Atomic Force Microscopy Investigations of DNA Lesion Recognition in Nucleotide Excision Repair

The overall goal of this atomic force microscopy experiment is to resolve interactions of DNA repair proteins with damage sites in DNA and to distinguish between different DNA interactions by various protein complexes. This method can help answer key questions in the DNA repair field, such as how a particular DNA repair system achieves the recognition of its target lesions in the DNA. The main advantage of this technique is that we can directly see and analyze the different types of complexes that are involved in the DNA lesion recognition process.

Demonstrating the procedure will be Nicolas Wirth, who used this approach during his bachelor research. To begin, prepare a suitable DNA substrate by generating a single-stranded DNA gap in a plasmid. Refill the gap with modified, single-stranded DNA oligonucleotides, and finally, linearize the plasma DNA using appropriate restriction enzymes.

For these experiments, the double-stranded DNA substrates are about 1, 000 base pairs long and contain a DNA lesion as well as an unpaired region called a DNA bubble for protein loading onto the DNA. Next, prepare a protein DNA sample for AFM analysis by first pipetting 10x Reaction Buffer and water into a microreaction tube. Then, add the DNA and proteins under investigation.

For example, here, 100 nanomolar of the DNA sample and one micromolar or each of the eukaryotic nucleotide excision repair proteins XPD and p44. Then, incubate the reaction for 30 minutes at 37 degrees Celsius in a heat block. Following the incubation, briefly spin down the sample.

Next, prepare a mica substrate to place the sample onto. Use a scalpel to cut a one-centimeter by one-centimeter piece of mica from a larger strip. Then, use a piece of adhesive tape to remove the top layers of the mica to reveal a clean, flat, anatomically smooth substrate surface.

Dilate the protein DNA sample fifty to a hundredfold in AFM deposition buffer, and immediately deposit 20 microliters of the diluted sample onto the mica surface. The dilution factor depends on the sample concentration. Immediately after depositing the sample on the mica surface, rinse the sample three to four times with a few milliliters of filtered, deionized water and blot off excess liquid.

Use a gentle stream of nitrogen to blow dry the sample. Finally, use adhesive tape to fix the sample at its edges onto a microscope slide. Place the sample in the middle of the AFM stage and use magnetic pads to fix the microscope slide on the stage.

Then, insert the AFM tip into the tip holder. Fix the tip in the holder under a clamp by tightening the screw so that it is finger tight. Once secured, enter the tip holder into the AFM measurement head.

Use the positioning screws to move the sample in a central position. Place the AFM measurement head on top of the sample, making sure the head stands stably with its legs inside the stage indentations. Next, align the AFM laser on the back of the cantilever for optimal signal strength.

Watch the reflection signal in the AFM video window to crudely position the laser. For this AFM model, turn the wheels of the right side and back of the AFM measurement head to adjust the X and Y positions of the AFM laser in order to direct it centrally onto the end of the cantilever. Then, optimize the detector sum signal by fine-tuning the laser position with the two wheels.

Direct the AFM laser reflection onto the detector center by zeroing the different signal from the top and bottom diodes of the detector array. For this step, turn the screw on the left-side of the measurement head for this AFM model. Next, determine the cantilever residence frequency by going into the master panel tune window in the software.

Choose an amplitude corresponding to a one-volt input for the Piezo that drives the cantilever oscillation and then set the oscillation frequency to negative 5%slightly lower than the residence frequency. Now perform an auto frequency tune and zero the phase of the oscillation. Leave the system to reach thermal equilibrium for about one hour before you start imaging, in order to avoid drift.

When you are ready to start imaging, in the software main panel, set a protecting set point and prepare to approach the tip to the sample surface by selecting engage. Lower the front wheel of the AFM head manually until the protective setting, or set point, is reached. Then, carefully lower the front wheel further until the Z sensor signal is fully extended to the left.

Activate the vibration oscillation table and close the acoustic isolation enclosure. Next, lower the set point in the AFM software using the hamster wheel to fine engage the AFM tip with the sample. To perform tapping mode imaging in the repulsive regime, lower the set point until the phase signal becomes slightly lower than the free level phase.

Then, begin scanning the sample. Use the scan speed of 2.5 micrometers per second in image surface areas of four micrometer by four micrometer or eight micrometer by eight micrometer squares with pixel resolutions of 2, 048 or 4, 096, respectively;and press the Do Scan button. Preselect relevant protein DNA complexes by direct visual inspection of the images in the AFM software.

For XPD samples, possible complexes include XPD p44 DNA, as well as XPD DNA and p44 DNA with distinctly different sizes due to the different molecular masses of XPD and p44. Measure volumes of individual protein peaks on the DNA by using the section tool in the analysis window to measure the height and diameter of the protein peak sections with the section window cursors. Use these values to determine the volume of the peaks using simple mathematical models to verify the complex type.

Finally, calibrate your AFM system with a range of proteins with known molecular weights to translate these volumes into approximate molecular weights of proteins and protein complexes. In order to determine additional features, such as DNA fragment lengths, the positions of protein complexes on the DNA and their target-site specificities or DNA band angles, see the accompanying text protocol. Shown here is an AFM image with three different types of DNA-bound complexes that can be distinguished based on their different sizes.

Class one complexes are consistent with only the helicase activating co-factor p44, class two complexes consist of only the XPD protein, and class three complexes consist of both XPD and p44 as legion recognition by XPD requires the activation of its helicase activity by p44, and only the class three complexes show lesion recognition. In order to identify different lesion recognition strategies, the locations of proteins on the DNA substrates were measured for protein loading at a DNA bubble in either the five prime or three prime directions from a DNA lesion shown in red for prokaryotic and eukaryotic NER helicases. In the protein position distributions, DNA lesion recognition can be seen as a peak due to enhanced binding at the DNA lesion position.

The prokaryotic NER helicase UVRB and its eukaryotic counterpart, XPD, show different strategies of CPD lesion recognition that indicate different DNA strand preferences. Specifically, CPD lesions are recognized on the translocated strand by UVRB, but preferentially on the opposite, non-translocated strand by XPD. Once mastered, this method can be done in a few hours or days including analysis.

It's important to work with highly pure protein and DNA samples to be able to interpret the features in the AFM images and to carefully design the DNA substrate depending on the biological system and on the question you want to address. In addition, ensemble methods, such as gel electrophoresis space, electromobility shift, or DNA incision assays are, of course, highly complementary to these AFM experiments;and these methods can help address additional questions, such as on DNA binding affinities or DNA lesion excision activities. This technique is a relatively fast and simple approach to directly visualize protein DNA complexes, and these complexes give us a good picture of the processes that occur in a biological system.

Of course, this is not only useful in understanding DNA repair processes, but it can also be applied to other protein DNA systems. After watching this video, you should have a pretty good idea of how to prepare a sample on your favorite protein DNA system, how to image it by AFM, and of how to extract useful parameters for an interpretation of your data.