Collecting and processing complex macromolecular mixtures

Abstract

This document provides methods and materials involved in collecting and processing complex macromolecular mixtures (e.g., stool samples). For example, stool collection devices, buffers for stabilizing nucleic acid and polypeptides present in stool, and kits for using sequence-specific capture probes (e.g., nucleic acid sequences designed to hybridize with particular target nucleic acids) to capture target nucleic acids directly from complex macromolecular mixtures (e.g., stool samples) without the need to perform prior steps to enrich, isolate, or purify the nucleic acid component are provided.

1 . A device for a stool sample, wherein said device comprises a container for housing a buffer and collected stool sample, and a lid for closing said buffer and collected stool sample within said container, wherein said lid comprises a stool handling extension and a sealable port. 
     
     
         2 . The device of  claim 1 , wherein said container comprises a piercable membrane configured to retain said buffer within said container. 
     
     
         3 . The device of  claim 1 , wherein said container is a tube. 
     
     
         4 . The device of  claim 1 , wherein said lid is configured to engage said container via threads. 
     
     
         5 . The device of  claim 1 , wherein said stool handling extension comprises a spatula for scooping stool. 
     
     
         6 . The device of  claim 1 , wherein said stool handling extension is removably attached to said lid. 
     
     
         7 . A method for collecting a stool sample with a device comprising a container for housing a buffer and collected stool sample, and a lid for closing said buffer and collected stool sample within said container, wherein said lid comprises a stool handling extension and a sealable port, wherein said method comprises:
 (a) handling said lid to collect said stool sample from stool via said stool handling extension, and   (b) attaching said lid onto said container, thereby placing said stool sample within said container.   
     
     
         8 . A buffer comprising between about 100 to about 300 mM of CDTA, between about 400 and about 600 mM of tris hydrochloride, between about 5 and about 15 mM of NaCl, and between about 0 and about 0.075% of a zwitterionic reagent. 
     
     
         9 . A method for stabilizing nucleic acid and polypeptides within a stool sample, wherein said method comprises contacting said stool sample with a buffer comprising between about 100 to about 300 mM of CDTA, between about 400 and about 600 mM of tris hydrochloride, between about 5 and about 15 mM of NaCl, and between about 0 and about 0.075% of a zwitterionic reagent. 
     
     
         10 . A method for obtaining target nucleic acid from a complex macromolecular mixture without performing a prior nucleic acid extraction or nucleic acid isolation step, wherein said method comprises:
 (a) contacting said complex macromolecular mixture with a sequence-specific capture probe comprising one member of a binding pair to form a probe/target nucleic acid complex if said complex macromolecular mixture comprises said target nucleic acid,   (b) isolating said probe/target nucleic acid complex if said probe/target nucleic acid complex is formed in (a).   
     
     
         11 . The method of  claim 10 , wherein said isolating comprises solid phase isolation. 
     
     
         12 . The method of  claim 10 , wherein said isolating comprises solution-based isolation. 
     
     
         13 . The method of  claim 10 , wherein said isolating comprises contacting said probe/target nucleic acid complex with magnetic material comprising another member of said binding pair to form a magnetic probe/target nucleic acid complex if said probe/target nucleic acid complex is formed, and applying magnetic force to isolate said magnetic probe/target nucleic acid complex from said complex macromolecular mixture if said magnetic probe/target nucleic acid complex is formed. 
     
     
         14 . The method of  claim 10 , wherein said complex macromolecular mixture is a stool sample. 
     
     
         15 . The method of  claim 10 , wherein said method is performed without a prior phenol/chloroform extraction. 
     
     
         16 . The method of  claim 10 , wherein said one member of said binding pair is biotin. 
     
     
         17 . The method of  claim 10 , wherein said another member of said binding pair is streptavidin. 
     
     
         18 . The method of  claim 13 , wherein said magnetic material is a bead. 
     
     
         19 . The method of  claim 13 , wherein said method comprises isolating said target nucleic acid from said isolated magnetic probe/target nucleic acid complex.