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Paul D. Carlson
Researcher at Cornell University
Publications - 13
Citations - 266
Paul D. Carlson is an academic researcher from Cornell University. The author has contributed to research in topics: RNA & Nucleic acid structure. The author has an hindex of 8, co-authored 13 publications receiving 165 citations. Previous affiliations of Paul D. Carlson include Northwestern University & University College of Engineering.
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Journal ArticleDOI
De novo-designed translation-repressing riboregulators for multi-input cellular logic.
Jongmin Kim,Jongmin Kim,Yu Zhou,Paul D. Carlson,Paul D. Carlson,Mario Teichmann,Chaudhary Soma,Friedrich C. Simmel,Friedrich C. Simmel,Pamela A. Silver,Pamela A. Silver,James J. Collins,James J. Collins,James J. Collins,Julius B. Lucks,Peng Yin,Peng Yin,Alexander A. Green +17 more
TL;DR: De novo RNA design is employed to develop two high-performance translational repressors with sensing and logic capabilities that detect transcripts with nearly arbitrary sequences, repress gene expression by up to 300-fold, and yield orthogonal sets of up to 15 devices.
Journal ArticleDOI
Computational design of three-dimensional RNA structure and function.
Joseph D. Yesselman,Daniel Eiler,Erik D. Carlson,Michael R. Gotrik,Anne E. d’Aquino,Alexandra N. Ooms,Wipapat Kladwang,Paul D. Carlson,Xuesong Shi,David A. Costantino,Daniel Herschlag,Julius B. Lucks,Michael C. Jewett,Jeffrey S. Kieft,Rhiju Das +14 more
TL;DR: Automated 3D design produces rapid and near-atomically accurate predictions of RNA tertiary structure as well as the ability to generate complex RNA machines such as functional single-stranded tethered ribosomes, and enhancement of the binding properties of small-molecule RNA aptamers.
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A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control.
TL;DR: This work determines the series of cotranscriptional folds and rearrangements that mediate antitermination by the Clostridium beijerinckii pfl ZTP riboswitch in response to the purine biosynthetic intermediate ZMP and reveals that an internal RNA strand displacement andriboswitch sequence play important roles in the process.
Journal ArticleDOI
Using in-cell SHAPE-Seq and simulations to probe structure–function design principles of RNA transcriptional regulators
Melissa K. Takahashi,Kyle E. Watters,Paul M. Gasper,Timothy R. Abbott,Paul D. Carlson,Alan A. Chen,Julius B. Lucks +6 more
TL;DR: A new structure-function design principle for attenuators is identified that enables the forward engineering of new RNA transcriptional repressors and establishes interior loops as an important structural element for designing synthetic RNA gene regulators.
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Characterizing the Structure-Function Relationship of a Naturally Occurring RNA Thermometer
TL;DR: Using the SHAPE-Seq RNA structure-probing method in vivo and in vitro, it is found that the regulator functions by a subtle shift in equilibrium RNA structure populations that leads to a partial melting of the helix containing the ribosome binding site.