Other

Eragen Biosciences, Inc.

Steven Albert Benner

Zunyi Yang

Nicole Aurora Leal

Shuichi Hoshika

Hyo-Joong Kim

Fei Chen

Daniel Hutter

Nilesh Karalkar

Roberto Laos

Albert Michael Sismour

Myong Jung Kim

Ryan W Shaw

Lukas Knecht

Diane Rowold

Nilesh B Karalkar

Ozlem Yaren

Patricia Moussatche

Nidhi Sharma

Ion Mircesti Scorei

Stephen Chamberlin

This invention claims ribonucleosides and their derivatives, including triphosphates, that have a 3′-ONHmoiety instead of a 3′-OH moiety.

Ribonucleoside derivatives with 3′-aminoxy groups

Disclosed here are compositions of matter that comprise DNA analogues that have been rectified by replacing the four standard components with alternative components that mitigate various problems frequently encountered during synthesis of these compounds, during the functioning of these compounds, and complex mixtures for information data storage.

Information storage with rectified dna

Processes described here exploit the utility of mismatching nucleobase analogs to create long segments of natural DNA to be constructed after fragments containing unnatural nucleotides are transliterated in at least two cycles of polymerase-catalyzed copying, or alternatively complete PCR, by guided mismatching.

Assembly of long DNA molecules by transliteration

Disclosed are PCR processes that transliterate target duplex DNA molecules containing 8 different nucleotide building blocks strategically arranged to allow efficient conversion of information in that target into DNA built from just four different nucleotides.

Directed transliteration of nucleotides in DNA

Nicotinamide ribose has many applications, including as a dietary supplement. This invention convers a process to prepare nicotinamide ribose it in its phosphorylated form. The instant invention is based on the discovery that nicotinamide ribose phosphate emerges in stable form by direct reaction of ribose-1,2-cyclic phosphate. It is based on the further conversion of the phosphorylated nicotinamide ribose product to unphosphorylated nicotinamide ribose upon treatment with an enzymatic phosphatase, most preferably in buffer containing borate. It is based on the further discovery that compositions of nicotinamide ribose with borate slow the decomposition of nicotinamide ribose, and therefore is more useful than compositions of nicotinamide ribose without borate.

Synthesis and stabilization of nicotinamide ribose and its derivatives

This invention claims processes that append a single nucleotide having a 3'-ONHmoiety to the 3&#x2032;-ends of an oligonucleotide primer using 3&#x2032;-deoxynucleoside triphosphates that have, instead of a 3&#x2032;-OH moiety, a 3&#x2032;-ONHmoiety, where the nucleotides contain both standard and non-standard nucleobases, and where as a key claim limitation, substantially no hydroxylamine is present in the solutions used in the claimed processes.

Processes using nucleoside triphosphates with stable aminoxy groups

This invention provides for processes for creating a long DNA molecule that is a concatamer that comprises a repeating oligonucleotide segment, wherein one or more of the nucleotides of said segment has one or more independently selected templating 'non-standard' nucleotides. These are nucleotide analogs that, when incorporated into oligonucleotides (DNA or RNA, collectively xNA), present to a pattern of hydrogen bonds that is different from the pattern presented by adenine, guanine, cytosine, and uracil. This disclosure provides a process for obtaining these using rolling circle amplification.

Binding molecules built from L-DNA with added nucleotides

This invention relates to processes that transcribe DNA molecules containing non-standard nucleotides using variants of T7 RNA polymerase to give RNA transcripts that contain their complementary non-standard nucleotides. Non-standard nucleotides pair during transcription using patterns of hydrogen bonding that are different from patterns that join the thymine-adenine and guanine-cytosine nucleobase pairs.

Enzymatic processes for synthesizing RNA containing certain non-standard nucleotides

Processes are disclosed that create derivative DNA molecules in large numbers under isothermal conditions, where amplification of a looped structure derived from a target is achieved by a process that separately or in combination includes (a) a displaceable probe that (b) may be captured in a separate site, optionally containing (c) components of an artificially expanded genetic information system, where the primers optionally contain (d) components of a self-avoiding molecular recognition system, and optionally (e) involving direct transfer of DNA or RNA from a sample from a capture medium with immobilized quaternary ammonium salts.

Isothermal amplification of oligonucleotides

The disclosed invention teaches processes to create a Watson-Crick complementary copy of a preselected oligonucleotide that contain non-standard nucleotides, which form nucleobase pairs fitting the standard Watson-Crick geometry, but here said pairs are joined by hydrogen bonding patterns different from those that join standard A:T and G:C pairs. The invention further relates to polymerases that incorporate those non-standard nucleotide analogs into oligonucleotide products using the corresponding triphosphate derivatives.

Polymerase incorporation of non-standard nucleotides

This invention relates to processes that amplify oligonucleotide analogs that incorporate non-standard nucleobase analogs from an artificially expanded genetic information system. These pair in DNA duplexes via patterns of hydrogen bonds that differ from patterns that join the thymine-adenine and guanine-cytosine nucleobase pairs.

Amplification of oligonucleotides containing non-standard nucleotides

This invention covers oligonucleotide analogs that fold in part by having a segment of consecutive pyrimidine analogs form pyrimidine analog:pyrimidine analog pairs with another a segment of consecutive pyrimidine analogs segment, and where the segments pair by pyrimidine analog:pyrimidine analog 'skinny' pairing. This pairing retains hydrogen bonding complementarity seen in standard DNA.

Molecular recognition systems with pyrimidine analog pairing

This invention relates to the use of analogs of purines that have two tautomeric forms, one formally complementary to thymidine, the other formally complementary to cytidine, and analogs of pyrimidines that have two tautomeric forms, one formally complementary to guanosine, the other formally complementary to adenosine. These uses include the polymerase chain reaction amplification of targets having polymorphisms in primer binding sites and ligation.

Applications for biversal nucleoside analogs

This invention claims processes that comprise the appending of nucleotides having a 3'-ONHmoiety to the 3&#x2032;-ends of oligonucleotide primers using 3&#x2032;-deoxynucleoside triphosphates of 2&#x2032;-deoxynucleoside derivatives that have, instead of a 3&#x2032;-OH moiety, a 3&#x2032;-ONHmoiety, where the nucleotides contain non-standard nucleobases.

Processes with terminal transferase, aminoxy nucleoside triphosphates, and nucleobase analogs

This invention provides for processes for binding to and/or chemically transforming a preselected target, where the process involves contacting said target to an oligonucleotide molecule that contains one or more 'non-standard' nucleotides, which are nucleotide analogs that, when incorporated into oligonucleotides (DNA or RNA, collectively xNA), present to a pattern of hydrogen bonds that is different from the pattern presented by adenine, guanine, cytosine, and uracil. This disclosure provides an example where such an oligonucleotide molecule is built from both D- and L-mirror image carbohydrates in the backbone. It also provides a process for obtaining these binders and/or transformers by a laboratory in vitro selection process that exploits rolling circle amplification rather than the polymerase chain reaction.

Growing community of inventors

Gainesville, FL, United States of America

Steven Albert Benner