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 with agarase to isolate a nucleic acid molecule within the microdrop after the isolating or detecting step.  
   
   
       6 . The method of  claim 1 , further comprising denaturing the nucleic acids 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 formamide 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.  
   
   
       11 - 35 . (canceled)  
   
   
       36 . A method of clinical analysis comprising: 
 encapsulating biological entities in gel microdrops, wherein said biological entities are from a tissue sample from a patient;    storing the microdrops for at least an hour; and    performing a clinical analysis on said encapsulated biological entities.    
   
   
       37 . The method of  claim 36 , wherein the microdrops are stored for at least six months.  
   
   
       38 . The method of  claim 36 , wherein the clinical analysis is performed on chromosomes from the microdrops.  
   
   
       39 . The method of  claim 36 , wherein the clinical analysis comprises 
 contacting the microdrops with a probe that is complementary to a nucleic acid molecule, the presence of which is indicative of a disease state and;    diagnosing the existence or prognosis of the disease from the hybridization or lack of hybridization of the probe to a nucleic acid molecule within an encapsulated cell.    
   
   
       40 . The method of  claim 39 , wherein the disease is a disease associated with a genetic defect.  
   
   
       41 . The method of  claim 39 , wherein the disease is cancer.  
   
   
       42 . The method of  claim 39 , wherein the probe is complementary to at an exonic segment of a gene.  
   
   
       43 . The method of  claim 39 , wherein the probe is complementary to at least two successive exons of a gene and specifically hybridizes to RNA expressed from the gene.  
   
   
       44 . The method of  claim 39 , wherein the disease comprises the presence of a virus.  
   
   
       45 . The method of  claim 39 , wherein the virus is a retrovirus.