MICROARRAY TRANSFORMER

Abstract

The invention relates to a method for microarray transformation, wherein, by using a cavity chip with transformation matrix, a template array can be copied onto a planar support, and the information or spatial arrangement is changed in the process, so that a transformed second array forms. The invention further relates to a device for carrying out such a method.

Claims

1. A method for microarray transformation comprising: a) provision of a template array, wherein the template array comprises multiple spots with template molecules, b) provision of a cavity chip comprising a transfer matrix, c) provision of a reaction mixture in the cavity chip, d) placement of the template array on the cavity chip, e) copying process, wherein the oligonucleotides of the spots of the template array are copied onto the cavity chip f) provision of an array surface, g) provision of a reaction mixture in the cavity chip, h) placement of the array surface on the cavity chip, i) copying process, wherein the oligonucleotides of the spots of the cavity chip are copied onto the array surface as DNA, RNA or protein, and wherein this newly formed additional array differs from the template array in terms of spot shape, spot size, spot position and/or in terms of information contained.

2. The method according to claim 1, wherein a modification, elongation, shortening, derivatization and/or inversion of the molecules occurs in the cavities of the cavity chip and/or during the copying process.

3. The method according to claim 1, wherein a) to e) are repeated at least once, wherein the same cavity chip but a different template array or the same template array in a different or in the same orientation is used.

4. The method according to claim 1, wherein the copying step comprises an amplification step.

5. The method according to claim 1, wherein the reaction mixture is a PCR mixture, an isothermal amplification mixture, a reverse transcription mixture, a transcription mixture or a cell-free expression mixture.

6. The method according to claim 1, wherein the template molecules are oligonucleotides.

7. The method according to claim 1, wherein the cavities of the cavity chips are coated with primers.

8. The method according to claim 7, wherein the primers, on the 3 end or on the 5 end, carry an additional DNA sequence.

9. The method according to claim 1, wherein multiple spots of the template array are merged in the cavity chip and/or additional array, so as to generate a mixture of template molecules or molecules derived therefrom and/or in order to generate a DNA or RNA which comprises multiple partial sequences or derivatives of these partial sequences of the template molecules from the respective spots.

10. The method according to claim 1, wherein spots of at least two template arrays are merged in the additional array, so as to generate a mixture of copies and/or to generate a copy which comprises multiple partial sequences or derivatives of these partial sequences of the template molecules from the respective spots.

11. The method according to claim 1, wherein at least one spot of the template array is subdivided in the additional array into multiple spots.

12. The method according to claim 1, wherein additional DNA molecules are added in solution, so that the molecules are elongated or changed by this DNA sequence.

13. The method according to claim 1, wherein the template molecules are DNA molecules all or some of which have short identical DNA sequences.

14. The method according to claim 8, wherein the additional sequences are used as barcode for position information and/or the primers can contain a sequence for the transcription and/or the cell-free synthesis.

15. The method according to claim 1, wherein the transformation is spatially and/or temporally limited.

16. A cavity chip for carrying out a method according to claim 1, comprising a transfer matrix with cavities, wherein the cavities are arranged so that a transformation can occur.

17. A device for carrying out a transformation according to claim 1, comprising the cavity chip the at least one template array, and the at least one array surface.

18. The method according to claim 6, wherein the template molecules in a) are DNA molecules or RNA molecules.

19. The method according to claim 13, wherein the short identical DNA sequences have 10-13 base pairs.

20. The method according to claim 13, wherein the additional sequences are used as barcode for position information and/or the primers can contain a sequence for the transcription and/or the cell-free synthesis.

Description

[0141] FIG. 1. Regressive transformation (large to small). An array of hexagons has been transformed into smaller circles. The figure shows a section of 2 hexagons.

[0142] FIG. 2. Progressive transformation (small to large) The array on the left with clearly larger cavities has been transformed into an array with large spots (right). Depending on the precise position of the original spots, different products can be generated here. In the example of the lower box, the lower red spot (A) has been transformed into a red circle (A) with clearly larger diameter. But the red spot (A) above has been fused with the overlying green spot (C) to form a yellow circle (B). Directly above this box, a green spot (left small, right large) is located, which in turn has been transformed in pure form. In the case of the top left box, 2 green (C) and 2 red spots (A) (left) were converted into a traffic light configuration (red (A), yellow (B), green (C) (right)).

[0143] FIG. 3. Allocation of the transformation The data from FIG. 2 has been superimposed here in order to represent the transformation more clearly. One can now see very well which small spots contributed as seeds of the larger spots. Some of the small red spots generated no signal in this experiment. For the green spots, a considerably clearer: allocation exists.

[0144] FIGS. 4 to 17 particularly preferred embodiments of the invention.

[0145] FIG. 4: Position optimization

[0146] Problem: Microarrays are printed, i.e., tiny drops are put on a surface and after that are of different size (A), not precisely in position (B) or inhomogeneous or have an irregular shape (C), etc. That is to say, the automated acquisition of the spots is difficult.

[0147] Solution: a transformation containing the optimal spatial position is carried out.

[0148] FIG. 5: Structure optimization

[0149] Problem: Microarrays are printed, i.e., the drops usually have circular to oval shapes and then any desired structures can then be generated.

[0150] Solution: A transformation is carried out, which gives an individual shape to each spot, including shapes which to date could not be produced.

[0151] FIG. 6: Reduction 1

[0152] Problem: The format of arrays is established by the printing process, i.e., there is a lower limit of the size of the spots due to the minimal deposition quantity, and likewise of their spacing in order to prevent running together of the spots.

[0153] Solution: Smaller spots can then be generated in the transformation.

[0154] FIGS. 7 and 8: Reduction 2a and 2b

[0155] Problem: The format of arrays is established by the printing process, i.e., there is a lower limit of the size of the spots due to the minimal deposition quantity, and likewise of their spacing in order to prevent running together of the spots.

[0156] Solution: Two transformations are carried out, one which contracts everything and then one which makes smaller spots.

[0157] FIG. 9: Enlargement 1

[0158] Problem: The format of arrays is established by the printing process, i.e., there is an upper limit of the size of the spots due to the maximum deposition quantity and concentration.

[0159] Solution: larger spots can then be generated in the transformation.

[0160] FIGS. 10, 11 and 12: Enlargement 2a, 2b and 2c

[0161] Problem: The format of arrays is established by the printing process, i.e., there is an upper limit of the size of the spots due to the maximum deposition quantity and concentration.

[0162] Solution: in a first transformation, the spots are spaced, then they are first reduced (!), in order to prevent contaminations, and then enlarged.

[0163] FIGS. 13 and 14: Position interchange a and b

[0164] Problem: The format of the array is established after the printing; a change in position automatically requires a new printing.

[0165] Solution: In a first transformation, the positions are interchanged, and, in a second transformation, the spot geometry is then reestablished.

[0166] FIG. 15: Merging

[0167] Problem: The DNA of individual spots cannot be fused or mixed later in order to thus bring about additive effects (for example, when two DNAs initially jointly interact with a protein) or allosteric effects (when a DNA is necessary in order to activate a protein or is activated by said protein, which then binds to another DNA, for example, initiation sequences or the lac-promoter or lac-repressor).

[0168] Solution: Two or more spots can be fused, and the DNAs can be next to one another or linearly one after the other.

[0169] FIG. 16: Division

[0170] Problem: Spots cannot be reduced again later, for example, in order to achieve a higher signal (under unsaturated conditions) or more rapid kinetics (ambient analyte theory).

[0171] Solution: In the transformation, the spot is divided into smaller spots

[0172] FIG. 17: Combinatory mixture

[0173] Problem: The generation of multiple DNA spots which, however, carry identical partial sequences is just as elaborate as the generation of completely incoherent sequences.

[0174] Solution: First, the DNA is removed from template 1, then it is removed from template 2 resulting in the generation of a combinatory mixture. Thus, with n and m spots on the original array, it is possible to generate a total of n*m combinatory mixtures.

[0175] A mixture can be implemented both as a juxtaposition (multiple DNA sequences are next to one another on the surface) and as abutting (the DNA sequences are linearly joined together one after the other, that is to say elongated). This can be implemented by selection of the primers and DNA sequences during the biochemical amplification step (all primers identical=usually next to one another, and primers matched=usually abutting=usually elongation PCR).

[0176] FIGS. 18 to 22 show particularly preferable devices of the invention.

[0177] FIG. 23 shows a diagrammatic representation of a typical transformation process. The transformation of a small spot into a larger-area spot as well as the transformation of a large-area spot into 3 smaller spots is represented. a: Filling of the cavity chip with a reaction mixture, for example, PCR mixture or cell-free expression system and placement of the original array on the cavity chip. b: Performance of a copying reaction, for example, a PCR. c: Opening, washing and blocking of the chip. d: Filling of the cavity chip with reaction mixture and closing thereof by means of an empty array surface. e: Performance of a copying reaction, for example, a PCR. f: Washing and blocking of the newly formed array (transformed array) and of the cavity chip.

[0178] FIG. 24 shows an additional example of a possible application.

ABBREVIATIONS AND EXPLANATIONS

[0179] Transfer chip Also referred to as cavity chip; device which can be used for stationary storage of biomolecules [0180] Primary array Also referred to as template array; microarray which is used as starting point and which has been prepared according to the current state of the art; preferably DNA or RNA array [0181] Secondary array Microarray which is produced after an array transformation is performed. It represents the final result of the array transformation. [0182] ST Spatial transformationChange of the information on the position and/or the geometry in comparison to the primary array [0183] ST zoom Spatial transformation zoomThe position information is maintained; however, the spots are represented either enlarged or reduced. [0184] ST rotation Spatial transformation rotationRotation of the primary array around certain point and by certain angle (in addition to the shift) [0185] ST shift Spatial transformation shiftPosition change of the array in comparison to the starting array [0186] ST stretch Redundancy for shape transformation [0187] ST merging Adding or connecting of new information to already existing information. The constitution of the original information is not changed in the process. [0188] ST resolution Spatial transformation resolution change; increase or reduction of the number of spots compared to the starting array [0189] ShaT Shape transformationChange of the original shape of the array spots of the primary array [0190] SeqT Sequence transformationChange of the biomolecules compared to the primary array [0191] (additive) SeqT addition Sequence transformation which enables the addition of new information to the already existing information [0192] (subtractive) SeqT Sequence transformation which enables the partial or subtraction complete removal of information

[0193] In accordance with the theory of affine and partially affine mappings from mathematics, all the transformations used can be bijective, injective and/or surjective and in addition additive, subtractive or identical. The following meanings apply here:

[0194] Bijective: Each cavity of the transfer chip encounters exactly one spot of the primary array. No spots are left out.

[0195] Injective: The cavities of the transfer chip encounter in each case one spot of the primary array. Spots may be left out.

[0196] Surjective: Each cavity of the transfer chip encounters one or more spots of the primary array. No spots are left out.

REFERENCES

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