Method for analyzing base sequence of nucleic acid

Abstract

A method for identifying an unknown base sequence present in a target single-stranded nucleic acid utilizing a probe array in which single-stranded nucleic acid probes are arranged as isolated spots on a substrate, where each probe has a base sequence complementary to one of the plural base sequences expected to be the unknown base sequence, and a fluorescence pattern of a sample on the probe array is compared with template patterns to identify the base sequence of the sample.

1 - 8 . (canceled)  
     
     
         9 . A method for identifying an unknown base sequence present in a target single-stranded nucleic acid comprising the steps of: 
 (a) preparing a probe array in which more than one of single-stranded nucleic acid probes are arranged as isolated spots on a substrate;    (b) reacting a first sample containing a single stranded nucleic acid, which has a base sequence fully complementary to a base sequence of one of the single-stranded nucleic acid probes and is fluorescence-labeled, with the probe array under such conditions that single-stranded nucleic acids complementary to each other form a double-stranded nucleic acid, removing the unreacted labeled single-stranded nucleic acid, and obtaining a two-dimensional fluorescent image of the array surface as a first template pattern of the first sample;    (c) performing the same operation as the step (b) for each of remaining single-stranded nucleic acid probes, and obtaining template patterns of No. 2 to No. n (n≧2) each as a two-dimensional fluorescent image of the array surface when one of the remaining single-stranded nucleic acid probes on the array forms a double-stranded nucleic acid with a single-stranded nucleic acid fully complementary to the respective base sequence;    (d) reacting the probe array with a second sample containing the target single-stranded nucleic acid under the same condition when the template patterns are obtained, and obtaining a two dimensional fluorescent image of the array surface as a sample pattern by the same operation as step (b); and    (e) comparing the sample pattern with n pieces of template patterns obtained in the steps (b) and (c), wherein the sample pattern is recognized as two-dimensional image information without using data conversion based on a relationship between a probe and fluorescent intensity, and identifying a template pattern showing substantially the same pattern as the sample pattern to identify the base sequence of the single-stranded nucleic acid used for the preparation of the identified template pattern as the unknown base sequence of the target single-stranded nucleic acid.    
     
     
         10 . The method according to  claim 9 , further comprising a treatment to compensate a difference in the sample pattern which is caused by a misplaced material on a surface of the substrate or an artifact during a hybridizing reaction when the patterns are compared in step (e).