Agilent Technologies, Inc.

University of Colorado

Zoltan Timar

Douglas J Dellinger

Geraldine F Dellinger

Marvin H Caruthers

Joel Myerson

Agnieszka Sierzchala

Holly Hogrefe

Jeffrey Robert Sampson

Robert A Ach

Brian Jon Peter

Victor R Mokler

Zoltan Kupihar

Gergo Hegedus

Geraldino Dellinger

Geraldine F Dellingen

A method of deprotecting a solid support bound polynucleotide comprising at least one 2'-protected ribonucleotide in which a step of contacting the polynucleotide with a composition comprising a diamine is performed under conditions sufficient to deprotect and cleave the polynucleotide which remains retained on the solid support.

Protected monomer and method of final deprotection for RNA synthesis

This disclosure provides a method comprising: a) clamping the top and bottom strands of a double stranded DNA molecule to produce a duplex in which the top and bottom strands are linked; b) denaturing the duplex to produce a denatured product; and c) renaturing the denatured product in the presence of a labeled oligonucleotide that is complementary to a sequence of nucleotides in the double stranded DNA molecule, thereby producing a D-loop-containing product. Kits for performing the method and products made by the method are also provided.

Target enrichment and labeling for multi-kilobase DNA

A method of deprotecting a solid support bound polynucleotide includes the step of contacting the polynucleotide with a composition comprising a diamine under conditions sufficient to deprotect the 2'-protected ribonucleotide residue. The solid support bound polynucleotide has at least one 2&#x2032;-protected ribonucleotide residue, which has the following structure: wherein Bis a protected or unprotected heterocycle; Ris a protecting group selected from a hydrocarbyl, a substituted hydrocarbyl, an aryl, and a substituted aryl; X is O or S; and PG is a thionocarbamate protecting group.

A method and compositions for sulfurizing at least one phosphite or thiophosphite linkage in an oligonucleotide. The methods employ a phenylacetyl disulfide reagent (known as PADS), phenylthioacetic acid (PTAA) in the presence or absence or N-alkyl imidazole in industrially preferred solvents or solvents that are derived from renewable resources. The use of PTAA eliminates the need to 'age' the PADS solution prior to its use in sulfurization reactions.

Use of thioacetic acid derivatives in the sulfurization of oligonucleotides with phenylacetyl disulfide

Methods of deprotecting polynucleotides are disclosed. One aspect of the method of deprotecting polynucleotides, among others, includes: providing a polynucleotide, wherein the polynucleotide includes at least one nucleotide monomer that has at least one protecting group selected from the following: a base having a protecting group, a 2'-hydroxyl protecting group, and a combination thereof, and deprotecting at least one of the protecting groups of the polynucleotide by introducing the polynucleotide to a solution including an &#x3b1;-effect nucleophile.

Solutions, methods, and processes for deprotection of polynucleotides

A computer-implemented method for confirming the nucleotide sequence of an oligonucleotide is provided. In certain embodiments, the method comprises: a) inputting the nucleotide sequence of an oligonucleotide; b) executing an algorithm that provides the predicted molecular formulas of fragments of the oligonucleotide; c) comparing the predicted m/z values of the predicted molecular formulas to experimentally-obtained m/z values obtained by analysis of the oligonucleotide by tandem mass spectrometry to determine if the predicted masses correspond with the experimentally-obtained masses. The method may be used, for example, to confirm the identity of an oligonucleotide after it is synthesized.

Method of oligonucleotide sequencing by mass spectrometry

Nucleotide monomers, polynucleotides, methods of making each, and methods of deprotecting each, are disclosed. An embodiment of the nucleotide monomer, among others, includes a nucleotide monomer having a heterobase protecting group selected from structures I through III as described herein. An embodiment of the polynucleotide, among others, includes a plurality of nucleotide moieties having a heterobase protecting group selected from one of structures I through III as described herein.

Monomer compositions for the synthesis of polynucleotides, methods of synthesis, and methods of deprotection

Embodiments of the invention include nucleotide and nucleoside monomers protected at the 5'- or 3&#x2032;-hydroxyls with thioether substituted aryl carbonate protecting groups. In certain cases, the carbonate protecting groups include an aryl moiety, e.g., a phenyl group, attached to the carbonate, where the aryl moiety further includes a thioether group, e.g., an alkyl or aryl thioether group, bound directly to the aryl ring. Aspects of the invention further include methods of synthesizing nucleic acids, e.g., oligonucleotides, using such protected nucleoside monomer monomers, as well as nucleic acids produced using methods of the invention and compositions thereof.

Thioether substituted aryl carbonate protecting groups

In various embodiments of the invention, novel compositions having a polynucleotide bound to a substrate via a cleavable linker are provided, and methods of cleaving a polynucleotide from a substrate are provided.

Cleavable thiocarbonate linkers for polynucleotide synthesis

Thiocarbonate linkers for polynucleotides

Nucleotide monomers, polynucleotides, methods of making each, methods of deprotecting each, and the like are disclosed herein.

Monomer compositions for the synthesis of RNA, methods of synthesis, and methods of deprotection

Cleavable linkers for polynucleotides

Compounds having a phosphorus group structure of: wherein:

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Boulder, CO, United States of America

Zoltan Timar