CN100349178C - Micro flow controlling chip DNA molecular memory - Google Patents
Micro flow controlling chip DNA molecular memory Download PDFInfo
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- CN100349178C CN100349178C CNB2004100828583A CN200410082858A CN100349178C CN 100349178 C CN100349178 C CN 100349178C CN B2004100828583 A CNB2004100828583 A CN B2004100828583A CN 200410082858 A CN200410082858 A CN 200410082858A CN 100349178 C CN100349178 C CN 100349178C
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Abstract
The present invention relates to a DNA molecule memory of a micro-flow control chip, which is composed of a storage medium, a reaction medium and a micro-flow control chip, wherein the storage medium comprises DNA storage unit molecules containing short chains of the known sequences, DNA empty molecules for starting operation and DNA storage molecules representing the overlapped result of biochemical reactions; at least a storage unit region, an enzyme cutting reaction region, an enzyme connecting reaction region and a result output region are arranged on the micro-flow control chip; the enzyme cutting reaction region, the enzyme connecting reaction region and the result output region are orderly connected by a micro-channel; the storage unit region is connected with the enzyme connecting reaction region by the micro-channel. The invention adopts micro-flow control chip technology to replace test tube operation or surface operation widely used in the current DNA calculation course for the first time and provides a practical possible platform for constructing a proper DNA computer by the characteristics of precise and controllable operation of the micro-flow control chip and high-flux large-scale integration.
Description
Technical field:
The present invention relates to computer science, molecular biology and micro-fluidic chip technology.A kind of DNA molecular computer with microflow controlled chips, micro flow controlling chip DNA molecular calculating device, micro flow controlling chip DNA molecular memory are provided especially, have reached a kind of kit that is specifically designed to the micro-fluidic chip of dna molecular computing machine and is specifically designed to the micro-fluidic chip of dna molecular computing machine.
Background technology:
It is a kind of new mode of thinking about calculating that DNA calculates, and also is simultaneously about the chemistry and the biological a kind of new mode of thinking.Although the biological process with mathematics has complicacy separately, but they have an important general character, be to obtain after all labyrinths of biosome are actually some simple processing of raw information process that are coded in the dna sequence dna, and ask a value that contains the computable function of variable W also can realize by a series of the compound of simple function that contain variable W.
The DNA principle of calculating is: with the data of the password in the dna molecular as storage, when finishing biochemical reaction in effect following moment of certain enzyme between dna molecular, can become another kind of genetic code from a kind of genetic code, if the genetic code before will reacting is as the input data, so reacted genetic code just can be used as operation result.Like this, the accurate controlled biochemical reaction by the dna double spiral is enriched comprises mark, increases or destroys original chain and finish various calculating process, just may be developed into a kind of with the novel computing machine of DNA as computation medium.Because what its adopted is a kind of arithmetic logic and storage mode that is different from traditional computer fully, when solving some challenge, will have traditional computer incomparable advantage.
Success of calculating as DNA and the most representative example, dna computer begins to tradition " inorganic " the computing machine challenge that with the integrated circuit is core just based on the biotechnology of continuous development.Because the complicacy of integrated circuit in the traditional computer, the storage limit of inorganic silicon chip, and the limitation of itself computing method, this makes realizes ultrastructure in traditional computer, the super large memory space and when some problem of processing the raising of computing number of speed magnitude have very big difficulty.
DNA calculates has the concurrency height, fast operation, the characteristics that information memory capacity is big.But up to now, the relative dna research work of calculating concentrates on two aspects substantially: the research of promptly early stage biomolecule Calculation and Study and recent automated biological molecular computing machine.All these are worked, and exist the limitation of following two aspects at least.The one, biology operation and corresponding results related in DNA calculates confirm to lack the complete integrated hardware unit that a support is calculated, and also can not control relevant parameter certainly; The 2nd, all these molecular computing work have only been carried out the automatic computing of dna molecular and have not been had and each computation process wherein can be write down and store, and store function is one of the major function of the computing machine of Modern Significance, also is the essential characteristic that dna computer is different from the DNA calculation element.
The micro-fluidic chip laboratory is meant specimen preparation related in the fields such as biological and chemical, biology and chemical reaction, basic operation units such as separation, detection are integrated or be integrated into substantially on more than one square centimeters the chip, in order to finishing different biological or chemical courses of reaction, and a kind of technology that its product is analyzed.Chip lab is applicable in principle from reaction, separation and the detection up to organic and inorganic micromolecular various dissimilar molecules of nucleic acid, protein, has related to biological and chemical problem greatly.
In a broad sense, chip lab is divided into two big classes, and a class is to be the array microwell plate chip of core with the affine hybridization technique of static state, there is not distribution network, do not separate, because more single-minded DNA and the protein of being applicable to is referred to as " biochip " by domestic medium usually.Another kind of based on microflow control technique, on chip, form network by the microchannel, run through total system with controlled fluid, be referred to as the micro-fluidic chip laboratory usually, be the main flow of chip lab.
The appearance of micro-fluidic chip technology and development, extensive integrated characteristics of the pacing items of the chip lab that it had and high flux particularly, for replacing test tube or surface operation, make up a proper dna computer a kind of possible platform is provided.
Summary of the invention:
The object of the present invention is to provide a kind of is dna molecular computing machine, dna molecular arithmetical unit, dna molecular storer, and a kind of kit that is specifically designed to the micro-fluidic chip of dna molecular computing machine and is specifically designed to the micro-fluidic chip of dna molecular computing machine of operating platform with the micro-fluidic chip.
The invention provides a kind of DNA molecular computer with microflow controlled chips, mainly comprise:
---with the dna molecular is computation medium, is the dna molecular arithmetical unit of operating platform with the micro-fluidic chip;
---with the dna molecular is storage medium, is the dna molecular storer of operating platform with the micro-fluidic chip;
---with robot calculator and detecting device is the control core device;
Controller connects with electrode on the micro-fluidic chip of dna molecular arithmetical unit and dna molecular storer respectively.
In the DNA molecular computer with microflow controlled chips of the present invention, described dna molecular as computation medium on the micro-fluidic chip of described dna molecular arithmetical unit, is finished the dna molecular computing according to the instruction that described controller sends.
In the DNA molecular computer with microflow controlled chips of the present invention, the importation correspondence of described dna molecular arithmetical unit be that the DNA that contains particular sequence calculates molecule and contains the DNA transfer of molecules of particular sequence, the output correspondence be to export molecule by the representative result of calculation DNA that enzyme is cut, biochemical process such as enzyme companys obtains.
In the DNA molecular computer with microflow controlled chips of the present invention, described dna molecular as storage medium, on the micro-fluidic chip of described dna molecular storer, the storage to described dna molecular calculating process and result is finished in the instruction of sending according to described controller.
In the DNA molecular computer with microflow controlled chips of the present invention, the importation correspondence of described dna molecular storer be blank molecule of DNA and the DNA storage unit molecule that contains known array, the output correspondence be by enzyme cut, the DNA storage molecule of the process " overlap-add operation " of biochemical process acquisition such as enzyme companys.
In the DNA molecular computer with microflow controlled chips of the present invention, the kind number of the DNA transfer of molecules in the kind number of described DNA storage unit molecule and the dna molecular arithmetical unit is corresponding.
In the DNA molecular computer with microflow controlled chips of the present invention, described detecting device detects at the DNA output molecule of dna molecular arithmetical unit, described robot calculator is made according to testing result and is screened judgement and to dna molecular arithmetical unit and dna molecular memory transmit instruction, make dna molecular finish the storage of dna molecular computing and dna molecular respectively on the micro-fluidic chip operating platform of arithmetical unit and storer.
In the DNA molecular computer with microflow controlled chips of the present invention, described detecting device can be laser induced fluorescence detector, electrochemical detector, UV-detector.
The invention provides a kind of micro flow controlling chip DNA molecular calculating device, constitute by computation medium, reaction medium and micro-fluidic chip:
Described computation medium is that the DNA that contains particular sequence calculates molecule, is used for containing particular sequence DNA transfer of molecules and representing the DNA of result of calculation to export molecule by biochemical reaction of intermediary operation;
Described reaction medium is the various biochemical enzymes that enzyme is cut, enzyme connects reaction that are used for;
At least be provided with the endonuclease reaction district, the enzyme that link to each other by the microchannel order on the described micro-fluidic chip and connect reaction zone, output area as a result.
In the micro flow controlling chip DNA molecular calculating device of the present invention, on the described micro-fluidic chip, it is corresponding with the kind number of transfer of molecules that enzyme connects the number of reaction zone.
In the micro flow controlling chip DNA molecular calculating device of the present invention, on the described micro-fluidic chip, be provided with the pcr amplification district as a result before the output area.
In the micro flow controlling chip DNA molecular calculating device of the present invention, on the described micro-fluidic chip, be provided with the zone of depositing various computation medium, various reaction mediums, these zones connect reaction zone by microchannel and each autocorrelative endonuclease reaction district or enzyme and link to each other.
In the micro flow controlling chip DNA molecular calculating device of the present invention, on the described micro-fluidic chip, be provided with the unified zone of depositing blank damping fluid and waste liquid respectively.
The invention provides a kind of micro flow controlling chip DNA molecular memory, constitute by storage medium, reaction medium and micro-fluidic chip:
Described storage medium comprise the short chain that contains known array DNA storage unit molecule, be used for the blank molecule of DNA of startup operation, represent the DNA storage molecule of stack result by biochemical reaction.
At least be provided with memory cell areas, endonuclease reaction district, enzyme on the described micro-fluidic chip and connect reaction zone and output area as a result.Endonuclease reaction district, enzyme connect reaction zone, the output area is linked to each other by the microchannel order as a result, and memory cell areas connects reaction zone with enzyme and linked to each other by the microchannel.
In the micro flow controlling chip DNA molecular memory of the present invention, on the described micro-fluidic chip, be provided with the pcr amplification district as a result before the output area.
In the micro flow controlling chip DNA molecular memory of the present invention, on the described micro-fluidic chip, be provided with the zone of depositing various storage mediums, various reaction mediums, these zones connect reaction zone by microchannel and each autocorrelative endonuclease reaction district or enzyme and link to each other.
In the micro flow controlling chip DNA molecular memory of the present invention, on the described micro-fluidic chip, be provided with the unified zone of depositing blank damping fluid and waste liquid respectively.
The present inventor is based on the basic technical scheme of above-mentioned dna molecular computing machine based on micro-fluidic chip, utilize existing equipment, a corresponding micro flow controlling chip DNA computing machine has also been built in design, and this dna computer is formed by micro-fluidic chip, micro-fluidic chip workstation and in order to three parts such as kit of finishing various molecular reactions particularly.
The dna computer micro-fluidic chip is formed by stacking by dull and stereotyped A and dull and stereotyped B of sealing-in that an one side is integrated with the complicated microchannel of many groups; Dull and stereotyped A has the complicated microchannel of many groups, and the width of this chip microchannel is 75 μ m.Two dull and stereotyped middle closed channels that form, dull and stereotyped A is provided with the import and export of passage.Concrete chip design as shown in Figure 3.Input, output, the computing function of dna computer finished in a group liquid pool and microchannel among Fig. 3, and store function is finished in b group liquid pool and microchannel.
In other words, the invention provides a kind of micro-fluidic chip that is used for the dna molecular computing machine, it is characterized in that: on this chip, be integrated with dna molecular arithmetical unit and dna molecular storer.
In a side of micro-fluidic chip, the integrated various operating units that can carry out the electrophoretic separation in enzyme company, endonuclease reaction, PCR reaction and the microchannel are in order to finish I/O function, computing function and the control function that dna molecular calculates;
Particularly, the present invention is used for the micro-fluidic chip of dna molecular computing machine, and described dna molecular arithmetical unit part is provided with an endonuclease reaction pond 1, two enzymes symmetrically and connects reaction tank 2, two PCR reaction tanks 3, buffer pool 4, two standard nucleic acid fragment ponds 5, a waste liquid pool 6.Endonuclease reaction pond 1 connects reaction tank 2, sequentially is connected with PCR reaction tank 3 with enzyme respectively; The detection zone of buffer pool 4, waste liquid pool 6 and a cross passage of two standard nucleic acid fragment pond 5 formations is a sample intake passage between two standard nucleic acid fragment ponds 5, is sense channel between buffer pool 4, the waste liquid pool 6; PCR reaction tank 3 connects the sample intake passage of detection zone; See Fig. 4.
At the opposite side of chip, designed a storing apparatus, comprising one " stack " arranged,, finish up to the instruction transmission in order to each result who calculates gained that adds up.
Particularly, the present invention is used for the micro-fluidic chip of dna molecular computing machine, and described dna molecular memory portion is provided with that two storage unit molecule liquid storage tanks 7, enzyme are cut, enzyme connects reaction tank 8, PCR reaction tank 3, buffer pool 4, waste liquid pool 6, sample waste liquid pool 9; Enzyme is cut, enzyme connects reaction tank 8 and links to each other with PCR reaction tank 3 with two storage molecule liquid storage tanks 7 respectively; PCR reaction tank 3, sample waste liquid pool 9, buffer pool 4, waste liquid pool 6 constitute the detection zone of a cross passage, are sense channel between buffer pool 4, the waste liquid pool 6, are sample intake passage between PCR reaction tank 3, the sample waste liquid pool 9; See Fig. 5.
The cross section of the microchannel of micro-fluidic chip is for falling trapezoidal or rectangle, and the microchannel width is 75 μ m.The liquid pool diameter is 2～6mm.
The micro-fluidic chip material can be a glass, quartz, plastics.Wherein plastic chip comprises: PDMS chip, PMMA chip, PC chip.
The micro-fluidic chip workstation is existing, the commonly used work system that is used for micro-fluidic chip of a cover, sees Fig. 2, partly is made up of incorporate chip electrophoresis platform, laser-Induced Fluorescence Detection, CCD monitoring, power supply and computer operating system etc.Have chip energy supply and signal collection function, and be concurrently in charge of hardware controls dna computer.
Can realize functions such as input, output, calculating and storage in order to make above-mentioned dna computer, also need a series of biochemical reaction reagent to match with it, for this reason, the present invention also provides a kind of dna computer micro-fluidic chip kit, and as shown in Figure 6, inner-box device has 1 dna computer micro-fluidic chip 11,1 cover restriction enzyme reaction reagent 22,1 cover connects enzyme reaction reagent 33,1 cover polymerase chain reaction 44,1 bottles of electrophoretic buffers 55 of PCR reaction reagent and standard nucleic acid fragments 66.Chip structure is seen Fig. 3, is integrated with the complicated microchannel of many groups, and input, output, the computing function of dna computer finished in a group liquid pool and microchannel, and store function is finished in b group liquid pool and microchannel.
Restriction enzyme reaction reagent comprises restriction enzyme and reaction buffer.The kind of restriction enzyme can be Fok I, Bgl I, BstX I, Sfi I etc.The ligase reaction reagent comprises T4 ligase and reaction buffer.The PCR reaction reagent comprises Taq enzyme, reaction buffer and deoxynucleoside triphosphate (dNTP).Described marker is as the length of internal standard compound with definite product D NA.
In a word, the present invention adopts the micro-fluidic chip technology to replace widely used test tube or surface operation in the present DNA computation process first, utilize micro-fluidic chip operation accurately controlled and can the extensive integrated characteristics of high flux, provide a kind of reality possible platform for making up a proper dna computer.
Description of drawings:
Fig. 1 is micro flow controlling chip DNA Computer Architecture figure;
Fig. 2 is the micro-fluidic chip workstation photo of dna computer;
Fig. 3 is a dna computer microfluidic chip structure synoptic diagram; A. be integrated with the flat board that many complicated microchannels of group and passage are imported and exported, B. sealing-in flat board;
Fig. 4 is an arithmetical unit design diagram on the dna computer micro-fluidic chip; Among the figure: 1. endonuclease reaction ponds, hole, hole 2. enzymes connect reaction tank, hole 3.PCR reaction tank, hole 4. buffer pools, hole 5. standard nucleic acid fragments, hole 6. waste liquid pools;
Fig. 5 is a reservoir designs synoptic diagram on the dna computer micro-fluidic chip; Among the figure: hole 7. storage molecule liquid storage tanks, hole 8. enzymes are cut, enzyme connects reaction tank, hole 3.PCR reaction tank, hole 4. buffer pools, hole 6. waste liquid pools, hole 9. sample waste liquid pools;
Fig. 6 is the used kit structural representation of dna computer;
Fig. 7 is that (a is b) with 3 states (S0, S1, finite-state automatas S2) for 2 incoming symbols;
Fig. 8 is leg-of-mutton syntactic structure;
Fig. 9 is the calculation process and the corresponding electrophoresis spectrogram of the finite-state automata of " aabbb " for incoming symbol;
Figure 10 is micro flow controlling chip DNA Computer Storage process and corresponding electrophoresis spectrogram.
Embodiment:
As seen from Figure 1, the micro flow controlling chip DNA computing machine mainly comprises micro-fluidic chip workstation, micro-fluidic chip and in order to finish the kit of various molecular reactions.The micro-fluidic chip workstation is made up of power supply, control device and output unit, has chip energy supply and signal collection function, and be concurrently in charge of the control of dna computer.The dc high-voltage origin system of workstation is connected with eight electrodes, can be as required each applies different voltage at the diverse location of micro-fluidic chip, the control reactant liquor flows at interchannel on demand.The detecting device of micro-fluidic chip workstation can move relative to chip, and the reaction product in arithmetic logic unit and the memory cell is detected respectively.Chip is the core of whole computing machine, and the calculation function and the store function of computing machine are all finished on chip.Dna molecular and all ingredients in the kit enter system by input block.
Fig. 2 is the micro-fluidic chip workstation of integrated form dna computer, it is existing equipment, have two kinds of type of drive of electric osmose and pressure concurrently, with the laser-induced fluorescence (LIF) is detection means, comprises laser-Induced Fluorescence Detection and ccd image monitoring optical system, eight electrode dc high-voltage origin systems, program control three-dimensional platform, control circuit system and software systems etc.The top of micro-fluidic chip workstation is chip stationary platform and electrode operating platform, can move up and down.The bottom is made up of incorporate optical detection system, comprising can be for the CCD and the optical detection recording section of the usefulness of focusing and pipeline monitoring.Design has and can select for the multi-wavelength for the position that substitutes the emitting fluorescence narrow band pass filter in the optical detection recording section.The workstation rear portion is made up of switchable high-voltage power supply and relevant circuit.
Fig. 3 is the core component micro-fluidic chip of dna computer.This chip has comprised functions such as input, output, calculating and storage, and respectively integrated endonuclease reaction, enzyme connect operating units such as reaction, PCR reaction and electrophoretic separation.Arithmetic logic unit (a) in a side of chip sees Fig. 4 for details, and hole 1 is that endonuclease reaction pond (1) is the input block of dna computer signal simultaneously, and all instruct all from entering here.Check point is an output terminal, by the laser-Induced Fluorescence Detection dna molecular, and transforms the software section that signal is transferred to the micro-fluidic chip workstation by A/D, goes accurate translation again, finishes output function.Passage in the chip and hole are to finish DNA to calculate necessary functional unit, in order to the biochemical reaction of realization DNA and the timely separation detection of reaction product, guarantee finishing of dna computer input, output function and computing function.Shown in storage one side (b) of chip, see Fig. 5 for details, designed a kind of " storehouse " memory, in order to store the result of each calculating gained.This " storehouse " memory has more important effect in context-free grammar identification.
The kit that Fig. 6 is adopted for the micro flow controlling chip DNA computing machine comprises micro-fluidic chip in the kit, finish the even reaction of endonuclease reaction, enzyme, PCR reaction and the required various chemicobiology reagent of electrophoretic separation.
The function of the micro flow controlling chip DNA computing machine among Fig. 1 and each component units of typical electronic computing machine is contrasted, and the result is as shown in table 1.
The function contrast of each component units of table 1. micro flow controlling chip DNA computing machine and exemplary electronic computing machine
| Unit | Input | Output | ALU | Memory | Control |
| Function | Realize the input of data and program | The realization visualization of data shows | Realization is to the processing of data | Realize the storage of operational process intermediate data | Miscellaneous part is controlled chronologically, made harmonious work |
| Robot calculator | Input equipment is as keyboard, mouse | Output device is as display | Arithmetic-logical block | Internal memory | Controller |
| The micro flow controlling chip DNA computing machine | Specific dna molecular and corresponding reaction reagent in the reaction tank | The collection of illustrative plates of the detected reaction of micro-fluidic chip workstation back molecule | DNA calculates required various reaction systems | Have the chip of memory function and the dna molecular of canned data | Computer-controlled program according to the design of the computation process of DNA |
The function of micro flow controlling chip DNA computing machine realizes;
Be convenient meter, (a is b) with 3 state (S to adopt 2 incoming symbols
0, S
1, S
2) finite-state automata realize above-mentioned every function of micro flow controlling chip DNA computing machine, as shown in Figure 7.This finite-state automata is based on that the thought of the syntactic structure pattern-recognition of isosceles triangle proposes.
Be without loss of generality, triangle can be regarded as by some little line segments and form, each line segment has identical length.These line segments are divided into three types of horizontal line, up oblique line and descending oblique lines etc., are to constitute leg-of-mutton elementary cell.On this basis this triangle is described as the character string that primitive is formed, triangle as shown in Figure 8 can be expressed as " aabbbcccc ".In the literary composition, the method for taking two limits to compare is based on calculate its end-state of above-mentioned finite-state automata by dna molecular, if end-state is S
0, represent both sides to equate, otherwise represent that these both sides do not wait.
The corresponding state transition rule of the finite-state automata among Fig. 7 is designed to:
T1
T2
T3
T4
T5
Transfer of molecules is designed to:
T1： T2：
T3： T4：
T5：
0 base-pair of the left end primer 2 of above-mentioned 5 kinds of transfer of molecules all is designed to different sequences.
Fig. 3 is the micro-fluidic chip design drawing of finite-state automata identification, can understand the principle of work and the implementation procedure of input, output, computing, control and the memory function of micro flow controlling chip DNA computing machine thus.
Specific dna molecular and corresponding reaction reagent add in the endonuclease reaction pond 1 of Fig. 4, with the input data.
1. dna molecular finishes in the 1-3 of hole respectively that enzyme is cut, enzyme connects and the PCR course of reaction, carries out the calculating of DNA,
2. carry out the electrophoretic separation detection in the passage between the hole 4-hole 6 and obtain collection of illustrative plates, output data.
3. according to the data of output, realize the storage of data by micro-fluidic chip workstation control storage area shown in Figure 5.
4. different storage molecules is put in hole 7, finishes in hole 8 and 3 that enzyme is cut, enzyme connects and the PCR reaction, realizes storage.
5. carry out the electrophoretic separation detection in the passage of reaction product between 4-hole, hole 6 and obtain collection of illustrative plates, the result of recording storage.
To how on micro-fluidic chip, realize being that the five functional of the dna computer of model is done one and specifically introduced below with the finite-state automata
(1) input
The input of the finite-state automata among Fig. 7 divides subsymbol to be:
a：ATCACG b：ACGGTA
TAGTGC TGCCAT
The Terminator molecule is GTACCT
CATGGA
With original state S0, the finite-state automata of incoming symbol " aabbb " is an example, obtains corresponding D NA input and divides
The solution that will contain the molecule of above-mentioned dna sequence dna imports in the hole 1 of a side chip among Fig. 3, realizes input process.
(2) output
Select the FokI restriction enzyme, its recognition site is 5 '-GGATG-3 ', and restriction enzyme site is (9,13), can form the cohesive end of one section 4bp after enzyme is cut, and its encoded combination of different conditions and symbol is as shown in table 2.
The combination of table 2 different conditions and symbol
The cohesive end that can form after enzyme is cut under the ligase effect with the corresponding transfer of molecules adhesion that has complementary cohesive end, form one section new dna fragmentation, the new state of encoding.
Detection molecules is used for the pairing state of trace routine operation result, so that the terminator state of automat all designs a relevant detection molecule is as follows:
D-S
0 D-S
1 D-S
2
Above-mentioned detection molecules is connected the back and forms reporter molecules (Report molecule) with the Output molecule, detected and note between the hole 4-6 in Fig. 4 chip.
(3) calculate
On micro-fluidic chip, realized calculation process as shown in Figure 9.
A-g is the electrophoresis spectrogram of input state, each intermediateness and output state correspondence among Fig. 9.The right side is that incoming symbol is the calculation process of the finite-state automata of " aabbb ".Fig. 9 a is the electrophoresis spectrogram of input molecule I nput-aabbb, and what Fig. 9 (b-f) represented is the electrophoresis spectrogram of each product in the computation process, and Fig. 9 g is the electrophoresis spectrogram of output molecule.With 100bp series standard nucleic acid fragment (DNA marker) as internal standard compound to determine the length of each target molecule (marking).In 100bp series DNA marker, the dna molecular length of being represented by left-to-right each peak corresponds to 100,200,300,400,500,600,700,800,900,1000,1500bp.Wherein the peak of 500bp is apparently higher than other peaks, so with its thing as a token of, mark in the drawings.Obvious displacement has taken place in the relative marker in peak that can obviously find out each target molecule among the a-g of Fig. 9, this show dna molecular through shown in the right side go on foot respectively that enzyme is cut, after enzyme connects reaction, variation has taken place in length.
(4) storage
In the micro flow controlling chip DNA computing machine, store by the data structure of " storehouse ".According to result calculated (transfer of molecules and corresponding incoming symbol), in the corresponding data typing storage molecule of micro-fluidic chip workstation control store chip handle, thereby realize its memory function in dna computer.
(5) control
Give workstation with the information feedback of result of calculation, the storage chip of being controlled the other end by the computer program of design in advance is in the corresponding data typing storage molecule.
1. pass through the A-D converter reflecting in the chip that the signals collecting of dna molecular information is in the micro-fluidic chip workstation;
2. the signal data that collects is converted into graphic file;
3. the transit time of dna molecular and its molecular length are directly proportional, the PCR product electrophoretogram that adds DNAmarker by the specific computer program analysis, can measure the length of PCR product more accurately, calculated value and ideal value are compared, just can determine the transfer of molecules in per step reaction.
4. display result and transmit a signal to the data storage end of dna computer writes down the data message of per step reaction by dna molecular.
5. the control of memory function
Micro-fluidic chip a side signal is transferred to workstation, and storage unit input Memory-a, Memory-b by its control chip b side finish up to the instruction transmission.
The realization of storer
Up to the present, because the restriction of test tube technical conditions can't realize the storage of DNA result calculated and intermediateness, and this memory function can realize in micro-fluidic chip system of the present invention.
Below we go through on micro-fluidic chip the process that realizes memory function.Linear data structure common in the computing machine has table, storehouse and formation, and these data structures have very important meaning to the development of dna computer.Below be example with incoming symbol " aab ", be implemented in the storehouse storage organization on the micro-fluidic chip.Be initially " sky " in the storage unit, promptly only contain " E " molecule.Import the particular sequence that a Memory-a or Memory-b make one section 13bp of storage molecule increase or 21bp respectively, finally by detecting the result of the length or the exportable storage of checking order.
The design of E molecule:
The PUC19 plasmid of buying from takara increases with primer L1 and R1, obtain the fragment that length is 304bp, wherein BamHI restriction endonuclease recognition site: GGATCC is contained in the 417-422 position, cuts with the BamHI enzyme then, generate the dna molecular that the left side has the 4bp cohesive end, be blank molecule " E ".
The design of storage unit molecule in the storehouse:
Memory-a and Memory-b molecule right-hand member have cohesive end, can link to each other with blank molecule " E ".Because they all contain the FokI restriction enzyme site, so enzyme connects product be divided into two parts again under the effect of FokI enzyme.According to the information that off status and symbol are arranged that transfer of molecules in the computation process provides, store.Deposit Memory-a or Memory-b in, blank molecule " E " has in fact increased by the particular sequence of one section 13bp or 21bp.Divide the period of the day from 11 p.m. to 1 a.m when being output as Terminator, storage finishes.Finally by detecting the result of the length or the exportable storage of checking order.
The specific operation process of storing process is as follows:
At first use the BamHI digestion with restriction enzyme to generate the blank molecule " E " of left end band cohesive end under 30 ℃ of conditions in hole 12, its length is 263bp.65 ℃ of heating 10min lose activity enzyme.Introduce storage unit molecule Memory-a or Memory-b (comprising the FokI restriction enzyme site) by result calculated.Connect 30min at 18 ℃ of enzymes, 65 ℃ of heating 10min lose activity enzyme.Connecting product with enzyme is that template is carried out PCR, and amplified production is with electrophoresis detection.Repeat aforesaid operations, divide the period of the day from 11 p.m. to 1 a.m when computation process is output as Terminator, storage finishes.Include the information that whole DNA is calculated in the storage molecule that finally obtains, can read at any time.
Is example with incoming symbol for the dynamic memory process of the finite-state automata of " aab ", and storing process is described:
Figure 10-a is the synoptic diagram of storehouse storing process and the electrophoresis spectrogram of each step storage product, and Figure 10-b is its corresponding calculating process.Transfer of molecules has comprised the information of state and symbol in the calculating process.Incoming symbol is followed successively by T1 for the transfer of molecules of the finite-state automata of " aab ", T2 and T3, and its corresponding symbol is followed successively by a, a, b.According to above information, with Memory-a, Memory-a and Memory-b deposit the E molecule successively in, obtain Ea, Eaa and Eaab.So just having finished an incoming symbol stores for the storehouse of " aab ".Utilize and the similar method of above-mentioned " storehouse " storing process, also can realize the dynamic memory process of formation and table.
Claims (3)
1, a kind of micro flow controlling chip DNA molecular memory is made of storage medium, reaction medium and micro-fluidic chip:
Described storage medium comprise the short chain that contains known array DNA storage unit molecule, be used for the blank molecule of DNA of startup operation, represent the DNA storage molecule of stack result by biochemical reaction;
Described micro-fluidic chip is provided with memory cell areas, endonuclease reaction district, enzyme and connects reaction zone, output area as a result; Endonuclease reaction district, enzyme connect reaction zone, the output area is linked to each other by the microchannel order as a result, and memory cell areas connects reaction zone with enzyme and linked to each other by the microchannel;
On the described micro-fluidic chip, be provided with the zone of depositing various storage mediums, various reaction mediums, these zones connect reaction zone by microchannel and each autocorrelative endonuclease reaction district or enzyme and link to each other.
2, according to the described micro flow controlling chip DNA molecular memory of claim 1, it is characterized in that: on the described micro-fluidic chip, be provided with the pcr amplification district as a result before the output area.
3, according to claim 1 or 2 described micro flow controlling chip DNA molecular memories, it is characterized in that: on the described micro-fluidic chip, be provided with the zone of depositing blank damping fluid and waste liquid respectively.
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| Application Number | Priority Date | Filing Date | Title |
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| CNB2004100828583A CN100349178C (en) | 2004-12-06 | 2004-12-06 | Micro flow controlling chip DNA molecular memory |
| PCT/CN2005/002098 WO2006060955A1 (en) | 2004-12-06 | 2005-12-06 | A dna molecular computer with a microfluidic control chip |
| US11/759,048 US20110177980A1 (en) | 2004-12-06 | 2007-06-06 | Microfluidic chip-based dna computer |
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| CNB2004100828583A CN100349178C (en) | 2004-12-06 | 2004-12-06 | Micro flow controlling chip DNA molecular memory |
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| US10020826B2 (en) * | 2014-04-02 | 2018-07-10 | International Business Machines Corporation | Generating molecular encoding information for data storage |
| CN111724841B (en) * | 2020-06-04 | 2022-06-10 | 中国科学院上海微系统与信息技术研究所 | Information storage method based on biological protein |
| CN112990462B (en) * | 2021-03-15 | 2023-03-21 | 华南理工大学 | Biochemical computer latch based on enzymatic reaction |
| CN114505105B (en) * | 2022-01-13 | 2022-11-11 | 电子科技大学 | Micro-fluidic chip based on memory calculation |
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| JP2000285120A (en) * | 1999-03-30 | 2000-10-13 | Japan Science & Technology Corp | Method and device for searching gene expression |
| CN1363074A (en) * | 2000-02-09 | 2002-08-07 | 索尼公司 | Information processing device and method, data holding device and program |
| WO2004104918A2 (en) * | 2003-05-20 | 2004-12-02 | Council Of Scientific And Industrial Research | Dna based number system and arithmetic |
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| JP2000285120A (en) * | 1999-03-30 | 2000-10-13 | Japan Science & Technology Corp | Method and device for searching gene expression |
| CN1363074A (en) * | 2000-02-09 | 2002-08-07 | 索尼公司 | Information processing device and method, data holding device and program |
| WO2004104918A2 (en) * | 2003-05-20 | 2004-12-02 | Council Of Scientific And Industrial Research | Dna based number system and arithmetic |
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