CN104991090A - Method for detecting single molecule horizontal intermolecular interaction by use of atomic force microscope (AFM) - Google Patents
Method for detecting single molecule horizontal intermolecular interaction by use of atomic force microscope (AFM) Download PDFInfo
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- CN104991090A CN104991090A CN201510378549.9A CN201510378549A CN104991090A CN 104991090 A CN104991090 A CN 104991090A CN 201510378549 A CN201510378549 A CN 201510378549A CN 104991090 A CN104991090 A CN 104991090A
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Abstract
The invention discloses a method for detecting single molecule horizontal intermolecular interaction by use of an atomic force microscope (AFM). The method comprises the following steps: modifying DNA1 on the surface of a substrate and modifying DNA2 on an AFM probe; when the AFM probe approaches the surface of the substrate, through complementary hybridization between the DNA1 and the DNA 2, forming a DNA1/DNA2 double-chain structure; identifying a specific sequence in double-chain DNA1/DNA2 by use of specificity of cutting endonuclease, and cutting off the single-chain DNA1; and then detecting the acting force between the DNAs by use of the AFM, and accordingly detecting the change of the interaction between the DNAs of DNA double chains before and after the cutting endonuclease is cut off.
Description
Technical field
The invention belongs to biological technical field, be specifically related to a kind of method that atomic force microscope detects single molecules level intermolecular interaction.
Background technology
Single Molecule Detection (single molecular detection, SMD) is the super sensitivity detection technology developed rapidly nearly ten years.Common molecular detection technique only can obtain the integrity attribute of general material, cannot express the interaction between individual molecule and individual molecule accurately and efficiently.And a lot of biomolecule (as protein, DNA, RNA etc.) has multiple conformation, and between molecule, there is interaction.Therefore, detect biomolecule from single molecules level, to identification, classification and quantitative description biomolecule, Real-Time Monitoring means of chemical reaction, in physiological conditions detectable biomolecule provide the information between molecular structure and function significant.
Single Molecule Detection is the event at nanometer scale space size measurement finite number object molecule or interaction of molecules.Under adopting the enzymatic reaction of atomic force microscope can realize nanometer or micron precision, the controlled of surface of solid phase carriers target molecule is fixed.Enzymatic nanoprocessing lithographic technique enzymatic reaction product can be provided to move with AFM probe and redeposited time topographical information.Such as, by fixing active enzyme molecules on AFM probe, to remove the biomolecule that is pre-existing in or to be translated into Small molecular, obtain negative map picture.For realizing high flux and flexible molecule printing, dip-pen nano processing lithographic technique (dip-pennanolithography, DPN) and microcontact printing techniques be applied to polynary DPN and polymer pen processing lithographic technique, and by atomic force microscope or fluorescence imaging visual.Because these technology relate to nanoscale operation, therefore need to set up controllable method to realize individual molecule fixing at substrate surface ad-hoc location.Individual molecule can be fixed on assigned address by atomic force microscope technology, has been applied to the research of unimolecule and other unimolecule mechanical spectrum technology.
Directly do not measure the interaction force between DNA by employing atomic force microscope in prior art, realize the cleavage reaction that on single molecules level, monitoring of DNA double-strand occurs under the effect of nicking restriction endonuclease, this present situation is urgently to be resolved hurrily.
Summary of the invention
The object of this invention is to provide a kind of atomic force microscope for detecting the method for single molecules level intermolecular interaction, the interaction force between DNA is directly measured by employing atomic force microscope, achieve the cleavage reaction that on single molecules level, monitoring of DNA double-strand occurs under the effect of nicking restriction endonuclease, for the enzymatic reaction on research single molecules level provides a kind of new method.
For achieving the above object, the present invention is achieved by the following technical solutions:
Atomic force microscope for detecting a method for single molecules level intermolecular interaction, substrate surface modifying DNA 1 and on AFM probe modifying DNA 2; When AFM probe and substrate surface near time, by the Complementary hybridization of DNA1 and DNA2, form DNA1/DNA2 duplex structure; Adopt the particular sequence in nicking restriction endonuclease specific recognition double-stranded DNA 1/DNA2, and single stranded DNA 1 is cut off; Then the acting force between atomic force microscope detection DNA is adopted.
Comprise the following steps:
(1) AFM probe modification DNA2: AFM probe is carried out hydroxylation modification, obtain the AFM probe of hydroxyl modified, the AFM probe of then activated hydroxyl groups modification, is fixed reaction by the AFM probe after activation and amido modified DNA2, take out AFM probe, aftertreatment is carried out to AFM probe.
(2) fixed dna 1 in gold substrate: pre-service gold substrate, is fixed reaction by the DNA1 of the gold substrate handled well and sulfydryl modification, and 37 DEG C are reacted more than 3 hours.
(3) atomic force microscope dynamometry: dropped in by buffer solution 3 in the gold substrate that obtains in step (2), be fixed on by drop on the scanner of atomic force microscope, surveys the interaction force F1 between DNA; When using nicking restriction endonuclease, by the mixed solution containing 1 × nicking restriction endonuclease damping fluid, nicking restriction endonuclease and described buffer solution 3, be added drop-wise in gold substrate, drop be fixed on the scanner of atomic force microscope, survey the interaction force F2 between DNA; Thus detect the change of DNA double chain Interaction Force of DNA before and after nicking restriction endonuclease is sheared.
In step (1), the process that described hydroxylation is modified is: AFM probe to be immersed in the mixed solution of the concentrated sulphuric acid and hydrogen peroxide (concentrated sulphuric acid (massfraction 95 ~ 98%): hydrogen peroxide (massfraction 30%)=7:3 (volume ratio)) 30 minutes, deionized water is cleaned, and obtains hydroxyl modified AFM probe.
In step (1), described reactivation process is: the AFM probe of hydroxyl modified being immersed in 200 μ l concentration is (note: NHS solution matching while using) in 100mMN-N-Hydroxysuccinimide (NHS) solution, after lucifuge places 30 minutes, deionized water rinsing is clean.
In step (1), the process of aftertreatment is: first rinse three times with buffer solution 2, then cleans with deionized water, air drying 30 minutes.The composition of described damping fluid 2: 300mM NaCl, 20mM Na
2hPO
4, 2mM ethylenediamine tetraacetic acid, 7mM lauryl sodium sulfate, pH=7.4; Effect: for cleaning AFM probe.
In step (1), the process of described fixation reaction is: the AFM probe being modified with DNA2 being immersed in 200 μ l concentration is in the amido modified DNA2 solution of 1 μM, and 25 DEG C are reacted more than 12 hours, and be preferably 12 ~ 24 hours, most preferred is 16 hours.
In step (2), the process of described pre-service gold substrate is: by gold substrate cleaning, drying.Process concrete is further: soak ultrasonic 10 minutes with cleaning fluid, and deionized water rinsing is clean, and nitrogen dries up.Described cleaning fluid is: the mixed solution of ammoniacal liquor and hydrogen peroxide, Qi Zhongshui: ammoniacal liquor: the volume ratio of hydrogen peroxide is 5:1:1.
In step (2), described fixation reaction process is: the gold substrate handled well being immersed in 1ml concentration is be fixed reaction in the sulfydryl modification DNA1 of 1 μM.
In step (2), the described reaction time is 3 ~ 24 hours.
In step (3), the process surveying the interaction force between DNA is: after AFM probe is put into liquid phase probe carriage, probe carriage is loaded atomic force flying-spot microscope.Open instrument switch, regulate probe carriage to make it decline, with the drop contact in gold substrate.Guarantee between gold substrate and probe carriage glass sheet after bubble-free, regulate hot spot.Select contact mode, inserting needle, residence time: 10000ms.Start the interaction force measured between DNA, thus detect the change of DNA double chain Interaction Force of DNA before and after nicking restriction endonuclease is sheared.
In step (3), described damping fluid 3 forms: 20mM Tris-HCl, 0.1M MgCl
2, pH=8.0, effect: the detection system of atomic force microscope dynamometry.
In step (3), described nicking restriction endonuclease is a class identification DNA distinguished sequence, and around recognition site or its, shear the restriction endonuclease of a DNA chain in dsRNA substrate.Described nicking restriction endonuclease is nicking restriction endonuclease Nb.BbvCI; Described 1 × nicking restriction endonuclease Nb.BbvCI damping fluid consist of potassium acetate, Tris-acetic acid, magnesium acetate and bovine serum albumin(BSA) (BSA), wherein the concentration of each component is respectively: 50mM potassium acetate, 20mM Tris-acetic acid, 10mM magnesium acetate, 100 μ g/ml BSA, pH 7.9.
Described DNA1 and DNA2 be two base complementrities treat surveyor's chain.
The invention has the beneficial effects as follows: the present invention establishes a kind of atomic force microscope (atomic force microscopy, AFM) and studies DNA double chain on single molecules level the method for cleavage reaction occurs under the effect of nicking restriction endonuclease.Select gold plaque as substrate, by Au-S covalent bond fixed dna 1 in gold substrate, make it and react by acid amides the DNA2 Complementary hybridization be fixed on AFM probe, thus form the DNA1/DNA2 duplex structure of complete complementary hybridization at substrate surface, and in double-strand, comprise the specific recognition site of nicking restriction endonuclease.Under the effect of nicking restriction endonuclease, the single stranded DNA 1 be fixed in gold substrate is cut to DNA1 ' and DNA1 ", wherein DNA1 ' is fixed in gold substrate.Compared with double-stranded DNA 1/DNA2, because DNA1 ' and the base number of DNA2 Complementary hybridization reduce, therefore DNA interaction force reduces.The present invention directly measures the interaction force between DNA by employing atomic force microscope, achieve the cleavage reaction that on single molecules level, monitoring of DNA double-strand occurs under the effect of nicking restriction endonuclease, for the enzymatic reaction on research single molecules level provides a kind of new method, and the interaction can expressed accurately and efficiently between individual molecule and individual molecule, for the significant process disclosing biological phenomena provides theoretical foundation, in fields such as analytical chemistry, clinical diagnosis and bioprocess dynamics, there is actual application value widely.
Accompanying drawing explanation
Fig. 1: on atomic force microscope technology research single molecules level, the schematic diagram of cleavage reaction occurs DNA double chain under the effect of nicking restriction endonuclease.
Embodiment
Below in conjunction with drawings and Examples, the present invention is further described.
In the present invention, AFM probe derives from basis nanometer Instrument Ltd. (contact mode), gold substrate derives from BioNavis company of Finland, DNA1 and DNA2 derives from Sangon Biotech (Shanghai) Co., Ltd., atomic force microscope derives from basis nanometer Instrument Ltd. CSPM5500 scanning probe microscopy (SPM) system, other reagent without specified otherwise all from commercial sources.
In the present invention, M represents mol/L, and mM represents mmol/L, μM expression μm ol/L.
Embodiment 1
The cleavage reaction (experimental principle as shown in Figure 1) that the present embodiment selects nicking restriction endonuclease Nb.BbvCI to occur under the effect of nicking restriction endonuclease to study single molecules level DNA double chain.Mainly comprise the following steps:
One, modifying DNA 1 on AFM probe:
1, buffer solution 1, buffer solution 2 and buffer solution 3 is prepared first respectively.
Buffer solution 1 forms: 25mM NaHCO
3, 5mM MgCl
2, 10% (v/v) dimethyl sulfoxide (DMSO), pH=8.5.Effect: for preparing DNA solution.
Buffer solution 2 forms: 300mM NaCl, 20mM Na
2hPO
4, 2mM ethylenediamine tetraacetic acid, 7mM lauryl sodium sulfate, pH=7.4.Effect: for cleaning AFM probe.
Buffer solution 3 forms: 20mM Tris-HCl, 0.1M MgCl
2, pH=8.0.Effect: the detection system of atomic force microscope dynamometry.
2, AFM probe to be immersed in the mixed solution of the concentrated sulphuric acid and hydrogen peroxide (concentrated sulphuric acid (massfraction 95%): hydrogen peroxide (massfraction 30%)=7:3 (volume ratio)) 30 minutes, deionized water is cleaned, obtain hydroxyl modified AFM probe, probe force constant is 0.2N/m.
3, hydroxyl modified AFM probe being immersed in 200 μ l concentration is (note: NHS solution matching while using) in 100mM N-hydroxy-succinamide (NHS) solution, activation AFM probe, after lucifuge places 30 minutes, deionized water rinsing is clean.
4, gained AFM probe being immersed in 200 μ l concentration is in the amido modified DNA2 solution of 1 μM, and 25 DEG C are reacted 16 hours, is fixed on AFM probe by DNA2 by acid amides reaction.
Wherein, the nucleotides sequence of DNA2 is classified as, as shown in SEQ ID NO:2:
5 '-GGTTACTATCACGCCTCAGCCTGAGGCATCAGCACGATTAGTAGTCATATTAGGTA GGG-3 ', 3 ' Amino End Group is modified.
5, AFM probe is taken out, first rinse three times with buffer solution 2, then clean with deionized water, air drying 30 minutes.
Two, fixed dna 2 in gold substrate:
1, before gold substrate uses, soak ultrasonic 10 minutes with cleaning fluid (composition of cleaning fluid: water: ammoniacal liquor: the volume ratio of hydrogen peroxide is 5:1:1), deionized water rinsing is clean, and nitrogen dries up.
2, the gold substrate handled well being immersed in 1ml concentration is in the sulfydryl modification DNA1 of 1 μM, and 37 DEG C are reacted 3 hours.
Wherein, the nucleotides sequence of described DNA1 is classified as, as shown in SEQ ID NO:1:
5 '-CCCTACCTAATATGACTACTAATCGTGCTGATGCCTCAGGCTGAGGCGTGATAGTA ACC-3 ', 3 ' end sulfydryl modification.
Three, atomic force microscope dynamometry
What 1,100 μ l buffer solution 3 are dropped in that step 2 obtains is fixed with in the gold substrate of DNA1, makes it form a large drop.Large drop is fixed on the scanner of atomic force microscope.
2, after AFM probe being put into liquid phase probe carriage, probe carriage is loaded atomic force flying-spot microscope.Open instrument switch, regulate probe carriage to make it decline, with the drop contact in gold substrate.Due to DNA1 and DNA2 sequence complete complementary, and comprise nicking restriction endonuclease Nb.BbvCI specific recognition site
(▲ represent clipped position).When AFM probe is close to substrate surface, DNA1 and DNA2 Complementary hybridization, forms DNA1/DNA2 duplex structure.
Guarantee between gold substrate and probe carriage glass sheet after bubble-free, regulate hot spot.
3, contact mode is selected, inserting needle, residence time: 10000ms.Start to measure.Measured the acting force (each position replicate determination 50 times) of 5 diverse locations respectively by atomic force microscope, the interaction force recorded between double-stranded DNA 1/DNA2 is 30.5 ± 3.7nN.
4, above-mentioned steps is adopted to obtain the AFM probe of DNA2 modification and the gold substrate of DNA1 modification.Add 10 μ l 10 × nicking restriction endonuclease damping fluids, 10U nicking restriction endonuclease, supplements volume to 100 μ l with damping fluid 3, is added drop-wise in the gold substrate of DNA1 modification.Make nicking restriction endonuclease Nb.BbvCI identify the shearing site of DNA1 in double-stranded DNA 1/DNA2, DNA1 be cut to DNA1 ' and DNA1 ", wherein DNA1 ' is fixed in substrate.After reaction terminates, regain AFM probe, the now DNA intermolecular forces of survey is reduced to 10.2 ± 3.7nN.The shearing site of nicking restriction endonuclease Nb.BbvCI specific recognition double-stranded DNA 1/DNA2 is described, and then the single stranded DNA 1 be fixed in gold substrate is cut into two parts DNA1 ' (18 bases) and DNA1 " (41 bases).Because DNA1 ' is fixed in gold substrate, compared with the double-stranded DNA 1/DNA2 before shearing (59 base-pairs), because DNA1 ' and the base number of DNA2 Complementary hybridization are reduced to 18 base-pairs, therefore DNA interaction force reduces, and achieves the detection of single molecules level enzymatic reaction.The method directly can provide the information of intermolecular interaction from single molecules level, for the significant process disclosing biological phenomena provides theoretical foundation, have actual application value widely in fields such as analytical chemistry, clinical diagnosis and bioprocess dynamics.
Wherein, described 1 × nicking restriction endonuclease Nb.BbvCI damping fluid consist of potassium acetate, Tris-acetic acid, magnesium acetate, BSA, wherein the concentration of each component is respectively: 50mM potassium acetate, 20mM Tris-acetic acid, 10mM magnesium acetate, 100 μ g/mlBSA, pH 7.9.
The present embodiment adopts atomic force microscope technology, establishes a kind ofly to study DNA double chain on single molecules level the method for cleavage reaction occurs under the effect of nicking restriction endonuclease.Difference modifying DNA 1 and DNA2 on substrate surface and AFM probe.When AFM probe and substrate surface near time, by the Complementary hybridization of DNA1 and DNA2, form DNA1/DNA2 duplex structure.Nicking restriction endonuclease can particular sequence in specific recognition double-stranded DNA 1/DNA2, and is cut off by single stranded DNA 1.Because the DNA hybridization length cut off on rear suprabasil DNA and AFM probe shortens, therefore when AFM probe upwards lifts, the interaction force recorded between DNA by atomic force microscope is reduced.
By reference to the accompanying drawings the specific embodiment of the present invention is described although above-mentioned; but not limiting the scope of the invention; one of ordinary skill in the art should be understood that; on the basis of technical scheme of the present invention, those skilled in the art do not need to pay various amendment or distortion that creative work can make still within protection scope of the present invention.
Claims (10)
1. atomic force microscope is for detecting a method for single molecules level intermolecular interaction, it is characterized in that: substrate surface modifying DNA 1 and on AFM probe modifying DNA 2; When AFM probe and substrate surface near time, by the Complementary hybridization of DNA1 and DNA2, form DNA1/DNA2 duplex structure; Adopt the particular sequence in nicking restriction endonuclease specific recognition double-stranded DNA 1/DNA2, and single stranded DNA 1 is cut off; Then adopt the acting force between atomic force microscope detection DNA, thus detect the change of DNA double chain Interaction Force of DNA before and after nicking restriction endonuclease is sheared.
2. the method for claim 1, it is characterized in that, the concrete grammar of described AFM probe modification DNA2 is: AFM probe is carried out hydroxylation modification, obtain the AFM probe of hydroxyl modified, then the AFM probe of activated hydroxyl groups modification, AFM probe after activation and amido modified DNA2 are fixed reaction, take out AFM probe, aftertreatment is carried out to AFM probe.
3. the method for claim 1, it is characterized in that, on described substrate surface, the concrete grammar of modifying DNA 1 is: substrate adopts gold substrate, first pre-service gold substrate, then the DNA1 of the gold substrate handled well and sulfydryl modification is fixed reaction, 37 DEG C are reacted more than 3 hours.
4. the method for claim 1, it is characterized in that, the concrete grammar of the acting force that described employing atomic force microscope detects between DNA is: dropped in by buffer solution 3 and be modified with in the gold substrate of DNA1, drop is fixed on the scanner of atomic force microscope, surveys the interaction force F1 between DNA; When using nicking restriction endonuclease, by the mixed solution containing 1 × nicking restriction endonuclease damping fluid, nicking restriction endonuclease and described buffer solution 3, be added drop-wise in gold substrate, drop be fixed on the scanner of atomic force microscope, survey the interaction force F2 between DNA; Thus detect the change of DNA double chain Interaction Force of DNA before and after nicking restriction endonuclease is sheared.
5. method as claimed in claim 2, is characterized in that: the process that described hydroxylation is modified is: AFM probe to be immersed in the mixed solution of the concentrated sulphuric acid and hydrogen peroxide 30 minutes, deionized water is cleaned, and obtains hydroxyl modified AFM probe.
6. method as claimed in claim 2, it is characterized in that: described reactivation process is: the AFM probe of hydroxyl modified being immersed in 200 μ l concentration is in 100mM N-hydroxy-succinamide (NHS) solution, after lucifuge places 30 minutes, deionized water rinsing is clean.
7. method as claimed in claim 2, is characterized in that: the process of aftertreatment is: first rinse three times with buffer solution 2, then cleans with deionized water, air drying 30 minutes; The composition of described damping fluid 2: 300mM NaCl, 20mMNa
2hPO
4, 2mM ethylenediamine tetraacetic acid, 7mM lauryl sodium sulfate, pH=7.4; Effect: for cleaning AFM probe.
8. method as claimed in claim 2, is characterized in that: the process of described fixation reaction is: the AFM probe being modified with DNA2 being immersed in 200 μ l concentration is in the amido modified DNA2 solution of 1 μM, and 25 DEG C are reacted more than 12 hours.
9. method as claimed in claim 3, is characterized in that: the process of described pre-service gold substrate is: by gold substrate cleaning, drying; Process concrete is further: soak ultrasonic 10 minutes with cleaning fluid, and deionized water rinsing is clean, and nitrogen dries up; Described cleaning fluid is: the mixed solution of ammoniacal liquor and hydrogen peroxide, Qi Zhongshui: ammoniacal liquor: the volume ratio of hydrogen peroxide is 5:1:1.
10. method as claimed in claim 3, is characterized in that: described fixation reaction process is: the gold substrate handled well being immersed in 1ml concentration is be fixed reaction in the sulfydryl modification DNA1 of 1 μM.
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