@misc{luo_leenay_beisel_2016, title={Current and future prospects for CRISPR-based tools in bacteria}, volume={113}, ISSN={["1097-0290"]}, DOI={10.1002/bit.25851}, abstractNote={ABSTRACT}, number={5}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Luo, Michelle L. and Leenay, Ryan T. and Beisel, Chase L.}, year={2016}, month={May}, pages={930–943} }
 @article{luo_beisel_2016, title={Engineering genes with CRISPR-Cas9}, volume={112}, number={9}, journal={Chemical Engineering Progress }, author={Luo, M. L. and Beisel, C. L.}, year={2016}, pages={36–41} }
 @article{luo_jackson_denny_tokmina-lukaszewska_maksimchuk_lin_bothner_wiedenheft_beisel_2016, title={The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers}, volume={44}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkw421}, abstractNote={Bacteria and archaea acquire resistance to foreign genetic elements by integrating fragments of foreign DNA into CRISPR (clustered regularly interspaced short palindromic repeats) loci. In Escherichia coli, CRISPR-derived RNAs (crRNAs) assemble with Cas proteins into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Cascade recognizes DNA targets via protein-mediated recognition of a protospacer adjacent motif and complementary base pairing between the crRNA spacer and the DNA target. Previously determined structures of Cascade showed that the crRNA is stretched along an oligomeric protein assembly, leading us to ask how crRNA length impacts the assembly and function of this complex. We found that extending the spacer portion of the crRNA resulted in larger Cascade complexes with altered stoichiometry and preserved in vitro binding affinity for target DNA. Longer spacers also preserved the in vivo ability of Cascade to repress target gene expression and to recruit the Cas3 endonuclease for target degradation. Finally, longer spacers exhibited enhanced silencing at particular target locations and were sensitive to mismatches within the extended region. These findings demonstrate the flexibility of the Type I-E CRISPR machinery and suggest that spacer length can be modified to fine-tune Cascade activity.}, number={15}, journal={NUCLEIC ACIDS RESEARCH}, author={Luo, Michelle L. and Jackson, Ryan N. and Denny, Steven R. and Tokmina-Lukaszewska, Monika and Maksimchuk, Kenneth R. and Lin, Wayne and Bothner, Brian and Wiedenheft, Blake and Beisel, Chase L.}, year={2016}, month={Sep}, pages={7385–7394} }
 @article{afroz_luo_beisel_2015, title={Impact of Residual Inducer on Titratable Expression Systems}, volume={10}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0137421}, abstractNote={Inducible expression systems are widely employed for the titratable control of gene expression, yet molecules inadvertently present in the growth medium or synthesized by the host cells can alter the response profile of some of these systems. Here, we explored the quantitative impact of these residual inducers on the apparent response properties of inducible systems. Using a simple mathematical model, we found that the presence of residual inducer shrinks the apparent dynamic range and causes the apparent Hill coefficient to converge to one. We also found that activating systems were more sensitive than repressing systems to the presence of residual inducer and the response parameters were most heavily dependent on the original Hill coefficient. Experimental interrogation of common titratable systems based on an L-arabinose inducible promoter or a thiamine pyrophosphate-repressing riboswitch in Escherichia coli confirmed the predicted trends. We finally found that residual inducer had a distinct effect on “all-or-none” systems, which exhibited increased sensitivity to the added inducer until becoming fully induced. Our findings indicate that residual inducer or repressor alters the quantitative response properties of titratable systems, impacting their utility for scientific discovery and pathway engineering.}, number={9}, journal={PLOS ONE}, author={Afroz, Taliman and Luo, Michelle L. and Beisel, Chase L.}, year={2015}, month={Sep} }
 @article{luo_mullis_leenay_beisel_2015, title={Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression}, volume={43}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gku971}, abstractNote={CRISPR-Cas systems have shown tremendous promise as heterologous tools for genome editing and transcriptional regulation. Because these RNA-directed immune systems are found in most prokaryotes, an opportunity exists to harness the endogenous systems as convenient tools in these organisms. Here, we report that the Type I-E CRISPR-Cas system in Escherichia coli can be co-opted for programmable transcriptional repression. We found that deletion of the signature cas3 gene converted this immune system into a programmable gene regulator capable of reversible gene silencing of heterologous and endogenous genes. Targeting promoter regions yielded the strongest repression, whereas targeting coding regions showed consistent strand bias. Furthermore, multi-targeting CRISPR arrays could generate complex phenotypes. This strategy offers a simple approach to convert many endogenous Type I systems into transcriptional regulators, thereby expanding the available toolkit for CRISPR-mediated genetic control while creating new opportunities for genome-wide screens and pathway engineering.}, number={1}, journal={NUCLEIC ACIDS RESEARCH}, author={Luo, Michelle L. and Mullis, Adam S. and Leenay, Ryan T. and Beisel, Chase L.}, year={2015}, month={Jan}, pages={674–681} }
 @article{gomaa_klumpe_luo_selle_barrangou_beisel_2014, title={Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems}, volume={5}, ISSN={["2150-7511"]}, DOI={10.1128/mbio.00928-13}, abstractNote={ABSTRACT}, number={1}, journal={MBIO}, publisher={American Society for Microbiology}, author={Gomaa, Ahmed A. and Klumpe, Heidi E. and Luo, Michelle L. and Selle, Kurt and Barrangou, Rodolphe and Beisel, Chase L.}, year={2014} }
 @article{foster_gongal_begaj_luo_2013, title={Embedded collagen deformation models for computational modeling of healthy, keratoconic, and crosslinked corneas}, volume={13}, number={3}, journal={Journal of Mechanics in Medicine and Biology}, author={Foster, C. D. and Gongal, D. and Begaj, T. and Luo, M.}, year={2013} }