TY - JOUR
T1 - Recovery of Information Stored in Modified DNA with an Evolved Polymerase
AU - Shroff, Raghav
AU - Ellefson, Jared W.
AU - Wang, Siyuan S.
AU - Boulgakov, Alexander A.
AU - Hughes, Randall A.
AU - Ellington, Andrew D.
N1 - Funding Information:
We would like to acknowledge support by the Welch Foundation (F-1654). R.S. was supported by the National Aeronautical Space Administration (NASA) Grant NNX15AF46G. J.W.E. was supported by the Defense Advanced Projects Research Agency (DARPA) Grant HR0011-12-2-0001. National Science Foundation (NSF) Graduate Research Fellowship (DGE-1610403) provided support to S.S.W. and A.A.B.
Publisher Copyright:
© 2022 American Chemical Society
PY - 2022/2/18
Y1 - 2022/2/18
N2 - DNA is increasingly being explored as an alternative medium for digital information storage, but the potential information loss from degradation and associated issues with error during reading challenge its wide-scale implementation. To address this, we propose an atomic-scale encoding standard for DNA, where information is encoded in degradation-resistant analogues of natural nucleic acids (xNAs). To better enable this approach, we used directed evolution to create a polymerase capable of transforming 2′-O-methyl templates into double-stranded DNA. Starting from a thermophilic, error-correcting reverse transcriptase, RTX, we evolved an enzyme (RTX-Ome v6) that relies on a fully functional proofreading domain to correct mismatches on DNA, RNA, and 2′-O-methyl templates. In addition, we implemented a downstream analysis strategy that accommodates deletions that arise during phosphoramidite synthesis, the most common type of synthesis error. By coupling and integrating new chemistries, enzymes, and algorithms, we further enable the large-scale use of nucleic acids for information storage.
AB - DNA is increasingly being explored as an alternative medium for digital information storage, but the potential information loss from degradation and associated issues with error during reading challenge its wide-scale implementation. To address this, we propose an atomic-scale encoding standard for DNA, where information is encoded in degradation-resistant analogues of natural nucleic acids (xNAs). To better enable this approach, we used directed evolution to create a polymerase capable of transforming 2′-O-methyl templates into double-stranded DNA. Starting from a thermophilic, error-correcting reverse transcriptase, RTX, we evolved an enzyme (RTX-Ome v6) that relies on a fully functional proofreading domain to correct mismatches on DNA, RNA, and 2′-O-methyl templates. In addition, we implemented a downstream analysis strategy that accommodates deletions that arise during phosphoramidite synthesis, the most common type of synthesis error. By coupling and integrating new chemistries, enzymes, and algorithms, we further enable the large-scale use of nucleic acids for information storage.
KW - 2′-O-methyl
KW - DNA data storage
KW - directed evolution
KW - nucleic acid analogues
KW - protein engineering
KW - reverse transcriptase
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U2 - 10.1021/acssynbio.1c00575
DO - 10.1021/acssynbio.1c00575
M3 - Article
C2 - 35113518
AN - SCOPUS:85124561109
SN - 2161-5063
VL - 11
SP - 554
EP - 561
JO - ACS Synthetic Biology
JF - ACS Synthetic Biology
IS - 2
ER -