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1. Poxvirus uracil-DNA glycosylase-An unusual member of the family I uracil-DNA glycosylases: Poxvirus Uracil-DNA Glycosylase

   https://doi.org/10.1002/pro.3058  

   Schormann, Norbert ; Zhukovskaya, Natalia ; Bedwell, Gregory ; Nuth, Manunya ; Gillilan, Richard ; Prevelige, Peter E. ; Ricciardi, Robert P. ; Banerjee, Surajit ; Chattopadhyay, Debasish ( December 2016 , Protein Science)
2. Salt-Dependent DNA-DNA Spacings in Intact Bacteriophage $\lambda$ Reflect Relative Importance of DNA Self-Repulsion and Bending Energies

   https://doi.org/10.1103/PhysRevLett.106.028102  

   ( January 2011 , Physical Review Letters)
3. Tethering-facilitated DNA ‘opening’ and complementary roles of β-hairpin motifs in the Rad4/XPC DNA damage sensor protein

   https://doi.org/10.1093/nar/gkaa909  

   Paul, Debamita ; Mu, Hong ; Tavakoli, Amirrasoul ; Dai, Qing ; Chen, Xuejing ; Chakraborty, Sagnik ; He, Chuan ; Ansari, Anjum ; Broyde, Suse ; Min, Jung-Hyun ( October 2020 , Nucleic Acids Research)

   Abstract XPC/Rad4 initiates eukaryotic nucleotide excision repair on structurally diverse helix-destabilizing/distorting DNA lesions by selectively ‘opening’ these sites while rapidly diffusing along undamaged DNA. Previous structural studies showed that Rad4, when tethered to DNA, could also open undamaged DNA, suggesting a ‘kinetic gating’ mechanism whereby lesion discrimination relied on efficient opening versus diffusion. However, solution studies in support of such a mechanism were lacking and how ‘opening’ is brought about remained unclear. Here, we present crystal structures and fluorescence-based conformational analyses on tethered complexes, showing that Rad4 can indeed ‘open’ undamaged DNA in solution and that such ‘opening’ can largely occur without one or the other of the β-hairpin motifs in the BHD2 or BHD3 domains. Notably, the Rad4-bound ‘open’ DNA adopts multiple conformations in solution notwithstanding the DNA’s original structure or the β-hairpins. Molecular dynamics simulations reveal compensatory roles of the β-hairpins, which may render robustness in dealing with and opening diverse lesions. Our study showcases how fluorescence-based studies can be used to obtain information complementary to ensemble structural studies. The tethering-facilitated DNA ‘opening’ of undamaged sites and the dynamic nature of ‘open’ DNA may shed light on how the protein functions within and beyond nucleotide excision repair inmore »cells.« less
4. Electro-hydrodynamic extraction of DNA from mixtures of DNA and bovine serum albumin

   https://doi.org/10.1039/D0AN00961J  

   Valley, Benjamin E. ; Crowell, Anne D. ; Butler, Jason E. ; Ladd, Anthony J. ( August 2020 , The Analyst)

   We report separation of genomic DNA (48 kbp) from bovine serum albumin (BSA) by the electro-hydrodynamic coupling between a pressure-driven flow and a parallel electric field. Electro-hydrodynamic extraction exploits this coupling to trap DNA molecules at the entrance of a microfluidic contraction channel, while allowing proteins and salts to be flushed from the device. Samples (10 μL) containing λ-DNA (1 ng) and BSA (0.3 mg) were injected directly into the device and convected to the contraction channel entrance by a flowing buffer solution. The DNA remains trapped in this region essentially indefinitely, while proteins and salts are eluted. The effectiveness of the concept has been assessed by fluorescence measurements of DNA and BSA concentrations. Electro-hydrodynamic extraction in a single-stage device was found to enhance the concentration of DNA 40-fold, while reducing the BSA concentration by four orders of magnitude. The relative concentrations of DNA to BSA at the contraction channel entrance can be as large as 1.5 : 1, corresponding to an A260/280 ratio of 1.9. The maximum yield of DNA from a salt-free solution is 50%, while salted (150 mM) solutions have a lower yield (38%).
5. Quantifying the stability of oxidatively damaged DNA by single-molecule DNA stretching

   https://doi.org/10.1093/nar/gky148  

   McCauley, Micah J ; Furman, Leah ; Dietrich, Catherine A ; Rouzina, Ioulia ; Núñez, Megan E ; Williams, Mark C ( March 2018 , Nucleic Acids Research)