Efficient optical analysis of polymers using arrays of nanostructures

Abstract

The invention is directed to methods and apparatus for detecting sequences of optical signals from parallel reactions on an array of nanostructures, such as nanopores, nanowells, or nanoparticles. In accordance with the invention, an array of nanostructures is provided, each nanostructure comprising a reaction site and each capable of confining a reaction that generates a sequence of optical signals, and the nanostructures of the array being arranged in clusters each comprising a number of nanostructures. Each different cluster is disposed within a different resolution limited area and the number of nanostructures in each cluster is either greater than one or a random variable with an average value greater than zero. Optical signals from reactions in the nanostructures are detected by an optical system operatively associated with the array.

What is claimed is: 
     
         1 . A device for analyzing polymers each having optical labels attached to a sequence of monomers, the device comprising:
 a nanopore array separating a first chamber and a second chamber, wherein nanopores of the nanopore array each connect the first chamber and the second chamber and are arranged in clusters such that each different cluster of nanopores is disposed within a different resolution limited area; and   a polymer translocating system for moving polymers in the first chamber to the second chamber through the nanopores of the nanopore array;   wherein said clusters are arranged in a rectilinear array or in a hexagonal array.   
     
     
         2 . The device of  claim 1  wherein each of said clusters comprises a plurality of nanopores or each of said clusters comprises a number of nanopores which is a random variable with an average value greater than zero. 
     
     
         3 . The device of  claim 1  wherein said polymers are polynucleotides and wherein said detection system determines numbers of functional nanopores within each of said resolution limited areas from said collected optical signals and varies an electrical field across said nanopore array to maximize a rate of sequence determination by said nanopore array. 
     
     
         4 . A method of analyzing polymers each having a sequence of optical labels comprising:
 providing a nanopore array wherein each nanopore has a bore capable of providing fluid communication between a first chamber and a second chamber, and the nanopore array having at least one resolution limited area containing a plurality of nanopores;   translocating polymers through nanopores of the nanopore array;   collecting and integrating optical signals from polymers translocating through nanopores in each of the resolution limited areas during a predetermined interval to obtain an integrated signal for each of the resolution limited areas; and   selecting a polymer concentration and/or polymer flux to maximize sequencing throughput of the nanopore array.   
     
     
         6 . The method of  claim 4  wherein said polymers are polynucleotides and said step of selecting comprises adjusting said polymer flux to maximize sequencing throughput by varying an electrical field strength across said nanopore array. 
     
     
         7 . A device for analyzing polymers each having a sequence of optical labels comprising:
 a solid phase membrane separating a first chamber and a second chamber, the solid phase membrane having an array of apertures each connecting the first chamber and the second chamber, the apertures of the array being arranged in clusters each having a plurality of apertures and each different cluster being disposed within a different resolution limited area; and   protein nanopores immobilized in the apertures, the immobilized protein nanopores having an active fraction wherein each immobilized protein of the active fraction is capable of translocating a polymer from the first chamber to the second chamber through a bore; and   wherein said polymers comprise polynucleotides and wherein said detection system determines numbers of functional nanopores within each of said resolution limited areas from said collected optical signals and varies an electrical field across said nanopore array to maximize a rate of determining said sequences of optical labels by said nanopore array.