Leland Stanford Junior University

Research Corporation Technologies, Inc.

University of Rochester

Illumina Corporation

Eric T Kool

Michael Previte

Molly Min He

Mostafa Ronaghi

Cheng-Yao Chen

Rigo Pantoja

Howard Yuan-Hao Chang

Willem Arend Velema

Jong Hwa Jung

Raphael M Franzini

James N Wilson

Nan Dai

Robert Carl Spitale

Hiroshi Abe

Jianmin Gao

Peter Joseph Crisalli

Yuki Tahara

This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.

Conformational probes and methods for sequencing nucleic acids

Reagents and methods to cloak and uncloak RNA polymers and applications thereof are provided. Photocloaking molecules are used to label RNA polymers. Radiant energy is used to remove photoreleaseable protecting adducts and revert a RNA polymer to its native form.

Photoreversible acylation reagents

Noncovalent small-molecule inhibitors of the enzyme OGG1, methods of their manufacture, and applications for their administration are provided. Small molecule inhibitors were shown to be selective for inhibiting OGG1 over multiple repair enzymes, including other base excision repair enzymes, and it displayed no toxicity in two human cell lines. The inhibitors provide a tool for the study of the role of OGG1 in multiple disease-related pathways, and a therapeutic target for the treatment thereof. Various embodiments include substituted 1,2,3,4-tetrahydroquinolines, such as compounds of the of the formula ABCDE: 

Substituted 1,2,3,4-tetrahydroquinolines as inhibitors of repair enzyme 8-oxoguanine deoxyribonucleic acid glycosylase activity

Methods for obtaining structural data from RNA in a sample, and RNA probes for performing the same, are provided. Methods of reversibly modifying RNA is a sample, in vitro or in vivo, and reversible probes for performing the same, are provided. The RNA probes may be SHAPE probes that include aryl or heteroaryl acyl imidazoles. The RNA probes may be reversible probes that include an aryl or heteroaryl ring substituted with a hydroxyl-reactive group and an azido-containing group. Also provided are methods of comparing in vitro and in vivo RNA structural data. Also provided are methods of diagnosing a cellular proliferative disease condition, e.g., by probing HOTAIR RNA. Aspects of the invention further include compositions, e.g., probes and kits, etc., that find use in methods of the invention.

Probes of RNA structure and methods for using the same

Probes comprising one or more selectively cleavable &#x3b1;-azidoether moieties are provided; and linkers comprising the one or more selectively cleavable &#x3b1;-azidoether moieties. The &#x3b1;-azidoether moiety will undergo a Staudinger reaction with a suitable reducing agent, resulting in cleavage. The probes find use in a variety of detection assays, e.g. specific polynucleotide binding assays, polypeptide binding assays, etc. The cleavable linkers are suitable for synthetic reactions, e.g. to prepare probes of the invention; in the synthesis of cleavable peptide conjugates; and the like.

Reductive release probes containing a chemoselectively cleavable &#x3b1;-azidoether linker and methods of use thereof

Nucleoside analogs are provided; and fluorescent sensors comprising the nucleoside analogs. The sensors comprise multiple chromophores built on a DNA backbone, in which all the natural DNA bases are replaced by excimeric or exciplex-forming fluorophores, ligands, quenchers and spacers in thousands of combinations. The sensors find use in the detection and identification of target analytes by fluorescence, e.g., detection of metal ions, neutral organic compounds and anions. The sensors find use in the detection and identification of molecular species in the vapor or gaseous phase, or the liquid phase. The sensors find use in qualitative and quantitative screening and detection methods.

Direct sensing of molecular species by polyfluors on a DNA backbone

Telomere-encoding nucleic acid nanocircles, methods for their preparation, and methods for their use are disclosed. The nanocircles can be constructed containing multiple repeats of the complement of telomere repeat sequences. The telomere-encoding nanocircles are useful for extending telomeres both in vitro and in vivo, for treating macular degeneration, the effects of skin aging, liver degeneration, and cancer. The nanocircles are further useful for treating cell cultures to produce long-lived non-cancerous cell populations. This use has wide applicability in scientific research, tissue engineering, and transplantation.

Telomere-encoding synthetic DNA nanocircles, and their use for the elongation of telomere repeats

Compositions and systems are provided for the high efficiency quenching small water-soluble oligomers, or oligofluors, of from about 1-10 kd in size, where the oligofluors comprise multiple excimeric or exciplex forming fluorophores arranged on a scaffold, which are efficiently quenched by a quencher entity linked to the oligomer through a cleavable moiety. Fluorophores of interest include, without limitation, aromatic fluorophores such as pyrenes, e.g. benzopyrene, perylene, pyrene, etc. In some embodiments the oligofluor/quencher combination provides for a Stern-Vollmer constant (K) of greater than about 10M, and may be greater than about 10M, greater than about 10M, or more. In some embodiments of the invention, the scaffold is a phosphodiester/glycoside backbone, e.g. an analog of a polynucleotide. The system of oligofluors and quenchers can be used in qualitative and quantitative screening and detection methods to detect any enzymatic, chemical or catalytic activity that can cleave the moiety between the quencher and scaffold.

Strongly quenching oligomeric excimer/quencher pairs for detection schemes

The present invention provides methods for synthesis and therapeutic use of DNA and RNA oligonucleotides and analogs. RNA oligonucleotides are synthesized using a small, circular DNA template which lacks an RNA polymerase promoter sequence. The RNA synthesis is performed by combining a circular single-stranded oligonucleotide template with an effective RNA polymerase and at least two types of ribonucleotide triphosphate to form an RNA oligonucleotide multimer comprising multiple copies of the desired RNA oligonucleotide sequence. Preferably, the RNA oligonucleotide multimer is cleaved to produce RNA oligonucleotides having well-defined ends. Preferred RNA oligonucleotide multimers contain ribozymes capable of both cis (autolytic) and trans cleavage.

Circular DNA vectors for synthesis of RNA and DNA

Novel compounds having a fluorescence quencher as a leaving group are disclosed. Nucleic acids and other molecules containing a fluorophore and a fluorescence quencher are disclosed as an embodiment of this invention. The use of the oligonucleotides in enzyme-free oligonucleotide ligation reactions results in an increase in fluorescence when the oligonucleotide also contains a nearby fluorophore. The ligation reactions can be performed in solution, on surfaces, or in cells.

Growing community of inventors

Rochester, NY, United States of America

Eric T Kool