Browsing by Author "Liu, David"

Now showing items 1-20 of 96

    • Adenine Base Editing in an Adult Mouse Model of Tyrosinaemia 

      Song, Chun-Qing; Jiang, Tingting; Richter, Michelle; Rhym, Luke H.; Koblan, Luke; Paz Zafra, Maria; Schatoff, Emma M.; Doman, Jordan; Cao, Yueying; Dow, Lukas E.; Zhu, Lihua Julie; Anderson, Daniel; Liu, David; Yin, Hao; Xue, Wen (Springer Science and Business Media LLC, 2019-02-25)
      Unlike traditional CRISPR-Cas9 homology-directed repair, base editing can correct point mutations without supplying a DNA-repair template. Here, we show in a mouse model of tyrosinemia that hydrodynamic tail-vein injection ...

    • Analytical Devices Based on Direct Synthesis of DNA on Paper 

      Glavan, Ana C; Niu, Jia; Chen, Zhen; Güder, Firat; Cheng, Chao-Min; Liu, David Ruchien; Whitesides, George McClelland (American Chemical Society (ACS), 2016)
      This paper addresses a growing need in clinical diagnostics for parallel, multiplex analysis of biomarkers from small biological samples. It describes a new procedure for assembling microarrays of ssDNA and proteins on ...

    • Anti-diabetic activity of insulin-degrading enzyme inhibitors mediated by multiple hormones 

      Maianti, Juan Pablo; McFedries, Amanda; Foda, Zachariah H.; Kleiner, Ralph; Du, Xiu Quan; Leissring, Malcolm A.; Tang, Wei-Jen; Charron, Maureen J.; Seeliger, Markus A.; Saghatelian, Alan; Liu, David Ruchien (Nature Publishing Group, 2014)
      Despite decades of speculation that inhibiting endogenous insulin degradation might treat type-2 diabetes, and the identification of IDE (insulin-degrading enzyme) as a diabetes susceptibility gene, the relationship between ...

    • Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker 

      He, Yu; Liu, David Ruchien (Nature Publishing Group, 2010)
      Multistep synthesis in the laboratory typically requires numerous reaction vessels, each containing a different set of reactants. In contrast, cells are capable of performing highly efficient and selective multistep ...

    • A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing 

      Mok, Beverly Y.; de Moraes, Marcos H.; Zeng, Jun; Bosch, Dustin E.; Kotrys, Anna V.; Raguram, Aditya; Hsu, FoSheng; Radey, Matthew C.; Peterson, S. Brook; Mootha, Vamsi K.; Mougous, Joseph D.; Liu, David (Springer Science and Business Media LLC, 2020-07-08)

    • Base editing of haematopoietic stem cells rescues sickle cell disease in mice 

      Newby, Gregory; Yen, Jonathan S.; Woodard, Kaitly J.; Mayuranathan, Thiyagaraj; Lazzarotto, Cicera R.; Li, Yichao; Sheppard-Tillman, Heather; Porter, Shaina N.; Yao, Yu; Mayberry, Kalin; Everette, Kelcee A.; Jang, Yoonjeong; Podracky, Christopher J.; Thaman, Elizabeth; Lechauve, Christophe; Sharma, Akshay; Henderson, Jordana M.; Richter, Michelle; Zhao, Kevin; Miller, Shannon; Wang, Tina; Koblan, Luke; McCaffrey, Anton P.; Tisdale, John F.; Kalfa, Theodosia; Pruett-Miller, Shondra M.; Tsai, Shengdar; Weiss, Mitchell J.; Liu, David (Springer Science and Business Media LLC, 2021-06-02)

    • The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing 

      Huang, Yun; Pastor, William Abraham; Shen, Yinghua; Tahiliani, Mamta V.; Liu, David Ruchien; Rao, Anjana; Liu, Jun (Public Library of Science, 2010)
      Background: We recently showed that enzymes of the TET family convert 5-mC to 5-hydroxymethylcytosine (5-hmC) in DNA. 5-hmC is present at high levels in embryonic stem cells and Purkinje neurons. The methylation status of ...

    • A biomolecule-compatible visible-light-induced azide reduction from a DNA-encoded reaction-discovery system 

      Chen, Yiyun; Kamlet, Adam S.; Steinman, Jonathan B.; Liu, David Ruchien (Nature Publishing Group, 2011)
      Using a system that accelerates the serendipitous discovery of new reactions by evaluating hundreds of DNA-encoded substrate combinations in a single experiment, we explored a broad range of reaction conditions for new ...

    • Broad Specificity Profiling of TALENs Results in Engineered Nucleases With Improved DNA Cleavage Specificity 

      Guilinger, John P.; Pattanayak, Vikram; Reyon, Deepak; Tsai, Shengdar Q.; Sander, Jeffry D.; Joung, J. Keith; Liu, David R. (2014)
      Although transcription activator-like effector nucleases (TALENs) can be designed to cleave chosen DNA sequences, TALENs have been shown to have activity against related off-target sequences. To better understand TALEN ...

    • Cellular uptake mechanisms and endosomal trafficking of supercharged proteins 

      Thompson, David B.; Villaseñor, Roberto; Dorr, B; Zerial, Marino; Liu, David Ruchien (Elsevier BV, 2012)
      Supercharged proteins can deliver functional macromolecules into the cytoplasm of mammalian cells with potencies that exceed those of cationic peptides. The structural features of supercharged proteins that determine their ...

    • Characterization of Protein-Metabolite and Protein-Substrate Interactions of Disease Genes 

      McFedries, Amanda Kathryn (2014-06-06)
      Discovery of protein-metabolite and protein-substrate interactions that can specifically regulate genes involved in human biology is an important pursuit, as the study of such interactions can expand our understanding of ...

    • A Chemical Screen for Biological Small Molecule-RNA Conjugates Reveals CoA-Linked RNA 

      Kowtoniuk, Walter Eugene; Shen, Yinghua; Heemstra, Jennifer M.; Agarwal, Isha; Liu, David Ruchien (National Academy of Sciences, 2009)
      Compared with the rapidly expanding set of known biological roles for RNA, the known chemical diversity of cellular RNA has remained limited primarily to canonical RNA, 3'-aminoacylated tRNAs, nucleobase-modified RNAs, and ...

    • Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors 

      Huang, Tony; Zhao, Kevin; Miller, Shannon; Gaudelli, Nicole; Oakes, Benjamin; Fellmann, Christof; Savage, David; Liu, David (Springer Science and Business Media LLC, 2019-05-20)
      Base editing requires that the target sequence satisfy the protospacer adjacent motif requirement of the Cas9 domain and that the target nucleotide be located within the editing window of the base editor. To increase the ...

    • A Class of Human Proteins that Deliver Functional Proteins into Mammalian Cells In Vitro and In Vivo 

      Cronican, James J.; Beier, Kevin T.; Davis, Tina N.; Tseng, Jen-Chieh; Li, Weida; Thompson, David B.; Shih, Allen F.; May, Erin M.; Cepko, Constance L.; Kung, Andrew L.; Zhou, Qiao; Liu, David Ruchien (Elsevier BV, 2011)
      We discovered a class of naturally occurring human proteins with unusually high net positive charge that can potently deliver proteins in functional form into mammalian cells both in vitro and also in murine retina, pancreas, ...

    • Continuous directed evolution of DNA-binding proteins to improve TALEN specificity 

      Hubbard, Basil P.; Badran, Ahmed H.; Zuris, John A.; Guilinger, John P.; Davis, Kevin M.; Chen, Liwei; Tsai, Shengdar Q.; Sander, Jeffry D.; Joung, J. Keith; Liu, David R. (2015)
      Nucleases containing programmable DNA-binding domains can alter the genomes of model organisms and have the potential to become human therapeutics. Here we present DNA-binding phage-assisted continuous evolution (DB-PACE) ...

    • Continuous Directed Evolution of Enzymes with Novel Substrate Specificity 

      Carlson, Jacob Charles (2013-07-05)
      Methodological advances in directed evolution have already made it possible to discover useful biomolecules within months to years. A further acceleration of this process might make it possible to address outstanding ...

    • Continuous evolution of B. thuringiensis toxins overcomes insect resistance 

      Badran, Ahmed H.; Guzov, Victor M.; Huai, Qing; Kemp, Melissa M.; Vishwanath, Prashanth; Kain, Wendy; Nance, Autumn M.; Evdokimov, Artem; Moshiri, Farhad; Turner, Keith H.; Wang, Ping; Malvar, Thomas; Liu, David R. (2016)
      The Bacillus thuringiensis δ-endotoxins (Bt toxins) are widely used insecticidal proteins in engineered crops that provide agricultural, economic, and environmental benefits. The development of insect resistance to Bt ...

    • Continuous evolution of SpCas9 variants compatible with non-G PAMs 

      Miller, Shannon; Wang, Tina; Randolph, Peyton; Arbab, Mandana; Shen, Max; Huang, Tony; Matuszek, Zaneta; Newby, Gregory; Rees, Holly; Liu, David (Springer Science and Business Media LLC, 2020-02-10)

    • Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by the MLL Partner TET1 

      Tahiliani, Mamta V.; Koh, Kian Peng; Shen, Yinghua; Pastor, William Abraham; Bandukwala, Hozefa S; Brudno, Yevgeny; Agarwal, Suneet; Iyer, Lakshminarayan M.; Liu, David Ruchien; Aravind, L; Rao, Anjana (American Association for the Advancement of Science, 2009)
      DNA cytosine methylation is crucial for retrotransposon silencing and mammalian development. In a computational search for enzymes that could modify 5-methylcytosine (5mC), we identified TET proteins as mammalian homologs ...

    • CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA 

      Mok, Beverly Y.; Kotrys, Anna V.; Raguram, Aditya; Huang, Tony P.; Mootha, Vamsi K.; Liu, David (Springer Science and Business Media LLC, 2022-04-04)
      The all-protein cytosine base editor DdCBE uses TALE proteins and a double-stranded DNA-specific cytidine deaminase (DddA) to mediate targeted C•G-to-T•A editing. To improve editing efficiency and overcome the strict ...