Technology Development

Our ongoing commitment in the Sobol Lab is to not only make groundbreaking discoveries but also to contribute to the research community by translating our methods and tools. To that end, we have made our vectors and cells available through respected sources like Addgene, ATCC, Kerafast, and ABMGood.

For more information on our technology development, we invite you to explore the dedicated page below. Together, let’s pave the way for transformative advancements in science!

Vectors Available at Addgene

Reagents Available from Kerafast

Lab reagents available at ABMGood (developed while at NIEHS in the Wilson lab):

Lab reagents available at ATCC (developed while at NIEHS in the Wilson lab):

DNA damage and repair analysis tools developed to date:

To quantitatively evaluate DNA repair capacity, we developed a method for the quantitative, real-time measurement of DNA glycosylase and AP endonuclease activities in cell nuclear lysates or by analysis of purified protein (DNA repair molecular beacon assay) (1,2).

A second tool we helped develop is for the quantitative analysis of genomic DNA damage – a Next Generation CometChip system. This ‘DNA repair on a Chip’ technology is based on a well-established assay for DNA damage, namely the Comet assay wherein damaged DNA migrates more readily than undamaged DNA when electrophoresed and can be visualized using standard microscopy. We have optimized the design and created a system that will enable a 3000% increase in throughput with increased accuracy that will function as a tool to quantify DNA damage and measure cellular DNA Repair capacity (3-5). Further, we have expanded this system to a 384-well platform (6).

Currently, we are developing novel probes for poly-ADP-ribose analysis (7,8) . Further, we have expanded this technology to include a Split-Luciferase LivePAR probe for live cell quantification of poly-ADP-ribose levels (9) . Efforts are ongoing to develop additional PAR-selective live-cell tools. To explore the role of these DNA repair pathways in an organism, we are also expanding our work to animal models. Most recently, we developed a mouse model with altered expression of the base excision repair (BER) protein DNA polymerase beta (Polb) (10) . Currently, we are working to develop additional mouse models to explore the biology of BER defects in an organism. If you are interested in the development of advanced DNA damage and repair analysis tools, please check our Visit Us page or contact us at Sobol.Lab@gmail.com.

References Cited

1. Li, J., Svilar, D., McClellan, S., Kim, J.H., Ahn, E.E., Vens, C., Wilson, D.M., 3rd and Sobol, R.W. (2018) DNA Repair Molecular Beacon assay: a platform for real-time functional analysis of cellular DNA repair capacity. Oncotarget, 9, 31719-31743.

2. Svilar, D., Vens, C. and Sobol, R.W. (2012) Quantitative, real-time analysis of base excision repair activity in cell lysates utilizing lesion-specific molecular beacons. Journal of visualized experiments : JoVE, e4168.

3. Ge, J., Ngo, L.P., Kaushal, S., Tay, I.J., Thadhani, E., Kay, J.E., Mazzucato, P., Chow, D.N., Fessler, J.L., Weingeist, D.M. et al. (2021) CometChip enables parallel analysis of multiple DNA repair activities. DNA Repair (Amst), 106, 103176.

4. Sykora, P., Witt, K.L., Revanna, P., Smith-Roe, S.L., Dismukes, J., Lloyd, D.G., Engelward, B.P. and Sobol, R.W. (2018) Next generation high throughput DNA damage detection platform for genotoxic
compound screening. Sci Rep, 8, 2771.

5. Sykora, P., Chiari, Y., Heaton, A., Moreno, N., Glaberman, S. and Sobol, R.W. (2018) Application of the CometChip platform to assess DNA damage in field-collected blood samples from turtles. Environ Mol Mutagen, 59, 322-333.

6. Li, J., Beiser, A., Dey, N.B., Takeda, S., Saha, L.K., Hirota, K., Parker, L.L., Carter, M., Arrieta, M.I. and Sobol, R.W. (2022) A high-throughput 384-well CometChip platform reveals a role for 3-methyladenine in the cellular response to etoposide-induced DNA damage. NAR Genom Bioinform, 4, lqac065.

7. Koczor, C.A., Saville, K.M., Andrews, J.F., Clark, J., Fang, Q., Li, J., Al-Rahahleh, R.Q., Ibrahim, M., McClellan, S., Makarov, M.V. et al. (2021) Temporal dynamics of base excision/single-strand break repair protein complex assembly/disassembly are modulated by the PARP/NAD(+)/SIRT6 axis. Cell reports, 37, 109917.

8. Koczor, C.A., Saville, K.M., Al-Rahahleh, R.Q., Andrews, J.F., Li, J. and Sobol, R.W. (2023) Quantitative Analysis of Nuclear Poly(ADP-Ribose) Dynamics in Response to Laser-Induced DNA Damage. Methods Mol Biol, 2609, 43-59.

9. Koczor, C.A., Haider, A.J., Saville, K.M., Li, J., Andrews, J.F., Beiser, A.V. and Sobol, R.W. (2022) Live Cell Detection of Poly(ADP-Ribose) for Use in Genetic and Genotoxic Compound Screens. Cancers (Basel), 14.

10. Koczor, C.A., Thompson, M.K., Sharma, N., Prakash, A. and Sobol, R.W. (2023) Polbeta/XRCC1 heterodimerization dictates DNA damage recognition and basal Polbeta protein levels without interfering with mouse viability or fertility. DNA Repair (Amst), 123, 103452.

Our ongoing commitment in the Sobol Lab is to not only make groundbreaking discoveries but also to contribute to the research community by translating our methods and tools. To that end, we have made our vectors and cells available through respected sources like Addgene, ATCC, Kerafast, and ABMGood.

For more information on our technology development, we invite you to explore the dedicated page below. Together, let’s pave the way for transformative advancements in science!