Orchid Biosciences, Inc.

Molecular Tool, Inc.

Beckman Coulter, Inc.

Orchid Biocomputer, Inc.

Philip Goelet

Jonathan Karn

Michael T Boyce-Jacino

Stephen P Anderson

Michael R Knapp

Steven R Head

Theo T Nikiforov

Yu-Hui Rogers

The present invention describes a novel nucleic acid sequencing reagent which consists of a capture moiety, a spacer region and a sequence specific hybridizing region of 4-8 bases. The nucleic acid sequencing reagent of the present invention can also contain an attachment moiety. The nucleic acid sequencing reagent can be arranged into a nested array. This array configuration can then be used to sequence a given template without prior knowledge (de novo) of the wild type or expected sequence in conjunction with primer extension in the presence of a labeled chain terminating nucleotide.

De novo or 'universal' sequencing array

This invention concerns a reagent composition comprising at least two different terminators of a nucleic acid template-dependent, primer extension reaction. This invention also concerns a method for determining the identity of a nucleotide base at a specific position in a nucleic acid of interest. This invention further concerns a method for determining the presence or absence of a particular nucleotide sequence in a sample of nucleic acids. This invention further concerns a method for identifying different alleles in a sample containing nucleic acids. This invention further concerns a method for determining the genotype of an organism at one or more particular genetic loci.

Reagent for nucleic acid typing by primer extension

De novo or &ldquo;universal&rdquo; sequencing array

The present invention provides a method for determining the nucleotide sequence of a nucleic acid molecule using primer oligonucleotides arrayed on a solid support and doing primer extension. By providing sequence information from both oligonucleotide primers in which the 3&prime; terminal nucleotide of the oligonucleotide primer is hybridized to the nucleic acid molecule and oligonucleotide primers in which the 3&prime; terminal nucleotide is not hybridized to the nucleic acid molecule the invention is advantageous in that less primers are needed to fully sequence a nucleic acid molecule. Where the 3&prime; terminal nucleotide of an oligonucleotide in the array does not hybridize to the nucleic acid molecule, the present invention provides for either not permitting oligonucleotides hybridized to nucleic acid molecules to be extended by polymerase-mediated incorporation of a single chain terminator nucleotide residue onto the 3&prime; terminus of said hybridized oligonucleotide, or permitting the removal of any non-hybridized nucleotide residues from the 3&prime; terminus of said hybridized oligonucloetides, so as to form a truncated primer oligonucleotide whose 3&prime; terminus is hybridized to said nucleic acid molecule. The invention also provides kits that can be used to implement the methods of the invention.

Method for analyzing the nucleotide sequence of a polynucleotide by oligonucleotide extension on an array

The invention concerns a reagent composition that employs at least two different terminators of a nucleic acid template-dependent primer extension reaction to determine the identity of a nucleotide base at a specific position in a nucleic acid of interest. The invention also concerns an immobilized method for determining such identification. The invention may be used to determine the presence or absence of a specific nucleotide sequence in a sample. It may also be employed in determination of genotype and in the identification of different alleles.

Method for determining nucleotide identity through extension of

A method is provided for determining the identity of a nucleotide at a preselected site in a nucleic acid molecule. The method involves the incorporation of a nucleoside triphosphate that is complementary to the nucleotide present at the preselected site onto the terminus of a primer molecule, and their subsequent ligation to a second oligonucleotide. The reaction is monitored by detecting a specific label attached to the reaction's solid phase or by detection in solution.

Ligase/polymerase-mediated genetic bit analysis of single nucleotide

The invention concerns a reagent composition that employs at least two different terminators of a nucleic acid template-dependent primer extension reaction to determine the identity of a nucleotide base at a specific position in a nucleic acid of interest. The invention also concerns the method for determining such identification. The invention may be used to determine the presence or absence of a specific nucleotide sequence in a sample. It may also be employed in determination of genotype and in the identification of different alleles.

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Reistertown, MD, United States of America

Philip Goelet