Abstract: Synthetic oligonucleotides, such as synthetic DNA, often contain sequence errors due to synthetic failures (e.g., side products and/or truncated products). Methods are provided herein for improving the sequence fidelity of synthetic double-stranded oligonucleotides by separative depletion of synthetic failures. Separation is effected by utilization of methodologies in a preparative mode under denaturing conditions. A preferred use of the methods relates to gene synthesis.

Abstract: A method for depositing biomolecule onto a solid support, the method including the steps of: immersing a tip of a spring probe into a solution of biomolecule; removing said tip from said solution to provide biomolecule solution adhered to said tip; and contacting said biomolecule solution with a solid support to thereby transfer biomolecule solution from said tip to said solid support. The spring probe has a planar tip but it otherwise identical to commercial spring probes. The solution of biomolecule contains a thickening agent in addition to biomolecule, where oligonucleotide is a preferred biomolecule.

Abstract: The present invention provide methods and an apparatus for performing amplification and other enzymatic reactions on nucleic acid molecules that have been printed onto a solid substrate, such as a silicon wafer or glass slide.

Abstract: Compositions and methods are provided for increasing the specificity of a probe nucleic acid for a target nucleic acid in a hybridization solution. An abasic residue, deoxyNebularine residue, or a hybotrope is used to increase specificity. A method is provided for identifying useful hybotropes, including salts, water miscible organic solvents, aprotic solvents and organic solvents, on the basis of enthalpy considerations. Hybotropic hybridization and modified oligonucleotides may be used in amplification reactions, such as PCR, sequence analysis methods, and genomic screening methods.

Abstract: A method and system for correlating characteristics (e.g., type of nucleotide) of biomolecules (e.g., DNA) to molecular tags with unique molecular weights that are associated with the biomolecule. In one embodiment, the molecular tags are applied to primers used when synthesizing the biomolecule. The system initially receives a mapping of each characteristic of the biomolecules to the corresponding molecular weight of the molecular tag. The system also receives an indication of the molecular weights detected when analyzing the biomolecules to which the molecular tags have been associated. For each molecular weight detected, the system determines based on the received mapping the characteristic corresponding to the detected molecular weight. The system then indicates that the analyzed biomolecule has the determined characteristic.

Abstract: Methods and compounds, including compositions therefrom, are provided for determining the sequence of nucleic acid molecules. The methods permit the determination of multiple nucleic acid sequences simultaneously. The compounds are used as tags to generate tagged nucleic acid fragments which are complementary to a selected target nucleic acid molecule. Each tag is correlative with a particular nucleotide and, in a preferred embodiment, is detectable by mass spectrometry. Following separation of the tagged fragments by sequential length, the tags are cleaved from the tagged fragments. In a preferred embodiment, the tags are detected by mass spectrometry and the sequence of the nucleic acid molecule is determined therefrom. The individual steps of the methods can be used in automated format, e.g., by the incorporation into systems.

Abstract: The present invention provide methods and an apparatus for performing amplification and other enzymatic reactions on nucleic acid molecules that have been printed onto a solid substrate, such as a silicon wafer or glass slide.

Abstract: An array of biomolecules is formed from a solid substrate comprising a surface, where said surface is at least partially covered with a layer of poly(ethylenimine) (PEI), and the layer is divided among a plurality of discrete first regions abutted and surrounded by a contiguous second region. The first regions are defined by the presence of a biomolecule and PEI. The second region is defined by the presence of PEI and the substantial absence of the biomolecule. The array may be prepared by a process including the steps of providing a solid substrate having a surface, wherein a layer of poly(ethylenimine) (PEI) covers at least a portion of the surface. The layer contains a plurality of discrete first regions abutted and surrounded by a contiguous second region. The process includes the step of depositing a biomolecule into the first regions while maintaining the second region substantially free of the biomolecule.

Abstract: Methods are provided for detecting the binding of a first member to a second member of a ligand pair, comprising the steps of (a) combining a set of first tagged members with a biological sample which may contain one or more second members, under conditions, and for a time sufficient to permit binding of a first member to a second member, wherein said tag is correlative with a particular first member and detectable by non-fluorescent spectrometry, or potentiometry, (b) separating bound first and second members from unbound members, (c) cleaving the tag from the tagged first member, and (d) detecting the tag by non-fluorescent spectrometry, or potentiometry, and therefrom detecting the binding of the first member to the second member.

Abstract: Oligonucleotides (ODNs) include a sequence that is complementary to a target sequence in single stranded RNA, or single or double stranded DNA, and an alkylating function which after hybridization alkylates the target sequence. ODNs adapted for alkylating single stranded RNA, such as messenger RNA, are complementary to the target sequence in the Watson Crick sense. ODNs adapted for alkylating double stranded DNA have at least two alkylating functions and are complementary to the target sequence in the Hoogsteen or reverse Hoogsteen sense. With these ODNs both strands of the target sequence are alkylated. A third class of ODNs have at least approximately 26 nucleotide units in a continous sequence which are complementary to the target sequence of double stranded DNA, and the alkylating function is covalently attached to a nucleotide unit in the continuous sequence. Alkylation or cross-linking with this class of ODNs occurs in the presence of a recombinase enzyme.

Abstract: This invention is directed to novel substituted nucleotide bases with a crosslinking arm which accomplish crosslinking between specific sites on adjoining strands of oligonucleotides or oligodeoxynucleotides. The invention is also directed to oligonucleotides comprising at least one of these crosslinking agents and to the use of the resulting novel oligonucleotides for diagnostic and therapeutic purposes. The crosslinking agents of the invention are of the following formula (I'):R.sub.1 --B--(CH.sub.2).sub.q --(Y).sub.r --(CH.sub.2).sub.m --A'(I')wherein,R.sub.1 is hydrogen, or a sugar moiety or analog thereof optionally substituted at its 3' or its 5' position with a phosphorus derivative attached to the sugar moiety by an oxygen and including groups Q.sub.1 Q.sub.2 and Q.sub.3 or with a reactive precursor thereof suitable for nucleotide bond formation;Q.sub.1 is hydroxy, phosphate or diphosphate;Q.sub.2 is .dbd.O or .dbd.S;Q.sub.3 is CH.sub.

Abstract: Compositions and methods for covalently immobilizing an oligonucleotide onto a polymer-coated solid support or similar structure are provided. Specifically, the polymer-coated support, such as a bead, possesses a large number of activatable moieties, preferably primary and secondary amines. An oligonucleotide is activated with a monofunctional or multifunctional reagent, preferably the homotrifunctional reagent cyanuric chloride. The resultant covalently immobilized oligonucleotides on the support serve as nucleic acid probes, and hybridization assays can be conducted wherein specific target nucleic acids are detected in complex biological samples. The beads or similar structures can be employed free in solution, such as in a microtiter well format; in a flow-through format, such as in a column; or in a dipstick. Additionally, dichlorotriazine oligonucleotides and processes for activating oligonucleotides by treatment with cyanuric chloride and derivatives are included in the present invention.

Abstract: Compositions and methods for covalently immobilizing an oligonucleotide onto a polymer-coated bead or similar structure are described. Specifically, the polymer-coated bead or similar structure possesses a large number of activatable moieties, preferably primary and secondary amines. An oligonucleotide is activated with a monofunctional or multifunctional reagent, preferably the homotrifunctional reagent cyanuric chloride. The resultant covalently immobilized oligonucleotides on the beads or similar structures can serve as nucleic acid probes on solid supports, and hybridization assays can be conducted wherein specific target nucleic acids are detected in complex biological samples.

Abstract: A solid support for oligonucleotide synthesis has the structure ##STR1## where CPG represents a controlled pore glass matrix, the wavy line represents a carbon chain covalently linking the NH group with the controlled pore glass matrix, X is 2,2'-dimethoxytrityl or H, and R is alkyl, aryl, arylalkyl, heteroalkyl, or heteroaryl. The dimethoxytrityl group is removed from the solid support by treatment with acid, and the oligonucleotide is built, step-by-step in a conventional synthesizer after attachment of the 3' end of the first oligonucleotide unit to the hydroxyl function connected to the R group.