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1. Lipid‐Polymer Hybrid “Particle‐in‐Particle” Nanostructure Gene Delivery Platform Explored for Lyophilizable DNA and mRNA COVID‐19 Vaccines

   https://doi.org/10.1002/adfm.202204462  

   Li, Zhongyu; Zhang, Xue‐Qing; Ho, William; Bai, Xin; Jaijyan, Dabbu_Kumar; Li, Fengqiao; Kumar, Ranjeet; Kolloli, Afsal; Subbian, Selvakumar; Zhu, Hua; et al (July 2022, Advanced Functional Materials)

   Abstract SARS‐CoV‐2 has led to a worldwide pandemic, catastrophically impacting public health and the global economy. Herein, a new class of lipid‐modified polymer poly (β‐amino esters) (L‐PBAEs) is developed via enzyme‐catalyzed esterification and further formulation of the L‐PBAEs with poly(d,l‐lactide‐coglycolide)‐b‐poly(ethylene glycol) (PLGA‐PEG) leads to self‐assembly into a “particle‐in‐particle” (PNP) nanostructure for gene delivery. Out of 24 PNP candidates, the top‐performing PNP/C12‐PBAE nanoparticles efficiently deliver both DNA and mRNA in vitro and in vivo, presenting enhanced transfection efficacy, sustained gene release behavior, and excellent stability for at least 12 months of storage at −20 °C after lyophilization without loss of transfection efficacy. Encapsulated with spike encoded plasmid DNA and mRNA, the lipid‐modified polymeric PNP COVID‐19 vaccines successfully elicit spike‐specific antibodies and Th1‐biased T cell immune responses in immunized mice even after 12 months of lyophilized storage at −20 °C. This newly developed lipid‐polymer hybrid PNP nanoparticle system demonstrates a new strategy for both plasmid DNA and mRNA delivery with the capability of long‐term lyophilized storage. 

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2. Overexpression of the WWE domain of RNF146 modulates poly-(ADP)-ribose dynamics at sites of DNA damage

   https://doi.org/10.1101/2023.12.29.573650  

   Al-Rahahleh, Rasha Q; Saville, Kate M; Andrews, Joel F; Wu, Zhijin; Koczor, Christopher A; Sobol, Robert W (December 2023, bioRxiv)

   Protein poly-ADP-ribosylation (PARylation) is a post-translational modification formed by transfer of successive units of ADP-ribose to target proteins to form poly-ADP-ribose (PAR) chains. PAR plays a critical role in the DNA damage response (DDR) by acting as a signaling platform to promote the recruitment of DNA repair factors to the sites of DNA damage that bind via their PAR-binding domains (PBDs). Several classes of PBD families have been recognized, which identify distinct parts of the PAR chain. Proteins encoding PBDs play an essential role in conveying the PAR-mediated signal through their interaction with PAR chains, which mediates many cellular functions, including the DDR. The WWE domain identifies the iso-ADP-ribose moiety of the PAR chain. We recently described the WWE domain of RNF146 as a robust genetically encoded probe, when fused to EGFP, for detection of PAR in live cells. Here, we evaluated other PBD candidates as molecular PAR probes in live cells, including several other WWE domains and an engineered macrodomain. In addition, we demonstrate unique PAR dynamics when tracked by different PAR binding domains, a finding that that can be exploited for modulation of the PAR-dependent DNA damage response. 

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3. Poly(ADP-ribose) binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions

   https://doi.org/10.1083/jcb.202006149  

   Kumbhar, Ramhari; Sanchez, Anthony; Perren, Jullian; Gong, Fade; Corujo, David; Medina, Frank; Devanathan, Sravan K.; Xhemalce, Blerta; Matouschek, Andreas; Buschbeck, Marcus; et al (May 2021, Journal of Cell Biology)

   The histone demethylase KDM5A erases histone H3 lysine 4 methylation, which is involved in transcription and DNA damage responses (DDRs). While DDR functions of KDM5A have been identified, how KDM5A recognizes DNA lesion sites within chromatin is unknown. Here, we identify two factors that act upstream of KDM5A to promote its association with DNA damage sites. We have identified a noncanonical poly(ADP-ribose) (PAR)–binding region unique to KDM5A. Loss of the PAR-binding region or treatment with PAR polymerase (PARP) inhibitors (PARPi’s) blocks KDM5A–PAR interactions and DNA repair functions of KDM5A. The histone variant macroH2A1.2 is also specifically required for KDM5A recruitment and function at DNA damage sites, including homology-directed repair of DNA double-strand breaks and repression of transcription at DNA breaks. Overall, this work reveals the importance of PAR binding and macroH2A1.2 in KDM5A recognition of DNA lesion sites that drive transcriptional and repair activities at DNA breaks within chromatin that are essential for maintaining genome integrity. 

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4. Encapsulation and Ultrasound-Triggered Release of G-Quadruplex DNA in Multilayer Hydrogel Microcapsules

   https://doi.org/10.3390/polym10121342  

   Alford, Aaron; Tucker, Brenna; Kozlovskaya, Veronika; Chen, Jun; Gupta, Nirzari; Caviedes, Racquel; Gearhart, Jenna; Graves, David; Kharlampieva, Eugenia (December 2018, Polymers)

   Nucleic acid therapeutics have the potential to be the most effective disease treatment strategy due to their intrinsic precision and selectivity for coding highly specific biological processes. However, freely administered nucleic acids of any type are quickly destroyed or rendered inert by a host of defense mechanisms in the body. In this work, we address the challenge of using nucleic acids as drugs by preparing stimuli responsive poly(methacrylic acid)/poly(N-vinylpyrrolidone) (PMAA/PVPON)n multilayer hydrogel capsules loaded with ~7 kDa G-quadruplex DNA. The capsules are shown to release their DNA cargo on demand in response to both enzymatic and ultrasound (US)-triggered degradation. The unique structure adopted by the G-quadruplex is essential to its biological function and we show that the controlled release from the microcapsules preserves the basket conformation of the oligonucleotide used in our studies. We also show that the (PMAA/PVPON) multilayer hydrogel capsules can encapsulate and release ~450 kDa double stranded DNA. The encapsulation and release approaches for both oligonucleotides in multilayer hydrogel microcapsules developed here can be applied to create methodologies for new therapeutic strategies involving the controlled delivery of sensitive biomolecules. Our study provides a promising methodology for the design of effective carriers for DNA vaccines and medicines for a wide range of immunotherapies, cancer therapy and/or tissue regeneration therapies in the future. 

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5. Two‐Dimensional Supramolecular Polymerization of DNA Amphiphiles is Driven by Sequence‐Dependent DNA‐Chromophore Interactions

   https://doi.org/10.1002/ange.202217814  

   Ghufran_Rafique, Muhammad; Remington, Jacob_M; Clark, Finley; Bai, Haochen; Toader, Violeta; Perepichka, Dmytro_F; Li, Jianing; Sleiman, Hanadi_F (May 2023, Angewandte Chemie)

   Abstract Two‐dimensional (2D) assemblies of water‐soluble block copolymers have been limited by a dearth of systematic studies that relate polymer structure to pathway mechanism and supramolecular morphology. Here, we employ sequence‐defined triblock DNA amphiphiles for the supramolecular polymerization of free‐standing DNA nanosheets in water. Our systematic modulation of amphiphile sequence shows the alkyl chain core forming a cell membrane‐like structure and the distal π‐stacking chromophore block folding back to interact with the hydrophilic DNA block on the nanosheet surface. This interaction is crucial to sheet formation, marked by a chiral “signature”, and sensitive to DNA sequence, where nanosheets form with a mixed sequence, but not with a homogeneous poly(thymine) sequence. This work opens the possibility of forming well‐ordered, bilayer‐like assemblies using a single DNA amphiphile for applications in cell sensing, nucleic acid therapeutic delivery and enzyme arrays. 

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