Searching journal content for articles similar to Kim et al. 22 (7): 1327.

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  1. Perspective: Enabling functional genomics with genome engineering
    • Isaac B. Hilton and
    • Charles A. Gersbach
    Genome Res. October 2015 25: 1442-1455; doi:10.1101/gr.190124.115
    ...understood. The recent development of engineering technologies has enabled precise interrogation of the function of these genomic features and their causal role in gene regulation. Additionally, these tools are facilitating the translation of this genomic information into tangible benefits for biotechnology...
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  2. Method: DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution
    • Juniper J. Elacqua,
    • Navpreet Ranu,
    • Sarah E. DiIorio,
    • and Paul C. Blainey
    Genome Res. January 2021 31: 75-87; Published in Advance December 21, 2020, doi:10.1101/gr.265223.120
    ...in Supplemental Table S1.Here, we built on SSB-seq (Baranello et al. 2014) to create degenerate and enrichment nick translations followed by sequencing (DENT-seq), a method capable of specifically identifying DNA nicks with single-nucleotide resolution in human genomic DNA. This method relies on an engineered...
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  3. Research: Mechanisms of precise genome editing using oligonucleotide donors
    • Yinan Kan,
    • Brian Ruis,
    • Taylor Takasugi,
    • and Eric A. Hendrickson
    Genome Res. July 2017 27: 1099-1111; Published in Advance March 29, 2017, doi:10.1101/gr.214775.116
    ...Mechanisms of precise editing using oligonucleotide donors Yinan Kan,1,2 Brian Ruis,1 Taylor Takasugi,1,3 and Eric A. Hendrickson1 1Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA The use of programmable...
  4. Method: Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins
    • Sojung Kim,
    • Daesik Kim,
    • Seung Woo Cho,
    • Jungeun Kim,
    • and Jin-Soo Kim
    Genome Res. June 2014 24: 1012-1019; Published in Advance April 2, 2014, doi:10.1101/gr.171322.113
    ...–92). Kim S, LeeMJ, KimH, KangM, Kim JS. 2011. Preassembled zinc-finger arrays for rapid construction of ZFNs. Nat Methods 8: 7. Kim E, Kim S, Kim DH, Choi BS, Choi IY, Kim JS. 2012. Precision engineering with programmable DNA-nicking enzymes.Genome Res 22: 1327–1333. Kim Y, Kweon J, Kim A, Chon JK, Yoo JY...
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  5. Method: 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors
    • Jacob Stewart-Ornstein,
    • Matthew J. Irby,
    • Marina K. Lilieholm,
    • Dylan Laprise,
    • Maria D. Collier,
    • Thomas Aunins,
    • Dewi Harjanto,
    • Aaron N. Chang,
    • Deepak Reyon,
    • and Jeremy S. Duffield
    Genome Res. September 2025 35: 2064-2075; Published in Advance August 5, 2025, doi:10.1101/gr.280164.124
    ...off-target sites. Here we show that PEG-seq is an important addition to the off-target detection toolkit, enabling off-target discovery for DNA nicking gene editors such as prime editors.Biochemical methods for identifying sites in genomic DNA that are recognized or acted on by a protein or protein...
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  6. Method: Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases
    • Seung Woo Cho,
    • Sojung Kim,
    • Yongsub Kim,
    • Jiyeon Kweon,
    • Heon Seok Kim,
    • Sangsu Bae,
    • and Jin-Soo Kim
    Genome Res. January 2014 24: 132-141; Published in Advance November 19, 2013, doi:10.1101/gr.162339.113
    ...nucleases constructed via modular assembly. Genome Res 19: 1279–1288. Kim S, LeeMJ, KimH, KangM, Kim JS. 2011. Preassembled zinc-finger arrays for rapid construction of ZFNs. Nat Methods 8: 7. Kim E, Kim S, Kim DH, Choi BS, Choi IY, Kim JS. 2012. Precision engineering with programmable DNA-nicking enzymes.Genome...
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  7. Method: Targeted chromosomal deletions and inversions in zebrafish
    • Ankit Gupta,
    • Victoria L. Hall,
    • Fatma O. Kok,
    • Masahiro Shin,
    • Joseph C. McNulty,
    • Nathan D. Lawson,
    • and Scot A. Wolfe
    Genome Res. June 2013 23: 1008-1017; Published in Advance March 11, 2013, doi:10.1101/gr.154070.112
    .... Genome Res 19: 1279–1288. Kim E, Kim S, Kim DH, Choi BS, Choi IY, Kim JS. 2012. Precision engineering with programmable DNA-nicking enzymes.Genome Res 22: 1327–1333. LeeHJ, KimE, Kim JS. 2010. Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome Res 20: 81–89. Lee HJ, Kweon J...
  8. Method: Precise and efficient nucleotide substitution near genomic nick via noncanonical homology-directed repair
    • Kazuhiro Nakajima,
    • Yue Zhou,
    • Akiko Tomita,
    • Yoshihiro Hirade,
    • Channabasavaiah B. Gurumurthy,
    • and Shinichiro Nakada
    Genome Res. February 2018 28: 223-230; Published in Advance December 22, 2017, doi:10.1101/gr.226027.117
    ...nicks. Cell Rep 17: 1872–1881. ↵Doudna JA, Charpentier E. 2014. Genome editing. The new frontier of engineering with CRISPR-Cas9. Science 346: 1258096. ↵Drum M, Kranaster R, Ewald C, Blasczyk R, Marx A. 2014. Variants of a Thermus aquaticus DNA polymerase with increased selectivity for applications...
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