Single-Point Genome Signature Tags

Abstract

Disclosed is a method for analyzing the organismic complexity of a sample through analysis of the nucleic acid in the sample. In the disclosed method, through a series of steps, including digestion with a type II restriction enzyme, ligation of capture adapters and linkers and digestion with a type IIS restriction enzyme, genome signature tags are produced. The sequences of a statistically significant number of the signature tags are determined and the sequences are used to identify and quantify the organisms in the sample. Various embodiments of the invention described herein include methods for using single point genome signature tags to analyze the related families present in a sample, methods for analyzing sequences associated with hyper- and hypo-methylated CpG islands, methods for visualizing organismic complexity change in a sampling location over time and methods for generating the genome signature tag profile of a sample of fragmented DNA.

Description

[0001]The present application is a continuation-in-part of U.S. patent application Ser. No. 10 / 113,916 filed on Apr. 1, 2002, the entire contents of which are incorporated by reference.[0002]This invention was made with Government support under contract number DE-AC02-98CH10886, awarded by the U.S. Department of Energy. The Government has certain rights in the invention.BACKGROUND OF THE INVENTION[0003]Research toward improving the ability to detect and identify microbial genomes has risen to prominence in part because of its application to defense against bio-terrorism and biological warfare. The steadily rising numbers of sequenced microbial genomes is also giving impetus to studies of natural populations in soil and water, with a view to understanding community composition and dynamics. Understanding of microbial community dynamics is also important in the field of infectious disease health care, particularly in view of the rise in the prevalence of antibiotic resistant strains o...

AI Technical Summary

Benefits of technology

The present invention provides a method for analyzing the nucleic acid of a sample to determine its organismic complexity and to track changes in organismic complexity over time. This is done by converting the nucleic acid of the sample to double-stranded DNA and then digesting it with a type II restriction enzyme to generate a plurality of DNA fragment species. These fragments are then captured with a specific binding pair and incubated with a duplex linker and a type IIS restriction enzyme to create recognition sequences for the type IIS enzyme. These recognition sequences, still attached to a solid support, are then analyzed using a type IIS restriction enzyme. This method provides a versatile tool for analyzing organismic complexity and can be used with various sample types and DNA fragmentation methods.

Problems solved by technology

(1991) Biotechniques 31:930-936), but utility is limited to analysis of relatively small fragments.

While VGS can provide a limited global survey for the presence or absence of a particular DNA fragment, it cannot directly identify novel sequences.

In addition, it would be unlikely that the methods would be applicable to identifying and quantitating the multiplicity of organisms in a natural, e.g., environmental, sample.

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