Gel Microdrops in Genetic Analysis

Abstract

The invention provides methods of nucleic acid analysis. Such methods entail forming a population of gel microdrops encapsulating a population of biological entities, each entity comprising a nucleic acid, whereby at least some microdrops in the population each encapsulate a single entity. The population of gel microdrops is then contacted with a probe under conditions whereby the probe specifically hybridizes to at least one complementary sequence in the nucleic acid in at least one gel microdrop. At least one gel microdrop is then analyzed or detected. The biological entities can be cells, viruses, nuclei and chromosomes.

1 . A method of nucleic acid analysis, comprising
 forming a population of gel microdrops encapsulating a population of biological entities, each entity comprising a nucleic acid, whereby at least some microdrops in the population each encapsulate a single biological entity;   contacting the population of gel microdrops with a probe under conditions whereby the probe specifically hybridizes to at least one complementary sequence in a nucleic acid within an encapsulated biological entity in a gel microdrop that contains a single biological entity; and   obtaining a digital image of the encapsulated biological entity comprising the hybridized probe.   
     
     
         2 . The method of  claim 1 , wherein the biological entities are selected from the group consisting of cells, viruses, nuclei, mitochondria, and chloroplasts. 
     
     
         3 . The method of  claim 1 , wherein the biological entities are not fixed chemically before the contacting step. 
     
     
         4 . The method of  claim 1 , further comprising amplifying one or more encapsulated nucleic acid species before the contacting step. 
     
     
         5 . The method of  claim 1 , further comprising digesting the gel of at least one isolated microdrop to isolate a nucleic acid molecule within the microdrop after obtaining the digital image. 
     
     
         6 . The method of  claim 1 , further comprising denaturing the nucleic acid in the microdrops before the contacting step. 
     
     
         7 . The method of  claim 1 , wherein the gel is agarose and the method further comprises crosslinking hydroxyl groups in the agarose with each other and with hydroxyl groups in the biological entity before the contacting step. 
     
     
         8 . The method of  claim 7 , wherein the hybridization is performed at a temperature of over 68° C. or in the presence of a form amide concentration greater than 20%. 
     
     
         9 . The method of  claim 1 , wherein the probe is a nucleic acid. 
     
     
         10 . The method of  claim 1 , further comprising labeling microdrops containing the biological entity with a label that does not label empty microdrops.