Multidentate Arrays

Abstract

A method of evaluating for the presence of a target polynucleotide in a sample, using an addressable array of multiple polynucleotide probes linked to a substrate. The sample is exposed to the array and a set of polynucleotide target probes, such that target polynucleotide which may be present will bind to a predetermined feature of the array through multiple target probes of the set by forming at respective target regions on a target molecule, simultaneous hybrids with anti-target regions of the multiple target probes. A binding pattern on the array is observed and the presence of the target polynucleotide evaluated based on the observed binding pattern. Kits using such arrays, and methods for selecting target probes are further provided.

1 . A method of evaluating for the presence of a target polynucleotide in a sample, using an addressable array of multiple polynucleotide probes linked to a substrate, the method comprising:
 (a) exposing the sample to the array and a set of polynucleotide target probes, such that target polynucleotide which may be present will bind to a predetermined feature of the array through multiple target probes of the set by forming at respective target regions on a target molecule, simultaneous hybrids with anti-target regions of the multiple target probes; and   (b) observing a binding pattern on the array and evaluating the presence of the target polynucleotide based on the observed binding pattern.   
     
     
         2 . A method according to  claim 1  wherein the target regions are of different sequence, and the set of target probes has at least two target probes with different sequence anti-target regions. 
     
     
         3 . A method according to  claim 1  wherein the presence of multiple different target polynucleotides is evaluated, and wherein the sample is exposed to multiple different sets of target probes such that each of the different target polynucleotides which may be present will bind to a corresponding predetermined features of the array through multiple target probes of a corresponding set by forming at respective target regions, simultaneous hybrids with the multiple probes of the corresponding set. 
     
     
         4 . A method according to  claim 3  wherein the respective target regions on each of the different targets are of different sequence, and each set of target probes has at least two target probes with different sequence anti-target regions. 
     
     
         5 . A method according to  claim 2  wherein the set of target probes has at least three polynucleotide target probes with different sequence anti-target regions. 
     
     
         6 . A method according to  claim 1  wherein the target probes are linked to the substrate at the predetermined feature prior to exposing the sample. 
     
     
         7 . A method according to  claim 1  wherein:
 the target probes are not linked to the substrate, and also include anti-capture regions; 
 the sample is also exposed to a set of capture probes, which have capture regions which will hybridize with respective anti-capture regions; 
 so that multiple molecules of target polynucleotide which may be present will each indirectly bind to the predetermined feature by the anti-target regions of the multiple target probes forming the simultaneous hybrids with the respective target regions and by the anti-capture regions hybridizing with the capture regions of the capture probes. 
 
     
     
         8 . A method according to  claim 1  wherein:
 the target probes are not linked to the substrate, and also include anti-capture regions; and 
 the predetermined feature of the array includes a set of capture probes linked thereto, and which have capture regions which will hybridize with respective anti-capture regions; 
 so that multiple molecules of target polynucleotide which may be present will each indirectly bind to the predetermined feature by the anti-target regions of the multiple target probes forming the simultaneous hybrids with the respective target regions and by the anti-capture regions hybridizing with the capture regions of the capture probes. 
 
     
     
         9 . A method according to  claim 8  wherein the target regions are of different sequence, and the set of target probes has at least two target probes with different sequence anti-target regions. 
     
     
         10 . A method according to  claim 9  wherein the anti-capture regions of the set are of the same sequence. 
     
     
         11 . A method according to  claim 2  wherein the target regions differ in sequence from one another by at least two nucleotides, and the anti-target regions of the set differ from one another by at least two nucleotides. 
     
     
         12 . A method according to  claim 2  wherein the target regions differ in sequence from one another by at least four nucleotides, and the anti-target regions of the set differ from one another by at least four nucleotides. 
     
     
         13 . A method according to  claim 1  wherein, based on the observed binding pattern, target polynucleotide is determined to have been present in the sample. 
     
     
         14 . An apparatus for evaluating for the presence of a target polynucleotide in a sample, comprising:
 (a) an addressable array of multiple polynucleotide probes linked to the substrate:   (b) a set of polynucleotide target probes which may or may not be linked to the substrate as part of the array, such that target polynucleotide which may be present in a sample exposed to the array will bind to a predetermined feature of the array through multiple target probes of the set by forming at respective target regions on a target molecule, simultaneous hybrids with anti-target regions of the multiple target probes.   
     
     
         15 . An apparatus according to  claim 14  wherein the target regions are of different sequence, and the set of target probes has at least two target probes with different sequence anti-target regions. 
     
     
         16 . An apparatus according to  claim 14  additionally comprising multiple different sets of target probes such that each of the different target polynucleotides which may be present will bind to a corresponding predetermined feature of the array through multiple target probes of a corresponding probe set by forming at respective target regions, simultaneous hybrids with the multiple probes of the corresponding probe set. 
     
     
         17 . An apparatus according to  claim 16  wherein the anti-target regions of the multiple target probes of the sets are all of different sequence. 
     
     
         18 . An apparatus method according to  claim 15  wherein the set of target probes has at least three target probes with different sequence anti-target regions. 
     
     
         19 . An apparatus according to  claim 14  wherein the target probes are linked to the substrate at the predetermined feature. 
     
     
         20 . An apparatus according to  claim 14  wherein:
 the target probes also include anti-capture regions; 
 the apparatus additionally comprises a set of capture probes, which have capture regions which will hybridize with respective anti-capture regions; 
 so that multiple molecules of target polynucleotide which may be present will each indirectly bind to the predetermined feature by the anti-target regions of the multiple target probes forming the simultaneous hybrids with the respective target regions and by the anti-capture regions hybridizing with the capture regions of the capture probes.