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Preparation of nucleic acid samplesRelated Patent Categories: Chemistry: Molecular Biology And Microbiology, Measuring Or Testing Process Involving Enzymes Or Micro-organisms; Composition Or Test Strip Therefore; Processes Of Forming Such Composition Or Test Strip, Involving Nucleic AcidPreparation of nucleic acid samples description/claimsThe Patent Description & Claims data below is from USPTO Patent Application 20070009939, Preparation of nucleic acid samples. Brief Patent Description - Full Patent Description - Patent Application Claims
RELATED APPLICATIONS [0001] This application claims the benefit of U.S. Provisional Application No. 60/162,739, filed Oct. 30, 1999, and U.S. Provisional Application No. 60/191,345, filed Mar. 22, 2000, both of which are fully incorporated herein by reference for all purposes BACKGROUND OF THE INVENTION [0002] Novel methods for enriching and labeling nucleic acids are needed For example, gene expression analysis techniques often employ isolation and labeling of ribonucleic acid (RNA) Because of the interest in identifying protein-encoding genes and in examining gene expression levels, it is often desirable to purify or enrich the messenger RNA (mRNA) The poly-adenine 3'-terminus (poly-A tail) of mRNA from eukaryotic cells can be used as a handle to bind to poly(dT) oligonucleotides, and this method is widely used to identify, purify and or label eukaryotic mRNA However, because prokaryotic mRNA generally lacks poly-A tails, there is a need for alternative methods for purifying and labeling mRNA samples which do not rely on the existence of a poly-A tail SUMMARY OF THE INVENTION [0003] The presently claimed invention provides methods of preparing a nucleic acid sample for analysis [0004] In a first embodiment, the presently claimed invention provides a method of preparing a nucleic acid sample for analysis comprising enriching for a population of interest within a mixed population of nucleic acids by contacting the nucleic acid sample with a bait molecule The bait molecule is capable of complexing specifically to unwanted target sequences within the nucleic acid sample, but is incapable of complexing with sequences from the population of interest The bait molecule is contacted with the target sequences forming bait target complexes which are then specifically removed from the nucleic acid sample The remaining enriched population of interest is then fragmented and a signal moiety is attached to the fragments [0005] In a second embodiment, the presently claimed invention provides a method of enriching for a population of interest within a mixed population of nucleic acids by contacting the nucleic acid with a bait molecule The bait molecule is capable of complexing specifically to unwanted target sequences within the nucleic acid sample, but is incapable of complexing with sequences from the population of interest The bait molecule is contacted with the target sequences forming bait target complexes which are then specifically removed from the nucleic acid sample Thus enriching for the population of interest [0006] In a third embodiment, the presently claimed invention provides a compound having the formula n-S-acetyl-PEO-sig where n is a polynucleotide, S is a thiol group, acetyl is an acetyl functional group, PEO is polyethelene oxide, and sig is a signal moiety [0007] In a fourth embodiment, the presently claimed invention provides a method for labeling a polynucleotide comprising contacting the polynucleotide with a PEO-iodoacetyl conjugated to a signal moiety under conditions such that the PEO-iodoacetyl will attach to said nucleotide [0008] In a fifth embodiment, the presently claimed invention provides a method for labeling a polynucleotide comprising contacting the polynucleotide with a reactive thiol group to form a thiolated polynucleotide and contacting the thiolated polynucleotide with either a signal moiety capable of reacting with said thiolated polynucleotide under appropriate conditions such that said signal moiety is attached to said polynucleotide [0009] In a sixth embodiment, the presently claimed invention provides a method for labeling prokaryotic mRNA comprising obtaining a population of RNA from a prokaryotic organism, enriching the population for mRNA by exposing the population to a plurality of DNA bait molecules which are complementary to at least a portion of the stable RNA in said population under such conditions as to allow for the formation of DNA RNA hybrids, exposing the DNA RNA hybrids to RNAse H to remove the RNA from said DNA RNA hybrids, exposing the remaining DNA to DNase I to remove the DNA, thus producing an enriched population of mRNA, fragmenting the enriched mRNA to form mRNA fragments, exposing the mRNA fragments to (--S-ATP and T4 kinase to produce reactive thiol groups at the 5' ends of the mRNA fragments, and exposing the thiolated mRNA fragments to PEO-Iodoacetyl-Biotin such that a stable thio-ether bond is formed between said thiolated mRNA fragments and said PEO-Iodoactyl-Biotin BRIEF DESCRIPTION OF THE DRAWINGS [0010] FIG. 1 depicts a schematic illustration of one embodiment of the presently claimed invention in which target sequences are depleted from a mixed population of nucleic acids [0011] FIG. 2 depicts a schematic illustration of one embodiment of the presently claimed invention wherein target sequences are complexed to a bait molecule and then specifically digested [0012] FIG. 3 depicts a schematic illustration of one embodiment of the presently claimed invention wherein bait molecules are synthesized by reverse transcriptase using target molecules as templates [0013] FIG. 4 depicts a schematic illustration of one embodiment of the presently claimed invention in which bait molecules are recycled to initiate repeated rounds of target depletion [0014] FIG. 5 depicts a schematic illustration of one embodiment of the presently claimed invention in which sequences from an enriched population of interest are labeled [0015] FIG. 6 is an image of unenriched RNA hybridized to a microarray [0016] FIG. 7 is an image of enriched RNA hybridized to a microarray [0017] FIG. 8 is a gel image showing the depletion of 23S and 16S RNA using the methods of the presently claimed invention [0018] FIG. 9 is a gel image showing the depletion of 23S and 16S RNA using the methods of the presently claimed invention including bait cycling [0019] FIG. 10 is an image of a Northern transfer showing the amount of mRNA transcript present during each round of rRNA depletion during a bait cycling experiment [0020] FIG. 11 is a gel image of biotin labeled mRNA fragments Continue reading about Preparation of nucleic acid samples... Full patent description for Preparation of nucleic acid samples Brief Patent Description - Full Patent Description - Patent Application Claims Click on the above for other options relating to this Preparation of nucleic acid samples patent application. ###  How KEYWORD MONITOR works... a FREE service from FreshPatents1. Sign up (takes 30 seconds). 2. Fill in the keywords to be monitored. 3. Each week you receive an email with patent applications related to your keywords. Start now! - Receive info on patent apps like Preparation of nucleic acid samples or other areas of interest. ### Previous Patent Application: Pgc-1beta, a novel pgc-1 homologue and uses therefor Next Patent Application: Primers, probes and reference plasmid for detection of meat adulteration Industry Class: Chemistry: molecular biology and microbiology ### FreshPatents.com Support Thank you for viewing the Preparation of nucleic acid samples patent info. 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