Device and method for producing a replicate or derivative from an array of molecules, and applications thereof

Abstract

A method of producing a replicate or derivative of an array of molecules, the array having a spatial arrangement of separate samples of molecules, includes creating, for each sample, at least one spatially limited effective area which is separate from the effective areas of the other samples, a surface, provided with a binding adapter or binding properties, of a carrier bordering on the effective areas. The molecules are amplified by means of amplifying agents in the effective areas for creating replicates or derivatives of the samples. The replicates or derivatives of the samples are bound to the carrier by means of the binding adapter or the binding properties, so that a spatial arrangement of the replicates or derivatives of the samples on the carrier corresponds to the spatial arrangement of the samples in the array. The carrier having the copies of the samples is removed from the array.

1 . A method of producing a replicate or derivative of an array of molecules method comprising:
 providing the array comprising a spatial arrangement of separate samples of the molecules,   creating, for each sample of the array, one or more spatially limited effective areas which is/are separate from spatially limited effective areas of the other samples, wherein the spatially limited effective areas provide a spatial arrangement of the samples of the molecules, and wherein a surface of a carrier, provided with one or more binding adapters or binding properties, borders on the effective areas;   amplifying the molecules in the spatially limited effective areas via of amplifying agents in the effective areas and creating replicates or derivatives of every one of the samples of molecules;   binding the replicates or derivatives of the samples of molecules to the surface of the carrier via the binding adapter or the binding properties, wherein a spatial arrangement of the replicates or derivatives of the samples of molecules on the surface of the carrier corresponds to the spatial arrangement of the samples of molecules in the array; and   removing the carrier comprising on the surface the replicates or derivatives of the samples of molecules from the array.   
     
     
         2 . The method as claimed in  claim 1 , wherein the spatially limited effective areas are spatially limited amplifying agent areas which are optionally defined, at least in part, by micro- or nanostructures within an array substrate of the array or within the carrier, wherein the micro- or nanostructures optionally comprise an unordered matrix or are optionally based on an ordered three-dimensional substrate. 
     
     
         3 . The method as claimed in  claim 2 , wherein the spatially limited effective areas are recesses,
 the amplifying agent is introduced into the recesses, and the recesses are closed off by the carrier, or   wherein the spatially limited amplifying agent areas are separated, at least in part, by phase boundaries between two liquids, a liquid and a gas, or a physical boundary,   and wherein, optionally, producing the at least one spatially limited amplifying agent area for each sample comprises providing the samples in separate droplets of liquid which comprise the amplifying agent and which are fixed, in the spatial arrangement, on the array, a thinner-bodied liquid being arranged between the droplets of liquid, and, optionally, arranging the carrier in relation to the array such that the surface of the carrier, provided with the binding adapter, faces the droplets of the liquid.   
     
     
         4 . The method as claimed in  claim 2 , wherein producing at least one spatially limited amplifying agent area comprises providing the carrier comprising at least one recess which is associated with each sample and comprises the binding adapter arranged therein, introducing the amplifying agent into the recesses, and closing off the recesses via the array substrate, so that the samples are exposed to the amplifying agent area. 
     
     
         5 . The method as claimed in  claim 2 , wherein the array is a sequencer chip or a nanowell plate. 
     
     
         6 . The method as claimed in  claim 1 , wherein
 the process of binding the replicates or derivatives to the carrier is performed simultaneously with the amplification, or   the spatial limitation of the effective area is that the binding adapters are present on the carrier, as complementary primers, in the form of a primer array that may comprise a regular or irregular distribution of spots, the spot size and spot density on the carrier being equal to or smaller than that on the array.   
     
     
         7 . The method as claimed in  claim 1 , wherein the spatial limitation of the effective area is effected by applying an energy field. 
     
     
         8 . The method as claimed in  claim 1 , wherein the molecules of the samples are bound to particles. 
     
     
         9 . The method as claimed in  claim 1 , wherein the array of molecules is a non-synthetic array of biomolecules, or the molecules are single- or double-stranded oligonucleotides, polynucleotides, DNA or synthetic molecules analogous to DNA (PNA), or the array comprises a sequencing process for deriving the genome, a sequencing process for deriving the transcriptome, a process of sequencing RNA, mRNA, tRNA, siRNA, or a process of sequencing mutations and variations, or
 via amplifying and binding to the carrier, copies are created which correspond to a DNA, a modified DNA, expressions of a DNA, an RNA, proteins or peptides; or   the amplifying agent effects a DNA amplification via polymerase chain reaction, an isothermal amplification, or a NASBA reaction, and the binding adapter comprises a matching primer, or   the method further comprises monitoring any changes in physical or chemical parameters within the effective areas.   
     
     
         10 . The method as claimed in  claim 1 , wherein the spatially limited effective areas comprise further molecules or DNA sequences or cells located therein which are part of the sample or are immobilized and which are needed for generating derivatives including expression vector sequences such as ori, promoters, ribosome binding sites, start codon, endoprotease cleaving sites, fusion sequences, reporter genes, terminators, antibiotics resistance genes, in-vitro translation systems, or cells. 
     
     
         11 . The method as claimed in  claim 1 , wherein primary, secondary and/or tertiary derivatives are generated, from a primary array or a replicate of the primary array, in that DNA is transcribed into RNA, the RNA is translated into protein, or in that a binder is enriched while using a produced protein, a produced RNA or a produced DNA or the copy thereof from a liquid phase, or in that a binder interacts, or
 a derivative is generated on the solid phase of a target array and is present there in an immobilized manner.   
     
     
         12 . The method of  claim 1 , further comprising:
 associating a reaction between a binder and an molecule in at least one of the samples with the DNA sequence of the molecule for genotype-phenotype coupling, or   associating a reaction wherein the molecule in at least one of the samples, its replicate or its derivative catalyzes a conversion of a substrate, with the DNA sequence of the molecule for genotype-phenotype coupling.   
     
     
         13 . (canceled) 
     
     
         14 . The method of  claim 8 , wherein the array is a liquid-particle array, and wherein the method further comprises sequencing replicates from the surface of the carrier in a sequencing device. 
     
     
         15 . The method of  claim 1 , wherein the method is carried out in a device comprising:
 a creator for creating, for each of the samples, at least one of the spatially limited effective areas,   the surface, provided with the binding adapter or binding properties, of the carrier bordering on the effective areas;   an amplifier for the amplifying the molecules via amplifying agents in the effective areas for creating the replicates or derivatives of the samples, and for binding the replicates or derivatives of the samples to the carrier via the binding adapter or the binding properties, so that a spatial arrangement of the replicates or derivatives of the samples on the carrier corresponds to the spatial arrangement of the samples wherein the carrier comprising the replicates or derivatives of the samples is removed from the array.   
     
     
         16 . The method of  claim 1 , wherein the array is a microarray and the spatially limited effective areas are cavities on the microarray. 
     
     
         17 . The method of  claim 1 , wherein, subsequent to the removing the carrier comprising on the surface the replicates or derivatives of the samples of molecules, the samples of molecules in the spatially limited effective areas are again amplified in the spatially limited effective areas via further amplifying agents and further replicates or derivatives of the samples of molecules are created. 
     
     
         18 . The method of  claim 17 , wherein the spatially limited effective areas are subjected to washing prior to adding the further amplifying agents. 
     
     
         19 . The method of  claim 2 , wherein the spatially limited amplifying agent areas are defined, at least in part, by micro- or nanostructures within an array substrate of the array or within the carrier. 
     
     
         20 . The method of  claim 19 , wherein the micro- or nanostructures comprise an unordered matrix based on a filter membrane, on a hydrogel or on an aerogel. 
     
     
         21 . The method of  claim 19 , wherein the micro- or nanostructures based on an ordered three-dimensional substrate.