System and method for nucleic acid amplification

Abstract

An embodiment of a method for generating a population of amplified concatamer products is described that comprises amplifying a template nucleic acid molecule using a first nucleic acid primer immobilized on a bead substrate and a second nucleic acid primer in solution to generate a population of substantially identical copies of the template nucleic acid molecule immobilized on the bead substrate; and amplifying the population of substantially identical copies of the template nucleic acid molecule using a concatamer primer that comprises a first region complementary to an end region of the population of substantially identical copies of the template nucleic acid molecule and a second region to generate a population of immobilized concatamer products of the substantially identical copies of the template nucleic acid molecule.

1 .- 19 . (canceled) 
     
     
         20 . A system for generating a population of amplified concatamer products, comprising a means for performing a method for generating a population of amplified concatamer products, comprising:
 amplifying a template nucleic acid molecule using a first nucleic acid primer immobilized on a solid phase substrate and a second nucleic acid primer in solution to generate a population of substantially identical copies of the template nucleic acid molecule immobilized on the solid phase substrate;   amplifying the population of substantially identical copies of the template nucleic acid molecule using a concatamer primer that comprises a first region complementary to a sequence of an end region of the population of substantially identical copies of the template nucleic acid molecule and a second region to generate a population of immobilized concatamer products of the substantially identical copies of the template nucleic acid molecule.   
     
     
         21 . The system of  claim 20 , wherein,
 each of the population of immobilized concatamer products comprise three or more concatamer copies of one of the substantially identical copies of the template nucleic acid molecule.   
     
     
         22 . The system of  claim 20 , wherein,
 the end region of the population of substantially identical copies of the template nucleic acid molecule comprises an adaptor region.   
     
     
         23 . The system of  claim 20 , wherein,
 the second region of the concatamer primer is complementary to the first nucleic acid primer immobilized on the solid phase substrate.   
     
     
         24 . The system of  claim 20 , wherein,
 the solid phase substrate which is fabricated from a material selected from the group consisting of cellulose, a cellulose derivative, an acrylic resin, glass, a silica gel, polystyrene, gelatin, polyvinyl pyrrolidone, a co-polymer of vinyl and acrylamide, a polystyrene cross-linked with divinylbenzene, polyacrylamide, a latex gel, polystyrene, dextran, rubber, silicon, a plastic, nitrocellulose, a natural sponge, a silica gel, control pore glass, a metal, a cross-linked dextran, and agarose gel.   
     
     
         25 . The system of  claim 20 , wherein,
 the template nucleic acid molecule has a length of up to 1000 nucleic acid residues.   
     
     
         26 . The system of  claim 20 , wherein,
 the template nucleic acid molecule comprises one or more additional functional elements selected from the group consisting of a primer sequence for amplification or sequencing methods, a quality control element, an adapter element, and a unique identifier.   
     
     
         27 . The system of  claim 26 , wherein,
 the unique identifier is a multiplex identifier (MID).   
     
     
         28 . The system of  claim 27 , wherein,
 the MID identifies a feature of a sample, wherein the feature is an experimental condition, a treatment, a species, an individual subject, a tissue type, or a cell type.   
     
     
         29 . The system of  claim 28 , wherein,
 the template nucleic acid molecule comprises more than one MID.   
     
     
         30 . The system of  claim 28 , wherein,
 a position of the MID in the template nucleic acid molecule is known relative to a feature of the template nucleic acid molecule or to an adaptor element coupled to the template molecule.   
     
     
         31 . The system of  claim 30 , wherein,
 the feature of the template nucleic acid molecule is a specific nucleic acid residue in the molecule, a recognizable sequence marker, or one or more primer elements.   
     
     
         32 . The system of  claim 31 , wherein the recognizable sequence marker is a Key element. 
     
     
         33 . The system of  claim 32 , wherein,
 the Key element or the one or more primer elements each has a known sequence composition.   
     
     
         34 . The system of  claim 20 , wherein,
 amplifying the population of substantially identical copies of the template nucleic acid molecule using a concatamer primer occurs via polymerase chain reaction (PCR) or emulsion PCR (emPCR).   
     
     
         35 . The system of  claim 20 , wherein,
 the solid phase substrate is a bead.   
     
     
         36 . The system of  claim 35 , wherein,
 the bead has a diameter of between about 1.4 μm and about 20 μm.   
     
     
         37 . The system of  claim 20 , wherein,
 the solid phase substrate is a planar substrate selected from the group consisting of a slide type substrate, a semiconductor chip comprising well type structures, a microwell array, a waveguide type reaction substrate, and a PTP array.