Die Plattengelelektrophorese (SGE) ist die effektivste Methode für die DNA-Fragmenttrennung 1 , 2 , 3 , 4 , 5 und gilt somit als vielseitiges Werkzeug in biochemischen und biologischen Analysen 6 , 7 , 8 . Allerdings zeigen viele Experimente, dass SGE durch die folgenden vier Probleme eingeschränkt wird: (1) die Trennungen dauern viele Stunden und sogar Tage; (2) der chemische verbrauch ist sehr hoch; (3) es erfordert eine komplizierte Apparatur ( z. B. 2D-Elektrophoresezelle, Elektrophorese-Stromversorgung und Gelbildgebungssystem); (4) Das Gelbildgebungssystem kann nur die abgetrennten DNA-Fragmente beobachten, wenn das Experiment beendet ist. Weiterhin wird Ethidiumbromid (EtBr), das üblicherweise in SGE 9 verwendet wird ,Ass = &quot;xref&quot;&gt; 10, ist mutagen und krebserregend 11 , 12 . So sollten Handschuhe bei der Übergabe von Gele mit EtBr getragen werden. Die Kapillarelektrophorese (CE) hat zahlreiche Vorteile 13 , 14 , 15 , 16 , 17 im Vergleich zu SGE, wie z. B. automatischer Betrieb, kurze Trennzeit und geringeren Verbrauch. Allerdings ist das CE-Instrument ziemlich teuer. Um diese Einschränkungen zu überwinden, wurde daher ein System entwickelt (Abbildung 1 ) für die Trennung von DNA. Ein solches System kann den Chemikalienverbrauch nicht nur stark reduzieren und die SGE-Experimentierzeit (&lt;8 min) speichern, sondern auch eine Echtzeit-Verfolgung des DNA-Trennprozesses im Agarosegel durch Smartphone durchführen. Durch die folgenden Verfahren in diesem Protokoll, Studenten schreienLd in der Lage sein, den SGE-Chip zu entwerfen und zu fertigen, das Agarosegel im Chip vorzubereiten, ein einfaches SGE-System mit einem Smartphone aufzustellen und den DNA-Migrationsprozess im Agarosegel aufzuzeichnen.

<table><tbody><tr><td>10&amp;times;TBE</td><td>Beijing Solarbio Science &amp;amp; Technology Co., Ltd.</td><td>T1051</td><td></td></tr><tr><td>50 bp DNA ladder</td><td>Takara Bio Inc.</td><td>3421A</td><td></td></tr><tr><td>100 bp DNA ladder</td><td>Takara Bio Inc.</td><td>3422A</td><td></td></tr><tr><td>1 kbp DNA ladder</td><td>Takara Bio Inc.</td><td>3426A</td><td></td></tr><tr><td>SYBR GREEN</td><td>Takara Bio Inc.</td><td>5760A</td><td></td></tr><tr><td>Agarose</td><td>Sigma-Aldrich Corporate</td><td>V900510</td><td></td></tr></tbody></table>

real-time tracking of dna fragment separation by smartphone

Die Plattengelelektrophorese (SGE) ist die häufigste Methode zur Trennung von DNA-Fragmenten; So wird es weitgehend auf das Gebiet der Biologie und andere angewendet. Allerdings ist das traditionelle SGE-Protokoll ziemlich langweilig, und das Experiment dauert lange. Darüber hinaus ist der Chemikalienverbrauch bei SGE-Experimenten sehr hoch. Diese Arbeit schlägt eine einfache Methode zur Trennung von DNA-Fragmenten auf Basis eines SGE-Chips vor. Der Chip wird von einer Graviermaschine hergestellt. Für die Anregungs- und Emissionswellenlängen des optischen Signals werden zwei Kunststoffplatten verwendet. Das Fluoreszenzsignal der DNA-Banden wird vom Smartphone gesammelt. Um diese Methode zu validieren, wurden 50, 100 und 1000 bp DNA-Leitern getrennt. Die Ergebnisse zeigen, dass eine DNA-Leiter kleiner als 5.000 bp innerhalb von 12 min aufgelöst werden kann und mit hoher Auflösung bei der Verwendung dieser Methode, was darauf hinweist, dass es ein idealer Ersatz für die traditionelle SGE-Methode ist.

<html> Fig. 4 , Fig. 5 und Fig. 6 stellen ein typisches Ergebnis nach der Gelelektrophorese von 50, 100 und 1000 bp DNA-Leitern dar. Nach dem Experiment waren die DNA-Fragmente gut getrennt. Weiterhin wurden die gleichen Proben in den 4 Kanälen des SGE-Chips getrennt, was zeigt, dass DNA-Fragmente gleicher Größe in jedem Experiment den gleichen Abstand bewegen. Die Trennleistung der DNA-Leiter kann du...

Watch this Scientific Journal Video about Real-time Tracking of DNA Fragment Separation by Smartphone at JoVE.com

Real-time Tracking of DNA Fragment Separation by Smartphone

Echtzeit-Tracking der DNA-Fragment-Trennung durch Smartphone

Traditionelle Plattengelelektrophorese (SGE) Experimente erfordern eine komplizierte Apparatur und einen hohen chemischen Verbrauch. Diese Arbeit stellt ein Protokoll vor, das eine kostengünstige Methode zur Trennung von DNA-Fragmenten innerhalb eines kurzen Zeitrahmens beschreibt.

Slab gel electrophoresis (SGE) is the most common method for the separation of DNA fragments; thus, it is broadly applied to the field of biology and ...

real-time-tracking-of-dna-fragment-separation-by-smartphone

Research

JoVE Journal

Biochemistry

14.5K Aufrufe.  University of Shanghai for Science and Technology.  Traditionelle Plattengelelektrophorese (SGE) Experimente erfordern eine komplizierte Apparatur und einen hohen chemischen Verbrauch. Diese Arbeit stellt ein Protokoll vor, das eine kostengünstige Methode zur Trennung von DNA-Fragmenten innerhalb eines kurzen Zeitrahmens beschreibt. 

Serie: Real-time Tracking of DNA Fragment Separation by Smartphone

Detection of Copy Number Alterations Using Single Cell Sequencing

Detection of genomic changes at single cell resolution is important for characterizing genetic heterogeneity and evolution in normal tissues, cancers, and microbial populations. Traditional methods for assessing genetic heterogeneity have been limited by low resolution, low sensitivity, and/or low specificity. Single cell sequencing has emerged as a powerful tool for detecting genetic heterogeneity with high resolution, high sensitivity and, when appropriately analyzed, high specificity. Here we provide a protocol for the isolation, whole genome amplification, sequencing, and analysis of single cells. Our approach allows for the reliable identification of megabase-scale copy number variants in single cells. However, aspects of this protocol can also be applied to investigate other types of genetic alterations in single cells.

Single cell sequencing is an increasingly popular and accessible tool for addressing genomic changes at high resolution. We provide a protocol that uses single cell sequencing to identify copy number alterations in single cells.

Der Nachweis von Copy Number Änderungen Single Cell-Sequenzierung

Detection of genomic changes at single cell resolution is important for characterizing genetic heterogeneity and evolution in normal tissues, cancers, and ...

Forschung

Genetik

Modified Terminal Restriction Fragment Analysis for Quantifying Telomere Length Using In-gel Hybridization

There are several different techniques for measuring telomere length, each with their own advantages and disadvantages. The traditional approach, Telomere Restriction Fragment (TRF) analysis, utilizes a DNA hybridization technique whereby genomic DNA samples are digested with restriction enzymes, leaving behind telomere DNA repeats and some sub-telomeric DNA. These are separated by agarose gel electrophoresis, transferred to a filter membrane and hybridized to oligonucleotide probes tagged with either chemiluminescence or radioactivity to visualize telomere restriction fragments. This approach, while requiring a larger quantity of DNA than other techniques such as PCR, can measure the telomere length distribution of a population of cells and allows measurement expressed in absolute kilobases. This manuscript demonstrates a modified DNA hybridization procedure for determining telomere length. Genomic DNA is first digested with restriction enzymes (that do not cut telomeres) and separated by agarose gel electrophoresis. The gel is then dried and the DNA is denatured and hybridized in situ to a radiolabeled oligonucleotide probe. This in situ hybridization avoids loss of telomere DNA and improves signal intensity. Following hybridization, the gels are imaged utilizing phosphor screens and the telomere length is quantified using a graphing program. This procedure was developed by the laboratories of Drs. Woodring Wright and Jerry Shay at the University of Texas Southwestern1,2. Here, we present a detailed description of this procedure, with some modifications.

In this article, a detailed protocol for quantifying telomere length using a modified terminal restriction fragment analysis is discussed that provides fast and efficient direct measurement of telomere length. This technique can be applied to a variety of cell sources of DNA for quantifying telomere length.

Modifizierte terminale Restriktionsfragmentanalyse zur Quantifizierung der Telomerenlänge mittels In-Gel-Hybridisierung

There are several different techniques for measuring telomere length, each with their own advantages and disadvantages. The traditional approach, Telomere ...

Krebsforschung

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

We describe a simple, robust and high throughput single molecule flow-stretching assay for studying 1D diffusion of molecules along DNA. In this assay, glass coverslips are functionalized in a one-step reaction with silane-PEG-biotin. Flow cells are constructed by sandwiching an adhesive tape with pre-cut channels between a functionalized coverslip and a PDMS slab containing inlet and outlet holes. Multiple channels are integrated into one flow cell and the flow of reagents into each channel can be fully automated, which significantly increases the assay throughput and reduces hands-on time per assay. Inside each channel, biotin-&#955;-DNAs are immobilized on the surface and a laminar flow is applied to flow-stretch the DNAs. The DNA molecules are stretched to &#62;80% of their contour length and serve as spatially extended templates for studying the binding and transport activity of fluorescently labeled molecules. The trajectories of single molecules are tracked by time-lapse Total Internal Reflection Fluorescence (TIRF) imaging. Raw images are analyzed using streamlined custom single particle tracking software to automatically identify trajectories of single molecules diffusing along DNA and estimate their 1D diffusion constants.

This protocol demonstrates a simple, robust and high throughput single molecule flow-stretching assay for studying one-dimensional (1D) diffusion of molecules along DNA.

Einfach, Robust und hohen Durchsatz Molekül fließen Stretching Assay-Implementierung für das Studium Transport von Molekülen entlang DNA

We describe a simple, robust and high throughput single molecule flow-stretching assay for studying 1D diffusion of molecules along DNA. In this assay, ...

Biochemie

Real-time Observation of the DNA Strand Exchange Reaction Mediated by Rad51

The DNA strand exchange reaction mediated by Rad51 is a critical step of homologous recombination. In this reaction, Rad51 forms a nucleoprotein filament on single-stranded DNA (ssDNA) and captures double-stranded DNA (dsDNA) non-specifically to interrogate it for a homologous sequence. After encountering homology, Rad51 catalyzes DNA strand exchange to mediate pairing of the ssDNA with the complementary strand of the dsDNA. This reaction is highly regulated by numerous accessary proteins in vivo. Although conventional biochemical assays have been successfully employed to examine the role of such accessory protein in vitro, kinetic analysis of intermediate formation and its progression into a final product has proven challenging due to the unstable and transient nature of the reaction intermediates. To observe these reaction steps directly in solution, fluorescence resonance energy transfer (FRET)-based real-time observation systems of this reaction were established. Kinetic analysis of real-time observations shows that the DNA strand exchange reaction mediated by Rad51 obeys a three-step reaction model involving the formation of a three-strand DNA intermediate, maturation of this intermediate, and the release of ssDNA from the mature intermediate. The Swi5-Sfr1 complex, an accessary protein conserved in eukaryotes, strongly enhances the second and third steps of this reaction. The FRET-based assays presented here enable us to uncover the molecular mechanisms through which recombination accessary proteins stimulate the DNA strand exchange activity of Rad51. The primary goal of this protocol is to enhance the repertoire of techniques available to researchers in the field of homologous recombination, particularly those working with proteins from species other than Schizosaccharomyces pombe, so that the evolutionary conservation of the findings presented herein can be determined.

Fluorescence resonance energy transfer-based real-time observation systems of the DNA strand exchange reaction mediated by Rad51 were developed. Using the protocols presented here, we are able to detect the formation of reaction intermediates and their conversion into products, while also analyzing the enzymatic kinetics of the reaction.

Echtzeit-Beobachtung der DNA-Strang Exchange Reaktion vermittelt durch Rad51

The DNA strand exchange reaction mediated by Rad51 is a critical step of homologous recombination. In this reaction, Rad51 forms a nucleoprotein filament ...

Application of DNA Fingerprinting using the D1S80 Locus in Lab Classes

In biological sciences, DNA fingerprinting has been widely used for paternity testing, forensic applications and phylogenetic studies. Here, we describe a reliable and robust method for genotyping individuals by Variable Number of Tandem Repeat (VNTR) analysis in the context of undergraduate laboratory classes. The human D1S80 VNTR locus is used in this protocol as a highly polymorphic marker based on variation in the number of repetitive sequences.
This simple protocol conveys useful information for teachers and the implementation of DNA fingerprinting in practical laboratory classes. In the presented laboratory exercise, DNA extraction followed by PCR amplification is used to determine genetic variation at the D1S80 VNTR locus. Differences in the fragment size of PCR products are visualized by agarose gel electrophoresis. The fragment sizes and repeat numbers are calculated based on a linear regression of the size and migration distance of a DNA size standard.
Following this guide, students should be able to:
&#8226;&#160; Harvest and extract DNA from buccal mucosa epithelial cells 
&#8226;&#160; Perform a PCR experiment and understand the function of various reaction components 
&#8226;&#160; Analyze the amplicons by agarose gel electrophoresis and interpret the results 
&#8226;&#160; Understand the use of VNTRs in DNA fingerprinting and its application in biological sciences

Application of DNA Fingerprinting using the D1S80 Locus in Lab Classes

Here we describe a simple protocol to generate DNA fingerprinting profiles by amplifying the VNTR locus D1S80 from epithelial cell DNA.

Anwendung von DNA Fingerprinting mit dem D1S80 Locus in Laborklassen

In biological sciences, DNA fingerprinting has been widely used for paternity testing, forensic applications and phylogenetic studies. Here, we describe a ...

Single-Molecule Dwell-Time Analysis of Restriction Endonuclease-Mediated DNA Cleavage

This novel total internal reflection fluorescence microscopy-based assay facilitates the simultaneous measurement of the length of the catalytic cycle for hundreds of individual restriction endonuclease (REase) molecules in one experiment. This assay does not require protein labeling and can be carried out with a single imaging channel. In addition, the results of multiple individual experiments can be pooled to generate well-populated dwell-time distributions. Analysis of the resulting dwell-time distributions can help elucidate the DNA cleavage mechanism by revealing the presence of kinetic steps that cannot be directly observed. Example data collected using this assay with the well-studied REase, EcoRV - a dimeric Type IIP restriction endonuclease that cleaves the palindromic sequence GAT&#8595;ATC (where &#8595; is the cut site) - are in agreement with prior studies. These results suggest that there are at least three steps in the pathway to DNA cleavage that is initiated by introducing magnesium after EcoRV binds DNA in its absence, with an average rate of 0.17 s-1 for each step.

Using quantum-dot-labeled DNA and total internal reflection fluorescence microscopy, we can investigate the reaction mechanism of restriction endonucleases while using unlabeled protein. This single-molecule technique allows for massively multiplexed observation of individual protein-DNA interactions, and data can be pooled to generate well-populated dwell-time distributions.

Einzelmolekül-Verweilzeitanalyse der Restriktionsendonuklilease-vermittelten DNA-Spaltung

This novel total internal reflection fluorescence microscopy-based assay facilitates the simultaneous measurement of the length of the catalytic cycle for ...

Smartphone als Analysegerät zur Quantifizierung von Proteinen mit Bradford-Assay

RGBradford: Protein Quantitation with a Smartphone Camera

Protein quantitation is an essential procedure in life sciences research. Amongst several other methods, the Bradford assay is one of the most used. Because of its widespread, the limitations and advantages of the Bradford assay have been exhaustively reported, including several modifications of the original method to improve its performance. One of the alterations of the original method is the use of a smartphone camera as an analytical instrument. Taking advantage of the three forms of the Coomassie Brilliant Blue dye that exist in the conditions of the Bradford assay, this paper describes how to accurately quantify protein in samples using color data extracted from a single picture of a microplate. After performing the assay in a microplate, a picture is taken using a smartphone camera, and RGB color data is extracted from the picture using a free and open-source image analysis software application. Then, the ratio of blue to green intensity (in the RGB scale) of samples with unknown concentrations of protein is used to calculate the protein content based on a standard curve. No significant difference is observed between values calculated using RGB color data and those calculated using conventional absorbance data.

Autor im Rampenlicht: Ein alternativer Ansatz zur Proteinquantifizierung durch Bradford-Assay mit einem Smartphone 

This paper provides a protocol for protein quantification using the Bradford assay and a smartphone as an analytical device. Protein levels in samples can be quantified using color data extracted from a picture of a microplate taken with a smartphone.

RGBradford: Proteinquantifizierung mit einer Smartphone-Kamera

Protein quantitation is an essential procedure in life sciences research. Amongst several other methods, the Bradford assay is one of the most used. ...

<meta charset="utf8"></head><body>CMG-vermittelte DNA-Dewindung durch Wachstum des ssDNA-RPA-Trakts beobachtet

Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase

Faithful genome duplication is essential for preserving the genetic stability of dividing cells. DNA replication is carried out during the S phase by a dynamic complex of proteins termed the replisome. At the heart of the replisome is the&#160;CDC45-MCM2-7-GINS (CMG) helicase, which separates the two strands of the DNA double helix such that DNA polymerases can copy each strand. During genome duplication, replisomes must overcome a plethora of obstacles and challenges. Each of these threatens genome stability, as failure to replicate DNA completely and accurately can lead to mutations, diseases, or cell death. Therefore, it is of great interest to understand how CMG functions in the replisome during both normal replication and replication stress. Here, we describe a total internal reflection fluorescence (TIRF) microscopy assay using recombinant purified proteins, which allows for real-time visualization of surface-tethered stretched DNA molecules by individual CMG complexes. This assay provides a powerful platform to investigate CMG behavior at the single-molecule level, allowing helicase dynamics to be directly observed with real-time control over reaction conditions.

<meta charset="utf8"></head><body>Autor im Rampenlicht: Entschlüsselung der Dynamik der eukaryotischen DNA-Replikation durch Einzelmolekül-Visualisierung

This protocol demonstrates performing a single-molecule assay for live visualization of DNA unwinding by CMG helicase. It describes (1) preparing a DNA substrate, (2) purifying fluorescently labeled Drosophila melanogaster CMG helicase, (3) preparing a microfluidic flow cell for total internal reflection fluorescence (TIRF) microscopy, and (4) the single-molecule DNA unwinding assay.

Einzelmolekül-Echtzeit-Visualisierung der DNA-Abwicklung durch CMG-Helikase

Faithful genome duplication is essential for preserving the genetic stability of dividing cells. DNA replication is carried out during the S phase by a ...

Echtzeit-Tracking der DNA-Fragment-Trennung durch Smartphone

Zusammenfassung

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RGBradford: Proteinquantifizierung mit einer Smartphone-Kamera

RGBradford: Proteinquantifizierung mit einer Smartphone-Kamera

RGBradford: Proteinquantifizierung mit einer Smartphone-Kamera

Einzelmolekül-Echtzeit-Visualisierung der DNA-Abwicklung durch CMG-Helikase