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  1. Article: Genome Editing Outcomes Reveal Mycobacterial NucS Participates in a Short-Patch Repair of DNA Mismatches.

    Islam, Tanjina / Josephs, Eric A

    bioRxiv : the preprint server for biology

    2023  

    Abstract: In the canonical DNA mismatch repair (MMR) mechanism in bacteria, if during replication a nucleotide is incorrectly mis-paired with the template strand, the resulting repair of this mis-pair can result in the degradation and re-synthesis of hundreds or ... ...

    Abstract In the canonical DNA mismatch repair (MMR) mechanism in bacteria, if during replication a nucleotide is incorrectly mis-paired with the template strand, the resulting repair of this mis-pair can result in the degradation and re-synthesis of hundreds or thousands of nucleotides on the newly-replicated strand (long-patch repair). While mycobacteria, which include important pathogens such as
    Language English
    Publishing date 2023-10-23
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.10.23.563644
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Selection of extended CRISPR RNAs with enhanced targeting and specificity.

    Herring-Nicholas, Ashley / Dimig, Hillary / Roesing, Miranda R / Josephs, Eric A

    Communications biology

    2024  Volume 7, Issue 1, Page(s) 86

    Abstract: As CRISPR effectors like Cas9 increasingly enter clinical trials for therapeutic gene editing, a future for personalized medicine will require efficient methods to protect individuals from the potential of off-target mutations that may also occur at ... ...

    Abstract As CRISPR effectors like Cas9 increasingly enter clinical trials for therapeutic gene editing, a future for personalized medicine will require efficient methods to protect individuals from the potential of off-target mutations that may also occur at specific sequences in their genomes that are similar to the therapeutic target. A Cas9 enzyme's ability to recognize their targets (and off-targets) are determined by the sequence of their RNA-cofactors (their guide RNAs or gRNAs). Here, we present a method to screen hundreds of thousands of gRNA variants with short, randomized 5' nucleotide extensions near its DNA-targeting segment-a modification that can increase gene editing specificity by orders of magnitude-to identify extended gRNAs (x-gRNAs) that effectively block any activity at those off-target sites while still maintaining strong activity at their intended targets. X-gRNAs that have been selected for specific target / off-target pairs can significantly out-perform other methods that reduce Cas9 off-target activity overall, like using Cas9 variants engineered for higher specificity in general, and we demonstrate their effectiveness in clinically-relevant gRNAs. Our streamlined approach to efficiently identify highly specific and active x-gRNAs provides a way to move beyond a one-size-fits-all model of high-fidelity CRISPR for safer and more effective personalized gene therapies.
    MeSH term(s) Humans ; CRISPR-Cas Systems ; RNA, Guide, CRISPR-Cas Systems ; Gene Editing ; RNA ; Genetic Therapy
    Chemical Substances RNA, Guide, CRISPR-Cas Systems ; RNA (63231-63-0)
    Language English
    Publishing date 2024-01-12
    Publishing country England
    Document type Journal Article
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-024-05776-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Selection of Extended CRISPR RNAs with Enhanced Targeting and Specificity.

    Herring-Nicholas, Ashley / Dimig, Hillary / Roesing, Miranda / Josephs, Eric A

    bioRxiv : the preprint server for biology

    2023  

    Abstract: For a CRISPR guide RNA (gRNA) with a specific target but activity at known "off-target" sequences, we present a method to screen hundreds of thousands of gRNA variants with short, randomized 5' nucleotide extensions near its DNA-targeting segment-a ... ...

    Abstract For a CRISPR guide RNA (gRNA) with a specific target but activity at known "off-target" sequences, we present a method to screen hundreds of thousands of gRNA variants with short, randomized 5' nucleotide extensions near its DNA-targeting segment-a modification that can increase Cas9 gene editing specificity by orders of magnitude with certain 5'- extension sequences,
    Language English
    Publishing date 2023-01-12
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.11.523593
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Selection of extended CRISPR RNAs with enhanced targeting and specificity

    Ashley Herring-Nicholas / Hillary Dimig / Miranda R. Roesing / Eric A. Josephs

    Communications Biology, Vol 7, Iss 1, Pp 1-

    2024  Volume 9

    Abstract: Abstract As CRISPR effectors like Cas9 increasingly enter clinical trials for therapeutic gene editing, a future for personalized medicine will require efficient methods to protect individuals from the potential of off-target mutations that may also ... ...

    Abstract Abstract As CRISPR effectors like Cas9 increasingly enter clinical trials for therapeutic gene editing, a future for personalized medicine will require efficient methods to protect individuals from the potential of off-target mutations that may also occur at specific sequences in their genomes that are similar to the therapeutic target. A Cas9 enzyme’s ability to recognize their targets (and off-targets) are determined by the sequence of their RNA-cofactors (their guide RNAs or gRNAs). Here, we present a method to screen hundreds of thousands of gRNA variants with short, randomized 5’ nucleotide extensions near its DNA-targeting segment—a modification that can increase gene editing specificity by orders of magnitude—to identify extended gRNAs (x-gRNAs) that effectively block any activity at those off-target sites while still maintaining strong activity at their intended targets. X-gRNAs that have been selected for specific target / off-target pairs can significantly out-perform other methods that reduce Cas9 off-target activity overall, like using Cas9 variants engineered for higher specificity in general, and we demonstrate their effectiveness in clinically-relevant gRNAs. Our streamlined approach to efficiently identify highly specific and active x-gRNAs provides a way to move beyond a one-size-fits-all model of high-fidelity CRISPR for safer and more effective personalized gene therapies.
    Keywords Biology (General) ; QH301-705.5
    Subject code 004
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: The "Duckweed Dip": Aquatic

    Islam, Tasmia / Kalkar, Swapna / Tinker-Kulberg, Rachel / Ignatova, Tetyana / Josephs, Eric A

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Duckweeds ( ...

    Abstract Duckweeds (
    Language English
    Publishing date 2023-08-22
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.08.21.554121
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Subspecialty Training in IR.

    Josephs, Shellie / Keller, Eric J / Vadlamudi, Venu / Annam, Aparna / Abi-Jaoudeh, Nadine

    Journal of vascular and interventional radiology : JVIR

    2023  Volume 34, Issue 12, Page(s) 2074–2075

    MeSH term(s) Humans ; Education, Medical, Graduate ; Education, Medical ; Internship and Residency
    Language English
    Publishing date 2023-11-24
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1137756-2
    ISSN 1535-7732 ; 1051-0443
    ISSN (online) 1535-7732
    ISSN 1051-0443
    DOI 10.1016/j.jvir.2023.08.015
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  7. Article ; Online: The "Duckweed Dip": Aquatic

    Islam, Tasmia / Kalkar, Swapna / Tinker-Kulberg, Rachel / Ignatova, Tetyana / Josephs, Eric A

    ACS synthetic biology

    2023  Volume 13, Issue 2, Page(s) 687–691

    Abstract: Duckweeds ( ...

    Abstract Duckweeds (
    MeSH term(s) Nanotubes, Carbon ; Plants/genetics ; DNA/metabolism ; Araceae/genetics ; Araceae/metabolism ; Gene Expression
    Chemical Substances Nanotubes, Carbon ; DNA (9007-49-2)
    Language English
    Publishing date 2023-12-21
    Publishing country United States
    Document type Journal Article
    ISSN 2161-5063
    ISSN (online) 2161-5063
    DOI 10.1021/acssynbio.3c00620
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  8. Article ; Online: Endonuclease-independent DNA mismatch repair processes on the lagging strand.

    Josephs, Eric A / Marszalek, Piotr E

    DNA repair

    2018  Volume 68, Page(s) 41–49

    Abstract: DNA mismatch repair (MMR) pathways coordinate the excision and re-synthesis of newly-replicated DNA if a mismatched base-pair has been identified by protein MutS or MutS homologues (MSHs) after replication. DNA excision during MMR is initiated at single- ... ...

    Abstract DNA mismatch repair (MMR) pathways coordinate the excision and re-synthesis of newly-replicated DNA if a mismatched base-pair has been identified by protein MutS or MutS homologues (MSHs) after replication. DNA excision during MMR is initiated at single-strand breaks (SSBs) in vitro, and several redundant processes have been observed in reconstituted systems which either require a pre-formed SSB in the DNA or require a mismatch-activated nicking endonuclease to introduce a SSB in order to initiate MMR. However, the conditions under which each of these processes may actually occur in living cells have remained obscured by the limitations of current MMR assays. Here we use a novel assay involving chemically-modified oligonucleotide probes to insert targeted DNA 'mismatches' directly into the genome of living bacteria to interrogate their replication-coupled repair processes quantitatively in a strand-, orientation-, and mismatched nucleotide-specific manner. This 'semi-protected oligonucleotide recombination' (SPORE) assay reveals direct evidence in Escherichia coli of an efficient endonuclease-independent MMR process on the lagging strand-a mechanism that has long-since been considered for lagging-strand repair but never directly shown until now. We find endonuclease-independent MMR is coordinated asymmetrically with respect to the replicating DNA-directed primarily from 3'- of the mismatch-and that repair coordinated from 3'- of the mismatch is in fact the primary mechanism of lagging-strand MMR. While further work is required to explore and identify the molecular requirements for this alternative endonuclease-independent MMR pathway, these findings made possible using the SPORE assay are the first direct report of this long-suspected mechanism in vivo.
    MeSH term(s) DNA Damage ; DNA Mismatch Repair ; DNA Replication ; DNA, Bacterial/metabolism ; Endonucleases/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins ; Mutagenicity Tests/methods
    Chemical Substances DNA, Bacterial ; Escherichia coli Proteins ; Endonucleases (EC 3.1.-)
    Language English
    Publishing date 2018-06-12
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2071608-4
    ISSN 1568-7856 ; 1568-7864
    ISSN (online) 1568-7856
    ISSN 1568-7864
    DOI 10.1016/j.dnarep.2018.06.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5555: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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  9. Article ; Online: Digital data storage on DNA tape using CRISPR base editors.

    Sadremomtaz, Afsaneh / Glass, Robert F / Guerrero, Jorge Eduardo / LaJeunesse, Dennis R / Josephs, Eric A / Zadegan, Reza

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 6472

    Abstract: While the archival digital memory industry approaches its physical limits, the demand is significantly increasing, therefore alternatives emerge. Recent efforts have demonstrated DNA's enormous potential as a digital storage medium with superior ... ...

    Abstract While the archival digital memory industry approaches its physical limits, the demand is significantly increasing, therefore alternatives emerge. Recent efforts have demonstrated DNA's enormous potential as a digital storage medium with superior information durability, capacity, and energy consumption. However, the majority of the proposed systems require on-demand de-novo DNA synthesis techniques that produce a large amount of toxic waste and therefore are not industrially scalable and environmentally friendly. Inspired by the architecture of semiconductor memory devices and recent developments in gene editing, we created a molecular digital data storage system called "DNA Mutational Overwriting Storage" (DMOS) that stores information by leveraging combinatorial, addressable, orthogonal, and independent in vitro CRISPR base-editing reactions to write data on a blank pool of greenly synthesized DNA tapes. As a proof of concept, this work illustrates writing and accurately reading of both a bitmap representation of our school's logo and the title of this study on the DNA tapes.
    MeSH term(s) Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA/genetics ; Gene Editing/methods ; DNA Replication ; Information Storage and Retrieval ; CRISPR-Cas Systems/genetics
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2023-10-13
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-42223-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Digital data storage on DNA tape using CRISPR base editors.

    Sadremomtaz, Afsaneh / Glass, Robert F / Guerrero, Jorge Eduardo / LaJeunesse, Dennis R / Josephs, Eric A / Zadegan, Reza

    bioRxiv : the preprint server for biology

    2023  

    Abstract: While the archival digital memory industry approaches its physical limits, the demand is significantly increasing, therefore alternatives emerge. Recent efforts have demonstrated DNA's enormous potential as a digital storage medium with superior ... ...

    Abstract While the archival digital memory industry approaches its physical limits, the demand is significantly increasing, therefore alternatives emerge. Recent efforts have demonstrated DNA's enormous potential as a digital storage medium with superior information durability, capacity, and energy consumption. However, the majority of the proposed systems require on-demand
    Language English
    Publishing date 2023-02-07
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.07.527074
    Database MEDical Literature Analysis and Retrieval System OnLINE

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