Becton Dickinson and Company Limited

Albert Einstein College of Medicine

Michael C Little

James G Nadeau

Paul Theodore Hamilton

George T Walker

Wayne F Beyer

Robert E Pearson

Julie A Dickson

Matthew P Collis

Oscar J Llorin

Melinda S Fraiser

Catherine A Spargo

Mark Van Cleve

Adriann H Walters

James A Down

James M Harris

Glenn P Vonk

Daniel L Woodard

Barry R Bloom

Patricia A Spears

William E Keating

Daryl D Shank

David J Wright

Deborah R Howard

Margaret S Dey

John Chan

Stewart Jurgensen

Paul Riska

David James Wright

The present invention relates to a method for disrupting cells by subjecting the cells to ultrasonic energy in the absence of beads. The present invention also relates to the enhancement of cell disruption methods using ultrasonic energy by reducing the surface tension of the liquid in which the cells are located.

Cell disruption method using sonication

The present invention relates to a method for reducing the amount of substances inhibitory to nucleic acid hybridization in samples. The method is practiced prior to release of target nucleic acid from cells of interest and involves contacting the sample with an agent which solubilizes the inhibitory substances and does not effectuate release of nucleic acids from cells in the sample, and then the cells from the agent.

Method for reducing inhibitors of nucleic acid hybridization

The present invention relates to kits and methods for conducting fluorescence based detection assays. The kits are configured in a manner to perform the method so as to reduce or eliminate interfering fluorescence signal.

Kit and method for fluorescence based detection assay

Methods employing internal oligonucleotide standards in isothermal nucleic acid amplification reactions to determine the efficacy of the amplification reaction and to quantify pre-amplification target levels.

Internal controls for isothermal nucleic acid amplification reactions

Strand Displacement Amplification methods (thermophilic SDA) which can be performed over a broad temperature range (37.degree. C. to 70.degree. C.). The preferred temperature range for thermophilic SDA is 50.degree. C. to 70.degree. C. It has been found that certain thermophilic restriction endonucleases are capable of nicking the hemimodified restriction endonuclease recognition/cleavage site as required by SDA and dissociating from the site. It has further been found that certain thermophilic polymerases are capable of extending from the nick while displacing the downstream strand. Thermophilic SDA, because of reaction temperatures higher than previously possible with conventional SDA enzyme systems, has improved specificity and efficiency, reduced nonspecific background amplification, and potentially improved yields of amplification products. In addition, the need to add the enzymes in a separate step after the initial heat denaturation of double stranded targets is eliminated when enzymes capable of tolerating the denaturation temperature are used.

Strand displacement amplification using thermophilic enzymes

Methods for using reporter mycobacteriophage (RM) and p-nitro-.alpha.-acetylamino-.beta.-hydroxy-propiophenone (NAP) to identify TB complex mycobacteria and distinguish these species from MOTT. RM-infected MOTT show little or no reduction in signal when treated with NAP. In contrast, TB complex mycobacteria infected with RM are distinguishable from RM-infected MOTT by a reduction in signal with NAP treatment.

Identification of mycobacterium tuberculosis complex species

Mycobacteriophage DS6A has been characterized and found to specifically infect all species of the TB complex, without any detectable infection of mycobacteria species other than those of the TB complex. DNA sequence analysis revealed several potential open reading frames, including one encoding a protein analogous to gp37 of mycobacteriophage L5 and a second encoding a protein with significant homology to the S. coelicolor DNA polymerase .beta. subunit. Based on the DNA sequence analysis, cloning sites can be identified for insertion of reporter genes, making DS6A useful as a reporter phage for specific detection and identification of species of the TB complex.

DNA polymerase III .beta.-subunit from mycobacteriophage DS6A

Methods for multiplex amplification of target nucleic acid sequences using a single pair of primers. Defined sequences are appended to the ends of multiple target sequences as part of the amplification reaction so that no steps in addition to amplification are required. The target sequences with the appended defined sequences need not be isolated prior to amplification. In one embodiment for coamplification of two target sequences, a sequence corresponding to a terminal segment of the first target sequence is appended to one end of the second target sequence and a sequence corresponding to a terminal segment of the second target sequence is appended to one end of the first target sequence. Amplification of the two targets then requires only a single pair of primers. Alternatively, a single defined sequence may be appended to the 5' and 3' ends of any number of selected targets. All such modified target sequences may then be amplified using a single pair of primers which hybridize to the defined end-sequences.

Simultaneous amplification of multiple targets

It has been found that certain glycoproteins, particularly mucins, are inhibitors of nucleic acid amplification reactions and that inhibition of the amplification reaction is associated with partial degradation of the carbohydrate chain. Partial degradation of the carbohydrate of a non-inhibitory glycoprotein renders it inhibitory, and partial degradation of the carbohydrate of a slightly inhibitory glycoprotein makes it more inhibitory. Sample processing prior to amplification may contribute to partial degradation of the carbohydrate chains of the glycoproteins which are present and increase their inhhibitory effect. In contrast, complete removal of the carbohydrate significantly reduces or completely eliminates the inhibitory effect. Methods for reducing or eliminating glycoprotein-associated inhibition of nucleic acid amplification reactions are also disclosed.

Methods for reducing inhibition of nucleic acid amplification reactions

Mycobacteriophage specific for the mycobacterium tuberculosis complex

Methods for processing samples which may contain mycobacteria which are compatible with both conventional culturing techniques and nucleic acid analysis. It has been found that the harsh chemical treatment previously thought necessary to obtain efficient lysis can be eliminated without loss of lysis efficiency, thereby eliminating reagents which may inhibit subsequent nucleic acid-based reactions. Heat alone is sufficient to lyse mycobacteria, even in buffers which do not contain detergents, chelators, enzymes, etc. Residual reagents introduced by conventional sample processing methods for culture can be successfully removed from the processed pellet without significant loss of microorganisms by at least two washings with saline, water, or buffers compatible with nucleic acid analysis and appropriate centrifugation.

Sample processing method for Mycobacterium tuberculosis

Genus- and species-specific oligonucleotide probes derived from the M. paratuberculosis 70 kD heat shock protein gene sequence. The probes are useful for detecting Mycobacteria and for identifying specific species of Mycobacteria.

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Raleigh, NC, United States of America

Michael C Little