CN109097437A - A method of research interfacial effect is to DNA two dimension origami structure stability influence - Google Patents
A method of research interfacial effect is to DNA two dimension origami structure stability influence Download PDFInfo
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Abstract
The invention discloses a kind of research interfacial effects to the method for DNA two dimension origami structure stability influence, synthesis including DNA triangle origami structure, on interface and solution in environmental factor change, and in particular to change interface on and solution in DNA origami structure local environment pH, Mg2+Concentration, temperature and ultraviolet irradiation and observe its appearance structure variation method.The present invention is based on the observation of scanning probe microscopy is simple to operation, pattern is clear, suitable for studying influence of the interfacial effect to a variety of two-dimension nano materials.Interface is constructed using mica sheet, it is easy to accomplish, and the factor that can be probed into is more, transplantability is strong；The method of the present invention is suitable for probing into influence of the interfacial effect to a variety of two-dimensional surface materials.
Description
Technical field
The present invention is based on scanning probe microscopy under atmosphere, a kind of research interfacial effect is disclosed to DNA two dimension paper folding knot
The method of structure stability influence.Specifically related to changing DNA triangle origami structure environmental condition on interface and in the solution,
The method for observing its morphology stability.The invention belongs to nanometer detection fields.
Background technique
DNA paper folding art is a kind of method of the preparation DNA nanostructure of simple general-purpose.It is specially that a long DNA is mono-
Chain and a series of not homotactic short chains are mixed into buffer solution and then in corresponding temperature condition according to a certain percentage
Lower slowly annealing, long-chain and short chain can fold out different shape and structures after the completion of all matching.
The features such as DNA origami structure is easy to modify due to its structure controllable precise, addressability and be widely used in tumor target
To pharmaceutical carrier (Chinese invention patent: a kind of preparation method of the DNA target for brain tumor to nano drug-carrying molecule, publication number:
CN104645338A), signal probe (Chinese invention patent: using DNA nanometers of origami structures as the detection of signal amplifying probe
Method, publication number: CN104133053A), biosensor (Chinese invention patent: the DNA paper folding nanometer based on aptamers modification
Structure-nanogold biosensor and its preparation method and application, publication number: CN104962615A) etc. research fields.And it is close
A little years for DNA conducting wire (Chinese invention patent: DNA guided nano granule assembles the preparation method of tree-shape wire, publication number:
CN1994862A), pH response (Chinese invention patent: the preparation method of the pH sensing element based on DNA molecular change of configuration, public affairs
The number of opening: CN104391119A) etc. characteristics research, and impart DNA nanostructure as nanometric circuit and prepare the unlimited of material
It may.
The realization of the various excellent performances of DNA nanostructure is built upon on the basis of itself structural intergrity.For
The stability of DNA nanostructure, some research work both domestic and external find its in high temperature, ethyl alcohol, in the organic solvents such as toluene all
Show excellent structural stability.But the problem of having one to be ignored jointly is exactly: unified standard DNA does not roll over for these researchs
Paper structure is in solid liquid interface or in solution.And at present do not there is also research to be related to solid liquid interface may be to DNA paper folding
The influence that structural stability generates does not have reliable research method as reference yet.
Summary of the invention
In view of the deficiencies of the prior art, it is an object of the invention to improve a kind of research interfacial effect to DNA two dimension paper folding
The method of the influence of structural stability.
The object of the invention passes through following proposal and realizes: a kind of research interfacial effect is to DNA two dimension origami structure stability
The method of influence, it is characterised in that the following steps are included:
(1) synthesis of DNA triangle paper folding:
208 short chains of staple are equally dissolved into MilliQ water, 200 nM of ultimate density of every chain is made, it will
M13mp18 single stranded DNA (100 nM) is blended in the short chain of DNA (200 nM) mixed with the ratio of molar concentration rate 1:10
1xTAE-Mg2+In solution, the 1xTAE-Mg2+Solution is by 40mM trishydroxymethylaminomethane (Tris), 20mM acetic acid, 2 mM second
Ethylenediamine tetraacetic acid (EDTA) (EDTA) and 12.5mM magnesium acetate, until pH 8.0, wherein the ultimate density of M13mp18 single stranded DNA is 5 nM,
Short chain ultimate density is 50 nM；Mixed solution is put into PCR instrument, set cycle of annealing from 95 DEG C of slow coolings to 4 DEG C,
Rate of temperature fall is 0.2 DEG C/10s；
(2) environment influences the Different Effects changed to solution and interface DNA structure:
The change of (2-1) pH
Where DNA triangle origami structure on interface pH change: the buffer of different pH is by 1xTAE-Mg2+ It is dripped in solution
Add the 1xTAE-Mg containing excessive hydrochloric acid or sodium hydroxide2+Buffer is made, and the buffer of different pH is added drop-wise to and is deposited with DNA
Triangle origami structure is simultaneously washed off and places certain time on the mica sheet that salinity is dried with nitrogen；
The change of the pH of solution where the paper folding of DNA triangle: being added directly into the buffer containing DNA triangle origami structure and boundary
The buffer of the identical component of used solution respective volume at face keeps its final pH identical with pH on corresponding interface, then
Place certain time；
The change of (2-2) temperature
The change of temperature on the interface of DNA triangle origami structure place: triangle paper folding is deposited on new removing mica sheet and is washed away
It after salinity drying, is placed under the controllable microscope of environment (Nanonavi E-Sweep, Seiko Inc, Japan), ring is set
Border temperature is different experimental temperature, and operation instrument makes it be rapidly heated to setting temperature and stablizes 10 min；
The change of the temperature of solution where DNA triangle origami structure: certain density triangle paper folding solution is placed in PCR instrument
In, setting program makes it be rapidly heated to different temperature and stablizes 10 min；
(2-3) Mg2+The change of concentration
Mg on interface where DNA triangle origami structure2+The change of concentration: by different Mg2+The buffer of concentration, which is added drop-wise to, to be deposited with
DNA triangle origami structure is simultaneously washed off on the mica sheet that salinity is dried with nitrogen, and certain time is placed；
The Mg of solution where the paper folding of DNA triangle2+The change of concentration: add directly into the buffer containing DNA triangle origami structure
Enter different Mg2+Concentration, but the identical buffer of other ion concentrations, make its final Mg2+Mg in concentration and corresponding interface2+
Concentration is identical, then places certain time；
The influence of (2-4) ultraviolet light
Ultraviolet irradiation is applied to the DNA triangle paper folding being deposited on interface: triangle paper folding will have been deposited and washes away salinity drying
Mica sheet lived with glass surface ware lid, be placed in measure and irradiate certain time below the ultraviolet lamp of eager to do well in everything degree；
DNA triangle paper folding in solution is applied ultraviolet: will be open containing the PCR pipe of a certain concentration DNA triangle paper folding solution
It is placed in below the ultraviolet lamp for measuring eager to do well in everything degree and irradiates certain time；
(3) scanning probe microscopy observes DNA triangle origami structure:
For DNA triangle paper folding morphology observation on interface: Q water washes out salinity on mica sheet, is dried with nitrogen to be placed under atmosphere and sweep
It retouches and is observed under probe microscope, wherein need to only be placed directly under atmosphere for changing one group of temperature and one group ultraviolet and scan probe
It is observed under microscope (Moltimode Nanoscope VII, VEECO)；
For DNA triangle paper folding morphology observation in solution: it takes 3 μ l solution to be added drop-wise on the mica sheet newly removed and deposits 3 min,
The salinity on interface is rinsed out with Q water and then is dried with nitrogen, and is finally placed under scanning probe microscopy and is observed.
The invention proposes a kind of experimental methods of influence to DNA two-dimensional nanostructure of probing into interfacial effect.Based on sweeping
The morphology observation for retouching probe microscope is easy to operate, and pattern is clear.Interface is constructed using mica sheet, it is easy to accomplish, and can probe into
Factor it is more, transplantability is strong.
The long-chain is M13mp18 phage single-chain, and 7249bp, the sequence of the staple chain is to be published in for 2006
Nature, entitled " the Folding DNA to create nanoscale shapes and on 440,297-302
Patterns " triangle paper folding sequence is identical.
The model Moltimode Nanoscope of scanning probe microscopy model Veeco company under used atmospheric gas
The instrument of VII, the imaging pattern are tapping-mode.
The buffer for being added drop-wise to difference pH on interface is by 1xTAE-Mg2+ It is added dropwise in solution a certain amount of containing excess
The 1xTAE-Mg of hydrochloric acid or sodium hydroxide2+Buffer is made, and does not change Mg in the process2+Concentration.
It is added drop-wise to difference Mg on interface2+The buffer of concentration is by 1xTAE-Mg2+ It is added dropwise in solution and is free of Mg2+'s
Buffer is made.
The method for changing interface environmental factor, is deposited on mica sheet using DNA origami structure and is formed by interface, blown
The pH buffer of sufficient amount is added dropwise directly above to submerge DNA origami structure after dry.
The method for changing environmental factor in solution is added dropwise into the buffer for saving DNA paper folding and contains excessive hydrochloric acid or hydrogen-oxygen
Change the 1xTAE-Mg of sodium2+Buffer is made.
The present invention has the advantages that the observation the present invention is based on scanning probe microscopy is simple to operation, pattern is clear, fits
For studying influence of the interfacial effect to a variety of two-dimension nano materials；Interface is constructed using mica sheet, it is easy to accomplish, and can probe into
Factor it is more, transplantability is strong；The method of the present invention is suitable for probing into influence of the interfacial effect to a variety of two-dimensional surface materials.Specifically
Are as follows:
(1) the invention proposes a kind of experimental methods of influence to DNA two-dimensional nanostructure of probing into interfacial effect.
(2) morphology observation based on scanning probe microscopy is easy to operate, and pattern is clear.Interface is constructed using mica sheet,
It is easily achieved, and the factor that can be probed into is more, transplantability is strong.
(3) this method is suitable for probing into influence of the interfacial effect to a variety of two-dimensional surface materials.
Detailed description of the invention
Fig. 1 is pattern comparison diagram of the DNA three-legged structure at different pH in interface and solution；
Fig. 2 is DNA three-legged structure interface and the pattern comparison diagram in solution at different temperatures；
Fig. 3 is DNA three-legged structure in different Mg2+Pattern comparison diagram under concentration in interface and solution；
Fig. 4 is pattern comparison diagram of the DNA three-legged structure under different ultraviolet irradiations in interface and solution.
Specific embodiment
Technical solution of the present invention is described further below by way of specific embodiment.Embodiment below is to this
The further explanation of invention, and do not limit the scope of the invention.
Embodiment 1
Morphology observation of the DNA triangle paper folding on interface when pH4:
Mica sheet is fixed on iron plate, the triangle paper folding solution (1nM) for taking 3 μ l to prepare is deposited on new removing mica sheet and washed
It removes salinity and is dried with nitrogen, the buffer of 20 μ l pH4 is then added dropwise to mica sheet surface again, and place 10 min, then uses again
Q water washes out salinity on mica sheet and is dried with nitrogen, and is placed under scanning probe microscopy and observes the variation of its pattern.
The morphology observation of DNA triangle paper folding in the solution when pH4:
The 1xTAE-Mg containing excessive hydrochloric acid is added dropwise into triangle paper folding solution2+Buffer makes its final pH 4, after being incubated for 7 min
It takes 3 μ l to deposit to wash away salinity on new removing mica sheet and be dried with nitrogen, is placed under scanning probe microscopy and observes the change of its pattern
Change.
Same method observes the variation of its pattern when pH3,10,11 under scanning probe microscopy.
If Fig. 1 is pattern comparison diagram of the DNA three-legged structure under different pH3,4,10 and 11 in interface and solution.
Embodiment 2
Morphology observation of the DNA triangle paper folding on interface at 80 DEG C of environment temperature:
Mica sheet is fixed on iron plate, the triangle paper folding solution for taking 3 μ l to prepare, 1 nM of concentration, deposits to new removing mica
On piece washes away salinity and is dried with nitrogen.Then iron plate is fixed under the controllable atomic force microscope of environment, setting temperature is 80
DEG C, operation program makes it be rapidly heated and observes the variation of its pattern after stablizing 10 min at 80 DEG C.
The morphology observation of DNA triangle paper folding in the solution at 80 DEG C of environment temperature:
Certain density DNA triangle paper folding solution is placed in PCR instrument, it is to 80 DEG C and steady that setting program makes it be rapidly heated
Fixed 10 min take 3 μ l to deposit to and wash away salinity on new removing mica sheet and be dried with nitrogen, are placed in scanning probe microscopy after cooling
Lower observation.
Same method, at 20,40,60 DEG C of temperature, the morphology observation such as Fig. 2 of DNA triangle paper folding in interface and solution
For the pattern comparison diagram in DNA three-legged structure at different temperatures interface and solution.
Embodiment 3
0.1xMg2+Morphology observation of the DNA triangle paper folding on interface under concentration:
Mica sheet is fixed on iron plate, the triangle paper folding solution (1 nM) for taking 3 μ l to prepare deposits on new removing mica sheet
It washes away salinity and is dried with nitrogen, 20 μ l 0.1xMg then are added dropwise to mica sheet surface again2+Buffer, and place 10 min, so
Salinity on mica sheet is washed off with Q water again afterwards and is dried with nitrogen, and is placed under scanning probe microscopy and is observed the variation of its pattern.
0.1xMg2+The morphology observation of DNA triangle paper folding in the solution under concentration:
It is added dropwise into DNA triangle paper folding solution and is free of Mg2+Buffer make its ultimate density 0.1x Mg2+, after being incubated for 7 min
It takes 3 μ l to be added drop-wise in the mica sheet surface newly removed and deposits 3 min, wash out salinity on mica sheet with Q water and be dried with nitrogen, set
The variation of its pattern is observed under scanning probe microscopy.
Same method, 0.5xMg2+Morphology observation of the DNA triangle paper folding on interface under concentration, if Fig. 3 is DNA triangle knot
Structure is in two difference Mg2+Pattern comparison diagram under concentration in interface and solution.
Embodiment 4
Morphology observation of the DNA triangle paper folding on interface under ultraviolet irradiation:
The DNA triangle paper folding being deposited on mica sheet is washed away into salinity and is dried up, mica sheet is lived with glass surface ware lid, is placed in survey
30 min of ultraviolet lamp lower section irradiation for measuring eager to do well in everything degree, which are placed under scanning probe microscopy, to be observed.
The morphology observation of DNA triangle paper folding in the solution under ultraviolet irradiation
Ultraviolet irradiation is applied to the DNA triangle paper folding in solution: the PCR of certain density DNA triangle paper folding solution will be contained
Tube opening, which is placed in below the ultraviolet lamp for measuring eager to do well in everything degree, irradiates 30 min.It takes 3 μ l to deposit on new removing mica sheet and washes away salinity
And be dried with nitrogen, it is placed under scanning probe microscopy and observes the variation of its pattern.
5 min are irradiated below same method ultraviolet lamp, the pattern of DNA triangle paper folding in the solution is in different ultraviolet irradiations
Between lower interface and the pattern comparison diagram in solution it is as shown in Figure 4.
Claims (8)
1. a kind of research interfacial effect is to the method for DNA two dimension origami structure stability influence, it is characterised in that change DNA triangle
The environmental condition of origami structure on interface and in the solution, observes its morphology stability, comprising the following steps:
(1) a kind of synthesis of known dna triangle paper folding sequence:
208 short chains of staple are equally dissolved into MilliQ water, 200 nM of ultimate density of every chain is made, it will
M13mp18 single stranded DNA (100 nM) with mix (the 200 short chains of nM DNA are blended in the ratio of molar concentration rate 1:10
1xTAE-Mg2+In solution, the 1xTAE-Mg2+Solution is by 40mM trishydroxymethylaminomethane (Tris), 20mM acetic acid, 2 mM second
Ethylenediamine tetraacetic acid (EDTA) (EDTA) and 12.5mM magnesium acetate composition, pH 8.0, wherein the ultimate density of M13mp18 single stranded DNA is 5
NM, short chain ultimate density are 50 nM；Mixed solution is put into PCR instrument, setting cycle of annealing is from 95 DEG C of slow coolings to 4
DEG C, rate of temperature fall is 0.2 DEG C/10s；
(2) environment influences the difference changed to solution and interface DNA structure, comprising:
The change of (2-1) pH:
Where DNA triangle origami structure on interface pH change: the buffer of different pH is by 1xTAE-Mg2+ It is dripped in solution
Add the 1xTAE-Mg containing excessive hydrochloric acid or sodium hydroxide2+Buffer is made, and the buffer of different pH is added drop-wise to and is deposited with DNA
Triangle origami structure is simultaneously washed off salinity, is placed on the mica sheet that is dried with nitrogen；
The change of the pH of solution where the paper folding of DNA triangle: being added directly into the buffer containing DNA triangle origami structure and boundary
The buffer of the identical component of used solution respective volume at face keeps its final pH identical with pH on corresponding interface, then
It places；
The change of (2-2) temperature:
The change of temperature on the interface of DNA triangle origami structure place: triangle paper folding is deposited on new removing mica sheet and is washed away
It after salinity, drying, is placed under the controllable microscope of environment (Nanonavi E-Sweep, Seiko Inc, Japan), ring is set
Border temperature is different experimental temperature, and operation instrument makes it be rapidly heated to setting temperature and stablizes 10 min；
The change of the temperature of solution where DNA triangle origami structure: triangle paper folding solution is placed in PCR instrument, and program is arranged
So that it is rapidly heated to different temperature and stablizes 10 min；
(2-3) Mg2+The change of concentration:
Mg on interface where DNA triangle origami structure2+The change of concentration: by different Mg2+The buffer of concentration, which is added drop-wise to, to be deposited with
DNA triangle origami structure simultaneously washes off salinity, on the mica sheet that is dried with nitrogen, places；
The Mg of solution where the paper folding of DNA triangle2+The change of concentration: add directly into the buffer containing DNA triangle origami structure
Enter different Mg2+Concentration but the identical buffer of other ion concentrations, make its final Mg2+Mg in concentration and corresponding interface2+It is dense
It spends identical, then places；
The influence of (2-4) ultraviolet light:
Ultraviolet irradiation is applied to the DNA triangle paper folding being deposited on interface: triangle paper folding will have been deposited and is washed away salinity, drying
Mica sheet lived with glass surface ware lid, be placed in measure and irradiate certain time below the ultraviolet lamp of eager to do well in everything degree；
DNA triangle paper folding in solution is applied ultraviolet: measurement will be placed in containing the PCR pipe of DNA triangle paper folding solution opening
Certain time is irradiated below the ultraviolet lamp of eager to do well in everything degree；
(3) scanning probe microscopy is observed:
For DNA triangle paper folding morphology observation on interface: Q water washes out salinity on mica sheet, is dried with nitrogen to be placed under atmosphere and sweep
Retouch probe, microscopically observation, wherein for changing the test group of temperature and the test group of ultraviolet irradiation, need to only be placed directly within
It is observed under scanning probe microscopy (Moltimode Nanoscope VII, VEECO) under atmosphere；
For DNA triangle paper folding morphology observation in solution: it takes 3 μ l solution to be added drop-wise on the mica sheet newly removed and deposits 3 min,
The salinity on interface is rinsed out with Q water, is then dried with nitrogen, is finally placed under scanning probe microscopy and observes.
2. the method as described in claim 1, which is characterized in that the change range of the temperature is at 20 to 80 DEG C.
3. the method as described in claim 1, which is characterized in that the change range of the pH is between 3-10.
4. the method as described in claim 1, the model of scanning probe microscopy model Veeco company under used atmospheric gas
The instrument of Moltimode Nanoscope VII, the imaging pattern are tapping-mode.
5. method as claimed in claim 1 or 3, which is characterized in that the buffer for being added drop-wise to difference pH on interface be pass through to
1xTAE-Mg2+ The 1xTAE-Mg containing excessive hydrochloric acid or sodium hydroxide is added dropwise in solution2+Buffer is made, in the process simultaneously
Do not change Mg2+Concentration.
6. the method as described in claim 1, which is characterized in that be added drop-wise to difference Mg on interface2+The buffer of concentration is to pass through
To 1xTAE-Mg2+ It is added dropwise in solution and is free of Mg2+Buffer be made, obtain 0.1-0.5xTAE-Mg2+ Solution.
7. the method as described in claim 1, which is characterized in that the method for changing interface environmental factor utilizes DNA paper folding knot
Structure, which is deposited on mica sheet, is formed by interface, the pH buffer of sufficient amount is added dropwise after drying directly above to submerge DNA folding
Paper structure.
8. the method as described in claim 1, which is characterized in that the method for changing environmental factor in solution, to preservation DNA paper folding
Buffer in be added dropwise the 1xTAE-Mg containing excessive hydrochloric acid or sodium hydroxide2+Buffer is made.
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Cited By (1)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN110488173A (en) * | 2019-08-19 | 2019-11-22 | 上海纳米技术及应用国家工程研究中心有限公司 | DNA paper folding Thin film conductive test method based on semi-conductor test instrument |
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| CN106834388A (en) * | 2016-12-20 | 2017-06-13 | 上海纳米技术及应用国家工程研究中心有限公司 | A kind of DNA structure element of ion concentration response and preparation and application |
| CN106893781A (en) * | 2017-03-08 | 2017-06-27 | 中国科学院上海应用物理研究所 | A kind of unimolecule methods of genotyping and its application based on DNA paper foldings probe specificity mark |
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| CN105760715A (en) * | 2016-02-05 | 2016-07-13 | 中国科学院上海应用物理研究所 | Image visualization method for detecting single molecule DNA duplication |
| CN106834388A (en) * | 2016-12-20 | 2017-06-13 | 上海纳米技术及应用国家工程研究中心有限公司 | A kind of DNA structure element of ion concentration response and preparation and application |
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| CN106893781A (en) * | 2017-03-08 | 2017-06-27 | 中国科学院上海应用物理研究所 | A kind of unimolecule methods of genotyping and its application based on DNA paper foldings probe specificity mark |
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| CN110488173A (en) * | 2019-08-19 | 2019-11-22 | 上海纳米技术及应用国家工程研究中心有限公司 | DNA paper folding Thin film conductive test method based on semi-conductor test instrument |
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