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1. Understanding the physical processes behind DNA-DNA proximity ligation assays

   https://doi.org/10.1101/2025.05.02.649190  

   Zubillaga_Herrera, Bernardo J; Das, Amit; Burack, Linden; Wang, Ailung; Di_Pierro, Michele (May 2025, bioRxiv)

   Abstract In the last decade, DNA-DNA proximity ligation assays opened powerful new ways to study the 3D organization of genomes and have become a mainstay experimental technology. Yet many aspects of these experiments remain poorly understood. We study the inner workings of DNA-DNA proximity ligation assays through numerical experiments and theoretical modeling. Chromosomes are modeled at nucleosome resolution and evolved in time via molecular dynamics. A virtual Hi-C experiment reproduces, in-silico, the different steps of the Hi-C protocol, including: crosslinking of chromatin to an underlying proteic matrix, enzymatic digestion of DNA, and subsequent proximity ligation of DNA open ends. The protocol is simulated on ensembles of different structures as well as individual structures, enabling the construction of ligation maps and the calculation of ligation probabilities as functions of genomic and Euclidean distance. The methods help to assess the effect of the many variables of the Hi-C experiment and of subsequent data processing methods on the quality of the final results. 

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2. 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)
3. Stabilizing DNA–Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA

   https://doi.org/10.3390/cryst12010049  

   Ward, Abigail R.; Dmytriw, Sara; Vajapayajula, Ananya; Snow, Christopher D. (January 2022, Crystals)

   Protein and DNA co-crystals are most commonly prepared to reveal structural and functional details of DNA-binding proteins when subjected to X-ray diffraction. However, biomolecular crystals are notoriously unstable in solution conditions other than their native growth solution. To achieve greater application utility beyond structural biology, biomolecular crystals should be made robust against harsh conditions. To overcome this challenge, we optimized chemical DNA ligation within a co-crystal. Co-crystals from two distinct DNA-binding proteins underwent DNA ligation with the carbodiimide crosslinking agent 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) under various optimization conditions: 5′ vs. 3′ terminal phosphate, EDC concentration, EDC incubation time, and repeated EDC dose. This crosslinking and DNA ligation route did not destroy crystal diffraction. In fact, the ligation of DNA across the DNA–DNA junctions was clearly revealed via X-ray diffraction structure determination. Furthermore, crystal macrostructure was fortified. Neither the loss of counterions in pure water, nor incubation in blood serum, nor incubation at low pH (2.0 or 4.5) led to apparent crystal degradation. These findings motivate the use of crosslinked biomolecular co-crystals for purposes beyond structural biology, including biomedical applications. 

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4. May the Road Rise to Meet You: DNA Deformation May Drive DNA Translocation

   https://doi.org/10.1016/j.bpj.2019.04.027  

   Jardine, Paul J. (June 2019, Biophysical Journal)
5. Tomography of DNA tiles influences the kinetics of surface-mediated DNA self-assembly

   https://doi.org/10.1016/j.bpj.2022.07.025  

   Zhang, Cuizheng; Paluzzi, Victoria E.; Mao, Chengde (December 2022, Biophysical Journal)