Study and Visualize DNA Replication Mechanisms with High Throughput

Part of: DNA Replication

Multiplexed force extension and manipulation of DNA-protein interactions

Here, multiple protein-coated DNA molecules are tethered between a bead and a glass surface. Using the AFS we can stretch the DNA molecules by pulling the beads away from the surface while measuring the z-position of each individual bead. This makes it possible to obtain the force-distance curve of many protein-coated DNA molecules in parallel.

AFS DNA-Protein Interactions General

Figure 1 shows the force-extension curve of a DNA molecule measured before (left) and after (right) the incubation of 1 μM of RecA – a protein involved in DNA repair. From the figure we can observe that RecA substantially lengthens the DNA as it forms filaments around the DNA structure, preventing it from coiling.

Figure 2 shows the normalized length-time traces of two individual DNA molecules in the presence of 0.5 μM RecA. At a constant force of 40 pN, the DNA length increases to >1.4x the contour length (Lc) because of RecA binding to the DNA. When the force is set to 2.5 pN again, the length of the DNA decreases due to RecA disassembly. This indicates that the RecA binding is strongly dependent on tension and is therefore enhanced by increased force. From the figure, we can also observe a slightly different behavior between the two molecules which underlies the importance of obtaining many single-molecule measurements.

Highly parallel measurements of DNA-protein interactions typically require that both constant and dynamic forces can be applied on the DNA. A high force and distance resolution and the ability to apply hundreds of picoNewtons to the DNA molecule are necessary to obtain the complete force-distance curve.

AFS AFS Force extension of RecA-DNA

1 Force-distance curves of DNA in the absence (left) and presence (right) of RecA.

AFS Time extension of RecA-DNA AFS

2 Normalized length-time traces of two individual DNA molecules in the presence of RecA. The figure shows a force-dependent binding behavior of the length increasing protein.

Data courtesy of Prof. Erwin Peterman and Prof. Gijs Wuite at the VU University Amsterdam.

Hill et al. (2017)

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Investigation of protein activity involved in DNA Replication

Multiple DNA tethers are attached at one end to the surface of the AFS chip and at the other to a polystyrene bead through RNA polymerase (RNAp) stalled on the DNA template. As the position of the bead changes proportional to the position of the protein on the DNA, we can study the enzymatic activity of the proteins by measuring the z-position of the beads while keeping the force constant.

AFS DNA Transcription

Figure 3 shows measurement data from a proof-of-concept experiment involving DNA molecules with stalled E. coli RNA polymerase (RNAp). Once transcription and replication are initiated we can precisely monitor the activity of many individual E. coli RNAp molecules in parallel by measuring the DNA elongation in real time.

The graph shows the typical complex nature of the protein activity: stochastically occurring elongation is frequently interrupted by pausing events of different nature.

AFS Enzymatic Activity

3 Activity bursts of multiple RNAp proteins.

Data courtesy of Anatoly Arseniev, Georgii Pobegalov and Mikhail Khodorkovskii at Peter the Great St. Petersburg Polytechnic University, Russia.

Investigation of the effect of inhibitors on enzymatic activity

Here, a single DNA tether is attached at one end to the surface of the AFS chip and at the other to a polystyrene bead through RNAp stalled on the DNA template. Next, constant force is applied to detect the activity of the RNAp in the presence of different known and unknown inhibitor molecules.

AFS DNA Transcription Small Molecules

In practice, the effect of two novel peptides, acinetodin and klebsidin, was investigated with respect to transcription elongation generated by RNA polymerase. The detection of transcription elongation was determined by the presence of varying concentrations of acinetodin, klebsidin and microcin J25; the last peptide being a known transcription inhibitor. Figure 4 shows that – just as microsin J25 – both acinetodin and klebsidin inhibit transcript elongation by E. coli RNAp, with the inhibitor activity of klebsidin being comparable to that of microcin J25 and more active than the activity of acinetodin.

The same experiment can be done with many single-molecules in parallel allowing you to collect properties, such as the rate and pausing events of each RNAp enzyme in singulo, and map their collective distribution in histograms. In this manner it is possible to identify the processivity properties of RNAp in the presence of different molecules leading to new insights.

AFS Effect of inhibitors on enzymatic activity

4 Representative elongation profiles for individual RNAp’s for various concentrations of microcin J25, klebsidin, and acinetodin and in the absence of inhibitors plotted as nucleotides transcribed vs time. Data were filtered by a 0.5 Hz low pass filter.

Figure 4 is reprinted with permission from ACS Chem. Bio., 2017, 12 (3), pp 814-824. Copyright 2018 American Chemical Society

Metelev et al. (2007)
ACS Chemical Biology



Parallel Single-Molecule Force Spectroscopy

Acoustic Force Spectroscopy is a new single-molecule and single-cell manipulation method capable of applying acoustic forces on hundreds of biomolecules in parallel for precise experimentation with high throughput. It enables scientists to probe thousands of individual molecules in parallel (such as RNA, DNA, proteins, and living cells), allowing statistical analysis of the mechanical properties of biological properties of biological systems based on a single experiment.

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