Arizona State University

Harvard College

Boston University

Massachusetts Institute of Technology

University of Florida Research Foundation Inc

University of Toronto

Alexander A Green

James Joseph Collins

Peng Yin

Keith Pardee

Duo Ma

Ahmed Yousaf

Anli Tang

Jongmin Kim

Melissa K Takahashi

Matthew Gilliam

Fan Hong

Qing Hua Wang

Yu Zhou

Thomas Ferrante

Guillaume Lambert

Dana Braff

Hao Yan

Neal W T Woodbury

Chris Diehnelt

Nicholas Stephanopoulos

Luhui Shen

Margot Karlikow

Ximo Chu

Abhishek Debnath

Soma Chaudhary

Kirstie Swingle

Kaiyue Wu

Masoud Norouzi

Peike Sheng

Mingyi Xie

Provided herein are methods, compositions and systems comprising synthetic nucleic acid molecules that enable inducible or conditional pri-miRNA processing, preferably in mammalian cells in vivo. Provided herein are synthetic nucleic acid molecules referred to as Orthogonal RNA Interference induced by Trigger RNA (ORIENTR) that switches between an inactive form and an active form upon interaction with one or more specific RNA-trigger molecules, which can be e.g., a synthetic RNA-trigger, or a disease-specific RNA signals, such as disease-specific mRNA, miRNA, or other cellular RNA products with sequences that characterize a disease state of a cell. The interaction between the RNA-trigger molecules and the ORIENTR is preferably mediated by hybridization, which exposes, facilitates the formation, and/or allows the formation of a correctly folded pri-miRNA scaffold substrate that can be processed by proteins of the RNAi pathway (such as Dicer), leading to RNAi-mediated repression of a target gene. Also provided herein are methods of using such ORIENTR molecules for the treatment or prevention of a disease in a subject, as well as detecting the presence or absence of a target RNA in a biological sample or in vivo.

miRNA switches for RNA-triggered control of RNA interference

Methods for detecting the presence of a pathogen infection are described. In particular, this document provides a method of detecting target nucleic acids, such as pathogen-specific RNA, in a biological sample obtained from a subject, where the method comprises using one or more toehold switch sensors and an isothermal amplification step to detect the target nucleic acid. Methods specific for detecting and identify the presence of a virus such as Zika virus are also provided.

Portable, low-cost pathogen detection and strain identification platform

Provided herein are methods and compositions for rapid, highly sensitive detection of SARS-CoV-2 in biological samples. In particular, provided herein is a rapid, low-cost method for detecting SARS-CoV-2 that provides reliable, visible test results and does not require PCR reagents, elaborate biosafety precautions, or sophisticated laboratory equipment.

Rapid low-cost detection of SARS-CoV-2 using isothermal amplification and sensing methods

Provided herein are synthetic nucleic acid molecules and methods of using such synthetic nucleic acid molecules for strong repression of target gene expression. In particular, provided herein are methods for altering expression of a protein in a cell, where the method comprises introducing into a cell a protein coding sequence operably linked to a near-threshold translational repressor having first and second trigger recognition sequences that are fully or partially complementary to a repressing trigger RNA; and introducing into a cell the repressing trigger RNA.

Synthetic near-threshold translational repressors

Provided herein are synthetic nucleic acid molecules known as loop-mediated riboregulators that have single-nucleotide polymorphism (SNP) sensitivity and ultralow OFF state signal levels. Loop-mediated riboregulators can activate or repress gene expression in response to trigger RNAs bearing completely arbitrary sequences. Also provided herein are methods of using such synthetic nucleic acid molecules for detecting the presence or absence of a particular target RNA in, for example, a biological sample.

Loop-mediated synthetic riboregulators

The invention provides novel and versatile classes of riboregulators, including inter alia activating and repressing riboregulators, switches, and trigger and sink RNA, and methods of their use for detecting RNAs in a sample such as a well and in modulating protein synthesis and expression.

Compositions comprising riboregulators and methods of use thereof

Provided herein are imaging probes and systems and methods employing such imaging probes for real-time, label-free, multiplexed imaging of RNAs in living cells. More particularly, aptamer-based sensors ('aptasensors') and molecular fuses comprising multiple aptasensors are genetically encoded imaging probes comprising RNA-target binding sequence and an intramolecular reconfiguration sequence. The probe is configured such that binding of a RNA target by the RNA-target binding sequence triggers the intramolecular reconfiguration sequence to reconfigure such that an optically detectable output is generated by the probe.

Molecular fuses for real-time, label-free, multiplexed imaging of RNAs in living cells

Methods and compositions for detecting the presence of a pathogen are described. In particular, this document provides a method of detecting a pathogen-associated nucleic acid in a biological sample of a subject, where the method comprises using one or more unimolecular aptamer-based sensors comprising an aptamer-fluorophore complex and an amplification step to detect the pathogen-associated nucleic acid. Methods specific for detecting the presence of malaria and other mosquito-borne virus infections are also provided.

Unimolecular aptamer-based sensors for pathogen detection

A polymerizable composition for 3D printing includes a photocurable polymer resin and metal diboride nanosheets. The resulting polymer nanocomposite includes a polymer matrix and metal diboride nanosheets dispersed throughout the polymer matrix. A method of synthesizing a nanomaterial-containing resin for 3D printing includes preparing a dispersion of metal diboride nanosheets in a solvent, and combining the dispersion with a liquid polymer resin to yield the nanomaterial-containing resin. A method of fabricating a nanocomposite structure from the nanomaterial-containing resin includes providing the nanomaterial-containing resin to a three-dimensional printer, forming a three-dimensional structure with the three-dimensional printer, and processing the three-dimensional structure to yield the nanocomposite structure.

3D-printed nanocomposites with metal diboride nanosheets

Provided herein are highly sensitive compositions and methods for detection of at least one specific nucleic acid molecule in a sample. The presence of a specific nucleic acid provides a positive indicator of a pathogenic agent, contaminant, non-canonical bases, and/or wild-type or mutated genes in a sample or a cell. Applications for which the compositions and methods are particularly well suited include point-of-care disease diagnosis or cellular RNA imaging.

Ultraspecific riboregulators having robust single-nucleotide specificity and in vitro and in vivo uses thereof

Integrated diagnostic devices comprising peptide-DNA conjugates for analyte detection, an embedded biomolecular computing system for sample analysis, and a layered device architecture are provided herein. In particular, provided herein are devices comprising a layered architecture that enables diagnostic reagents, sample components, and reaction products to flow through the system with minimal user intervention.

Integrated diagnostic devices having embedded biomolecular computing systems and uses thereof

Ultraspecific, programmable nucleic acid sensors capable of detecting and preferentially amplifying target DNA molecules comprising a particular SNP or mutation are provided. In some cases, the ultraspecific programmable nucleic acid sensors are useful for detecting SNP-containing DNA molecules indicative of cancer such as cell-free DNA circulating in the blood or indicative of organ transplant rejection Also provided are methods for construction of such ultraspecific nucleic acid sensors and methods for preferential amplification of target DNA molecules containing a mutation of interest, as well as testing systems for early cancer screening and routine monitoring of circulating cancer DNA using liquid biological samples such as serum, plasma, or saliva.

Ultraspecific nucleic acid sensors for low-cost liquid biopsies

Provided herein are methods and compositions for rapid, highly sensitive detection of Valley fever in biological samples. In particular, provided herein is a low-cost method for detecting Valley fever that provides reliable, visible test results and does not require elaborate biosafety precautions or sophisticated laboratory equipment.

Rapid low-cost detection of valley fever using isothermal amplification and sensing methods

Provided herein, in some embodiments, are artificial ribosomes that synthesize nonribosomal peptides, polyketides, and fatty acids with full control over peptide sequence. Also provided herein are methods for programmed synthesis of nonribosomal peptides, polyketides, and fatty acids. In particular, provided herein are methods for scalable synthesis of a wide range of antibacterial, antifungal, antiviral, and anticancer compounds.

Growing community of inventors

Scottsdale, AZ, United States of America

Alexander A Green