Browsing by Author "Kim, Jangwon"

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    Metastable hybridization-based DNA information storage to allow rapid and permanent erasure
    (Springer Nature, 2020) Kim, Jangwon; Bae, Jin H.; Baym, Michael; Zhang, David Yu; Bioengineering; Systems, Synthetic, and Physical Biology; Center for Theoretical Biological Physics
    The potential of DNA as an information storage medium is rapidly growing due to advances in DNA synthesis and sequencing. However, the chemical stability of DNA challenges the complete erasure of information encoded in DNA sequences. Here, we encode information in a DNA information solution, a mixture of true message- and false message-encoded oligonucleotides, and enables rapid and permanent erasure of information. True messages are differentiated by their hybridization to a "truth marker” oligonucleotide, and only true messages can be read; binding of the truth marker can be effectively randomized even with a brief exposure to the elevated temperature. We show 8 separate bitmap images can be stably encoded and read after storage at 25 °C for 65 days with an average of over 99% correct information recall, which extrapolates to a half-life of over 15 years at 25 °C. Heating to 95 °C for 5 minutes, however, permanently erases the message.
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    A Study on Developing a New Method for Storing Data on DNA and on Building Epigenetic Panel for Diagnosis of Colorectal Cancer
    (2021-06-22) Kim, Jangwon; Zhang, David Yu
    The thesis is divided into two parts. In the first half of the thesis, a new method on storing data on DNA, which enables rapid and easy erasure of the data will be discussed; The potential of DNA as an information storage medium is rapidly growing due to technological advances in DNA synthesis and sequencing. However, the chemical stability of DNA-encoded information results in challenges in the complete erasure of information encoded in the sequence of DNA. For information that is both highly important and highly confidential, a mechanism for rapid and permanent erasure is needed that is compatible with long-term information storage. Here, we present a method for encoding information in a metastable aqueous-phase DNA information solution, comprising a mixture of DNA oligonucleotides encoding true messages and false messages. True messages are differentiated by their hybridization to a “truth marker” oligonucleotide; because the half-life of DNA hybridization is exponentially dependent on ambient temperature, even a brief exposure to elevated temperatures can effectively randomize the binding partners of the truth markers. Experimentally, we show that 8 separate bitmap images can be stably encoded and read after storage at 25 ◦C for 65 days with an average of over 99% correct information recall, which extrapolates to a half-life of over 15 years at 25 ◦C. Heating to 95 ◦C for just 5 minutes, however, permanently erases the message. This is, to our knowledge, the first technique in DNA data storage to use the physical or chemical properties of DNA to realize a behavior that is not a simple analog of conventional data storage. In the second half of the thesis, we will discuss on how we developed a novel epigenetic diagnostic panel for colorectal cancer using the concept of ’Epigenetic Instability’.; DNA methylation-based biomarkers have been recognized as effective tools for early detection of cancer. However, discovering epigenetic biomarkers usually accompanies whole genome sequencing or bead array, which take a lot of time and cost for a single run. Here we introduce a targeted bisulfite sequencing-based colorectal cancer diagnosis panel, where we can detect the cancer in much earlier stage than conventional methods by using a concept of methylation heterogeneity. In this way, the test can be done within a day, costing only $50 per sample. In addition, we developed a new metric that can effectively show the overall status of epigenetic instability across biomarker regions to determine the current stage of the cancer. 12 clinical were tested to verify our protocol and metric; When colorectal cancer and healthy tissue samples from the same patients were compared, the values calculated based on our metric gave more than 50% differences in average, showing robustness of the metric.