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Title: Sulfide-linked 3,4,5-trimethoxyphenyl-thiosemicarbazide/triazole hybrids: Synthesis, antioxidant, antiglycation, DNA cleavage and DNA molecular docking studies
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Results in Chemistry
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National Science Foundation
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  1. With the rapid increase of available digital data, we are searching for a storage media with high density and capability of long-term preservation. Deoxyribonucleic Acid (DNA) storage is identified as such a promising candidate, especially for archival storage systems. However, the encoding density (i.e., how many binary bits can be encoded into one nucleotide) and error handling are two major factors intertwined in DNA storage. Considering encoding density, theoretically, one nucleotide (i.e., A, T, G, or C) can encode two binary bits (upper bound). However, due to biochemical constraints and other necessary information associated with payload, currently the encoding densities of various DNA storage systems are much less than this upper bound. Additionally, all existing studies of DNA encoding schemes are based on static analysis and really lack the awareness of dynamically changed digital patterns. Therefore, the gap between the static encoding and dynamic binary patterns prevents achieving a higher encoding density for DNA storage systems. In this paper, we propose a new Digital Pattern-Aware DNA storage system, called DP-DNA, which can efficiently store digital data in the DNA storage with high encoding density. DP-DNA maintains a set of encoding codes and uses a digital pattern-aware code (DPAC) to analyze the patterns of a binary sequence for a DNA strand and selects an appropriate code for encoding the binary sequence to achieve a high encoding density. An additional encoding field is added to the DNA encoding format, which can distinguish the encoding scheme used for those DNA strands, and thus we can decode DNA data back to its original digital data. Moreover, to further improve the encoding density, a variable-length scheme is proposed to increase the feasibility of the code scheme with a high encoding density. Finally, the experimental results indicate that the proposed DP-DNA achieves up to 103.5% higher encoding densities than prior work. 
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  2. Abstract

    DNA helicase activity is essential for the vital DNA metabolic processes of recombination, replication, transcription, translation, and repair. Recently, an unexpected, rapid exponential ATP‐stimulated DNA unwinding rate was observed from anArchaeoglobus fulgidushelicase (AfXPB) as compared to the slower conventional helicases fromSulfolobus tokodaii, StXPB1 and StXPB2. This unusual rapid activity suggests a “molecular wrench” mechanism arising from the torque applied by AfXPB on the duplex structure in transitioning from open to closed conformations. However, much remains to be understood. Here, we investigate the concentration dependence of DNA helicase binding and ATP‐stimulated kinetics of StXPB2 and AfXPB, as well as their binding and activity in Bax1 complexes, via an electrochemical assay with redox‐active DNA monolayers. StXPB2 ATP‐stimulated activity is concentration‐independent from 8 to 200 nM. Unexpectedly, AfXPB activity is concentration‐dependent in this range, with exponential rate constants varying from seconds at concentrations greater than 20 nM to thousands of seconds at lower concentrations. At 20 nM, rapid exponential signal decay ensues, linearly reverses, and resumes with a slower exponential decay. This change in AfXPB activity as a function of its concentration is rationalized as the crossover between the fast molecular wrench and slower conventional helicase modes. AfXPB‐Bax1 inhibits rapid activity, whereas the StXPB2‐Bax1 complex induces rapid kinetics at higher concentrations. This activity is rationalized with the crystal structures of these complexes. These findings illuminate the different physical models governing molecular wrench activity for improved biological insight into a key factor in DNA repair.

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