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1. Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology

   https://doi.org/10.3390/s20247019  

   Saran, Runjhun; Wang, Yong; Li, Isaac T. (December 2020, Sensors)

   null (Ed.)

   The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA’s bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA’s rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines. 

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2. DP-DNA: A Digital Pattern-Aware DNA Encoding Scheme to Improve Encoding Density of DNA Storage

   https://doi.org/10.1109/MASCOTS59514.2023.10387655  

   Li, Bingzhe; Ou, Li; Yuan, Bo; Du, David H.C. (October 2023, IEEE)

   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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3. A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction

   https://doi.org/10.1186/s12859-019-3011-2  

   Moreland, Blythe S.; Oman, Kenji M.; Bundschuh, Ralf (December 2019, BMC Bioinformatics)
4. A Cooperative DNA Catalyst

   https://doi.org/10.1021/jacs.1c07122  

   Taylor, Dallas N.; Davidson, Samuel R.; Qian, Lulu (September 2021, Journal of the American Chemical Society)
5. Specificity versus Processivity in the Sequential Modification of DNA: A Study of DNA Adenine Methyltransferase

   https://doi.org/10.1021/acs.jpcb.7b10349  

   Barel, Itay; Naughton, Brigitte; Reich, Norbert O.; Brown, Frank L. (January 2018, The Journal of Physical Chemistry B)