JP2006058094A - Effective size determining method of molecule, method for bonding molecule to substrate, and molecule detection device - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To provide a technique capable of controlling the deposit density of a molecule bonded to the surface of a solid to clear the structure or behavior in the solution of the molecule bonded to the surface of the solid and capable of realizing the enhancement of the reliability and sensitivity of a device using the molecule bonded to the surface of the solid. <P>SOLUTION: When the molecule having charge is bonded to a substrate, an electrolyte is allowed to coexist in a solution containing the molecule and, by adjusting the screening effect due to the electrolyte and considering the effective size of the molecule in the solution, the deposit density of the molecule is controlled. The effective size of the molecule having charge in the solution containing the electrolyte and the molecule having the charge can be estimated from the screening effect due to the electrolyte. <P>COPYRIGHT: (C)2006,JPO&NCIPI

Description

  The present invention relates to a method for attaching molecules to a substrate and a device produced using the method, which are used for biochips, DNA chips, and the like.

  In part due to the influence of the nanotechnology initiative advocated in the United States in 2000, nanotechnology has become a keyword that attracts many people in recent years. In particular, the field of nanobiotechnology, which is a fusion of semiconductor microfabrication technology (semiconductor nanotechnology) and biotechnology, is a new field that has the potential to solve existing problems from the ground up. Came to be.

The key technology for nanobiotechnology is how to attach biomolecules such as DNA and proteins to solids such as semiconductors and metals, and to have functions on the solid surface. A method of attaching molecules to a solid surface represented by an LB (Langmuir Brodgett) film by physical adsorption has been widely known for a long time. However, with physical adsorption alone, peeling of the molecule occurs with time or repeated use. . For this reason, in recent years, adhesion of molecules by chemical adsorption utilizing a chemical reaction between a solid surface and molecules has become common. In particular, a method of attaching molecules by chemical adsorption using an SH (thiol) group at one end of a molecule and utilizing a covalent bond between S (sulfur) and a metal or semiconductor has been proposed and widely used in research and development. (For example, see Non-Patent Document 1)
When a molecule having an alkyl chain in which an SH group is arranged at one end is used as a molecule, a regularly arranged film of one molecule can be arranged on a solid by van der Waals force of the alkyl chain. The method for producing this film is easy. That is, when the solid surface is immersed in a solution containing this molecule, a monomolecular film (self-assembled monomolecular film) is spontaneously formed on the solid surface.

By attaching a functional group having DNA or protein and other functions to a part of the alkyl chain, a monomolecular film having a function on the surface can be formed. (For example, see Non-Patent Document 2)
“Chemical Reviews”, 1996, Vol. 96, p. 1533-1554 “Bioconjugate Chemistry”, 1997, Vol. 8, p. 31-37 “Nucleic Acids Research”, 2001, Vol. 29, p. 5163-5168 “Journal of American Chemical Society”, 1997, Vol. 119, p. 8916-8920

  However, when the solid surface is modified by simply using molecules having an alkyl chain having functional groups having various functions, the density of molecules having an alkyl chain attached to the surface (in the present invention, the solid surface such as a substrate) It is difficult to control the density of molecules attached to the substrate (referred to as “attachment density”).

In addition, it is known that chemisorption of such molecules depends on diffusion, and an example of observing changes in the adhesion density of molecules with time has been reported. Therefore, it is difficult to obtain a low adhesion density with a wide reproducibility by time control so that the influence of molecular interaction is negligible because the intermolecular-molecule spacing is wide. (For example, see Non-Patent Document 3)
Furthermore, biomolecules such as DNA and proteins are relatively large molecules compared to normal molecules with alkyl chains, and only a dense (ie, high-density biomolecule) self-assembled monolayer was produced. In this case, the steric hindrance between the biomolecules becomes large, and there is a problem that the free movement of the biomolecules is inhibited. On such a surface, the reaction between biomolecules, the signal related to the thermal motion of the biomolecule (for example, the signal related to fluctuation motion and bending motion) cannot be obtained sufficiently.

  On the other hand, in the field of biosensors that use such reactions between molecules and molecular movements for sensing technology, techniques for controlling adhesion density and producing low adhesion density with high reproducibility are very important. Accordingly, there is a strong need for a technique for controlling the adhesion density of molecules attached to a solid surface.

  DNA has a negative charge in the phosphate group which is the backbone in aqueous solution. For this reason, DNA repels each other in an aqueous solution. In an aqueous solution containing an electrolyte, it is known that ions having a positive charge surround the DNA and exhibit an action (also called a screening effect or Debye effect) that cancels the charge of the DNA.

  This screening effect depends on the electrolyte concentration. That is, by controlling the electrolyte concentration, the closest distance between DNAs can be controlled, and the final adhesion density of molecules having a charge such as DNA may be controlled.

However, although there is a report confirming this effect, it is only a qualitative examination, and the adhesion density cannot be predicted. (For example, see Non-Patent Document 4)
Furthermore, many of the string-like molecules such as DNA are unclear what structure is taken in an aqueous solution, making handling of such molecules even more difficult.

  An object of the present invention is to solve the above-described problems and to develop a technique capable of controlling the adhesion density of molecules adhering to a solid surface.

  In addition, the purpose is to develop a technology that can clarify the structure and behavior of molecules attached to the solid surface in a solution, and realize high reliability and high sensitivity of devices using molecules attached to the solid surface. Yes.

  Still other objects and advantages of the present invention will become apparent from the following description.

  According to one aspect of the present invention, there is provided a method for determining the effective size of a molecule having a charge, which estimates the effective size of the molecule having a charge in a solution containing the electrolyte and the molecule having a charge from the screening effect by the electrolyte. The

  According to the embodiment of the present invention, it is possible to know the effective size of a molecule having a charge for controlling the adhesion density of molecules adhering to a solid surface.

  According to another aspect of the present invention, when a molecule having a charge is attached to a substrate, the electrolyte is allowed to coexist in a solution containing the molecule, the screening effect by the electrolyte is adjusted, and the effectiveness of the molecule in the solution is adjusted. Considering the size provides a method for attaching charged molecules to a substrate that controls the adhesion density of the molecules.

  According to the aspect of the present invention, a desired adhesion density can be realized.

  It is preferable to estimate the effective size of the charged molecule in the solution containing the electrolyte and the charged molecule from the screening effect by the electrolyte as described above, and use this effective size as the effective size.

  In any of the above embodiments, any electrolyte may be used. However, the use of an electrolyte composed of a monovalent cation and a monovalent anion, the monovalent cation and the monovalent cation. The electrolyte composed of an anion is preferably NaCl or KCl or a mixture thereof.

  According to still another aspect of the present invention, there is provided an apparatus for attaching charged molecules to a substrate, wherein the molecule attaching method to the substrate is used to control the density of molecules attached to the substrate. Provided. According to the aspect of the present invention, a substrate having a desired adhesion density can be obtained.

  According to still another aspect of the present invention, using the above-described method for attaching molecules to a substrate, the molecule-molecule distance to be attached to the substrate is at least twice or less than the effective length of the molecule. Thus, there is provided a molecular detection device that uses a substrate, the adhesion density of which is controlled, as a molecular detection unit.

  According to the embodiment of the present invention, the structure and behavior of molecules attached to a solid surface in a solution can be clarified. In addition, a highly reliable device with excellent sensitivity can be realized.

  It is preferable that the substrate is made of a conductive material, a semiconductor, or an insulator, and particularly that the substrate is made of gold or platinum.

  In each of the above embodiments, the charged molecule is a protein, DNA, RNA, antibody, natural or artificial single-stranded nucleotide body, natural or artificial double-stranded nucleotide body, aptamer, or antibody. Products obtained by limited degradation with degrading enzymes, organic compounds having affinity for proteins, biopolymers having affinity for proteins, complexes thereof, positively or negatively charged ionic polymers and the like It is preferable that the substance contains a substance selected from the group consisting of any combination of the above, that the molecule having a charge has a thiol group, and that the molecule having a charge contains a fluorescent dye.

  According to the present invention, the adhesion density of molecules adhering to the solid surface can be controlled, whereby the structure and behavior of the molecules adhering to the solid surface in the solution can be clarified. In addition, high reliability and high sensitivity of the device using molecules attached to the solid surface can be realized.

  Embodiments of the present invention will be described below with reference to the drawings, examples and the like. In addition, these figures, Examples, etc. and description illustrate the present invention and do not limit the scope of the present invention. It goes without saying that other embodiments may belong to the category of the present invention as long as they match the gist of the present invention.

  When attaching a necessary molecule to a solid surface, a method of immersing the solid in a solution containing the molecule is generally used. At this time, electrostatic repulsion of the molecule occurs by using a molecule that is charged (has an electric charge) in a solution for the molecule to be attached, or a substance in which a substance having an electric charge is bonded. For this reason, other molecules cannot approach the molecules once attached to the solid surface due to electrostatic repulsion.

  In the present invention, a molecule having a charge, a molecule in which a substance having a charge is bound, and the like are collectively referred to simply as a “molecule having a charge” or a “charged molecule”. Details will be described later.

  When an aqueous solution containing an electrolyte is used as the solution, ions having a charge opposite to that of the molecule (counter ion) cover the molecule at a certain existence probability distance and neutralize the charge of the molecule. . The action of canceling the charge between molecules in this way is called a screening effect, and this counter ion layer is called a diffusion electric double layer.

The thickness of the diffusion electric double layer depends on the salt concentration (ion concentration) of the electrolyte, and the higher the salt concentration of the electrolyte, the thinner the layer. The thickness of this layer is widely known as the Debye length (L _Debye), for example, 1: 1 type electrolyte (monovalent cation and an electrolyte consisting of a monovalent anion) in be expressed by the following equation Can do.

^{_{L Debye = (2000N A cz 2}} e 2 / (ε r ε 0 kT)) -1/2 (m) ··· (1)
Here, N _A is Avogadro's number, c is the ion concentration (moL / L) of the electrolyte, z is the valence of the electrolyte ion, e is the unit charge, ε _r is the relative dielectric constant of the medium, and ε ₀ is the dielectric constant of the vacuum , K is a Boltzmann constant, and T is an absolute temperature.

From this equation, the change in L _Debye when the ion concentration of the electrolyte is changed can be easily estimated. FIG. 1 shows changes in L _Debye when the ion concentration of a 1: 1 type electrolyte such as NaCl is changed. It can be seen that in the region where the ion concentration of the electrolyte is high, L _Debye is small and the screening effect is large. That is, in such an ion concentration region of the electrolyte, electrostatic repulsion between charged molecules is suppressed, and it can be predicted that a charged molecule film having a high adhesion density can be produced. Furthermore, by taking into consideration the screening effect and the size of charged molecules in the solution, the adhesion density can be more accurately controlled.

Thus, if ions used as the electrolyte are determined, L _Debye can be uniquely calculated. In addition, if the size of the charged molecule in the aqueous solution is known, the density of the charged molecule, which varies depending on the ion concentration of the electrolyte, can be predicted by calculation by considering the size and L _Debye .

  Hereinafter, a case where negatively charged spherical charged molecules having a radius of 1 nm are attached to the solid surface will be described as an example.

Assuming that electrostatic repulsion of charged molecules does not occur and when adsorption of a single layer of molecules is considered on a flat solid surface, a hexagonal molecular film is formed as a close-packed structure as shown in FIG. Can be considered. In this case, the molecular adhesion density (closest surface density) is calculated by using the radius r of the molecule,
Adhesion density = 1 / (2r ² √3) (cm ⁻² ) (2)
It can be expressed as. A molecule having r of 1 nm has a constant adhesion density of 2.9 × 10 ¹³ cm ⁻² .

In consideration of electrostatic repulsion of charged molecules and taking L _Debye into consideration, the adsorbed molecule layer is separated from the molecule by L _Debye × 2 as shown in FIG. ,
Adhesion density = 1 / (2 (r + L _Debye ) ² √3) (cm ⁻² ) (3)
It can be expressed. For a molecule having a 1: 1 type electrolyte such as NaCl and having an r of 1 nm, the adhesion density can be controlled by changing the ion concentration of the electrolyte as shown in FIG.

  The above is a case where the size of the charged molecule in the aqueous solution is known, but even if it is unknown, the charged molecule adhesion density at a predetermined electrolyte ion concentration is once measured by an experiment. The size of an unknown molecule can be estimated from the value, and by taking the size and screening effect into consideration, it is possible to predict the dependence of the adhesion density on the ion concentration of the electrolyte.

  That is, in the method for determining the effective size of the charged molecule according to the present invention, the effective size of the charged molecule in the solution containing the electrolyte and the charged molecule is estimated from the screening effect by the electrolyte.

  Specifically, for example, when the Debye length is obtained from the ion concentration of the electrolyte using the equation (1), and this Debye length and the measured adhesion density data of charged molecules are applied to the equation (3), the charged molecule Can be obtained as the molecular radius. In this case, the adhesion density is determined by using XPS, focusing on a specific element of the adhering molecule, by quantifying the adhering molecule with a radioactive element label attached beforehand, It can be determined by a method of measuring and quantifying the redox current of the redox marker to be summed.

  The electrolyte used in this case may be any one as long as it does not violate the gist of the present invention, but a 1: 1 type electrolyte such as NaCl or KCl is preferable from the viewpoint of simplifying the influence on the electric resistance molecule. This mixture may be used.

  As described above, the “charged molecule” in the present invention includes a simple molecule having a charge as well as a substance having a charge bonded to a molecule having a charge or a molecule having no charge. Substances and molecules have a charge as a whole, or substances that do not have a charge bind to a molecule that has a charge, so that the substance and molecules have a charge as a whole Also included. In the latter two cases, the group is the “charged molecule” according to the present invention. In this case, the “bond” may be a chemical bond or a physical bond, but the former is preferable because of high bond stability.

  Substances in the above are obtained by subjecting proteins, DNA, RNA, antibodies, natural or artificial single-stranded nucleotide bodies, natural or artificial double-stranded nucleotide bodies, aptamers, and antibodies to limited degradation with proteolytic enzymes. Selected from the group consisting of products, organic compounds with affinity for proteins, biopolymers with affinity for proteins, complexes thereof, positively or negatively charged ionic polymers and any combinations thereof Substances that can bind to such substances are preferred, and those having the property of specifically binding to these substances are preferred.

  Therefore, as the “charged molecule” according to the present invention, protein, DNA, RNA, antibody, natural or artificial single-stranded nucleotide body, natural or artificial double-stranded nucleotide body, aptamer, and antibody are proteolytic enzymes. Products obtained by limited decomposition with, organic compounds having affinity for proteins, biopolymers having affinity for proteins, complexes thereof, positively or negatively charged ionic polymers and any of them Those comprising a substance selected from the group consisting of: As the “charged molecule” according to the present invention, one having a thiol group is preferable in order to facilitate attachment to the substrate.

  Here, in the present invention, the “nucleotide body” means any one of the group consisting of mononucleotide, oligonucleotide and polynucleotide, or a mixture thereof. Such materials are often negatively charged. Single strands or double strands can be used. It can also be made part of the charged molecule by hybridization. In addition, protein, DNA, and a nucleotide body may be mixed. Biopolymers include those derived from living organisms, those obtained by processing those derived from living organisms, and synthesized molecules.

The above "product" is obtained by subjecting an antibody to limited digestion with a proteolytic enzyme. As long as it meets the gist of the present invention, an antibody Fab fragment or (Fab) ₂ fragment, an antibody Fab fragment or (Fab) ) Any fragment such as a fragment derived from ₂ fragments or a derivative thereof can be included.

As the antibody, for example, a monoclonal immunoglobulin IgG antibody can be used. In addition, as a fragment derived from an IgG antibody, for example, an Fab fragment or (Fab) ₂ fragment of an IgG antibody can be used. Furthermore, fragments derived from such Fab fragments or (Fab) ₂ fragments can also be used. Examples that can be used as organic compounds having affinity for proteins include enzyme substrate analogs such as nicotinamide adenine dinucleotide (NAD), enzyme activity inhibitors, neurotransmission inhibitors (antagonists), and the like. Examples of biopolymers having affinity for proteins include proteins serving as protein substrates or catalysts, and elemental proteins constituting a molecular complex.

The “charged molecule” in the present invention has a role of making the substrate surface hydrophobic or hydrophilic by adhering to the substrate, or by adsorbing special molecules such as DNA and proteins to the surface, It is possible to have a role to give functions that the original solid surface did not have. Specifically, the surface is covered with —CH ₃ to make it hydrophobic, or covered with NH ³⁺ or COO ⁻ to make it a + charged surface or a −charged surface, making them hydrophilic, respectively, DNA or protein The formation of a monomolecular film having functionality by adsorbing on the surface can be exemplified.

  In the method for attaching charged molecules to the substrate according to the present invention, when the charged molecules are attached to the substrate, the electrolyte is allowed to coexist in the solution containing the molecules, and the screening effect by the electrolyte is adjusted. Also consider the effective size of the molecules in the solution.

  For example, since the adhesion density, Debye length, and effective size of the molecule are linked by the equation (3), the desired Debye length is calculated from the effective size of the molecule to be attached and the desired adhesion density, and the Debye length is calculated. Thus, the type of electrolyte and ion concentration can be determined. In this manner, molecules can be attached to the substrate so as to obtain a substrate surface having a desired molecular adhesion density.

  In this case, when the effective size of the molecule is known, the effective size may be used. When the effective size of the molecule is unknown, the effective size of the charged molecule in the solution containing the electrolyte and the charged molecule may be estimated from the screening effect by the electrolyte as described above. As the electrolyte in this case, it is preferable to use a 1: 1 type electrolyte.

  By adopting such a method, it is possible to obtain an apparatus for attaching charged molecules to a substrate, which can control the density of molecules attached to the substrate. Such an apparatus may be any apparatus as long as it meets the object of the present invention. For example, this system is a precision system that combines and miniaturizes multiple functional parts such as machinery, optics, and fluid, which are manufactured using technology that makes very fine products based on semiconductor processing technology. MEMS (Micro Electro Mechanical Systems) or μTAS (Micro Total Analysis System), a chemical analysis system that integrates micro pumps, micro valves, sensors, etc. Can do. Specifically, the MEMS or μTAS includes an ion sensor such as a pH sensor or a gas sensor, a DNA chip or a protein chip used for detection of charged molecules that are fully or partially charged, such as DNA and protein. Such a molecular detection device can be exemplified. In the present invention, “detection” includes determining whether or not a charged molecule or a molecule that specifically binds to the charged molecule is present, or binding to the charged molecule or the charged molecule. This includes determining the type, size and quantity of the substance.

  With this device, the charged molecule adhesion density on the substrate can be set to a desired value, and the movement of charged molecules can be observed without any influence between charged molecules, or the influence between charged molecules can be examined. Is possible.

  As a molecule detection device used for detecting charged molecules for observing the movement of charged molecules in a state where there is no mutual influence between charged molecules, the molecule attached to the substrate using the above-described method for attaching molecules to the substrate is used. -A substrate that controls the adhesion density so that the distance between molecules is at least twice the effective length of the molecule and prevents the molecules from physically contacting each other is used as a molecule detection unit. preferable.

  In addition, as a molecular detection device used for detection of charged molecules in order to examine the influence between charged molecules, the above-described method for attaching molecules to a substrate is used. It is preferable to use a substrate in which the adhesion density is controlled so as to be less than twice the effective length of the substrate and the molecules are in physical contact with each other as the molecule detection unit.

  In addition, the distance between molecules in the above can be obtained from the adhesion density.

  In such a molecular detection device, any known method may be used as a method for detecting a molecule. For example, a method of applying a voltage between a substrate and a solution containing an electrolyte and taking out the response as an electric signal, a method of attaching a fluorescent dye to a charged molecule, and detecting this fluorescence can be exemplified.

  FIG. 7 shows an example of a molecular detection device that attaches a fluorescent dye to a charged molecule and detects this fluorescence. The molecular detection device 1 of FIG. 7 has a charged molecule 5 having a fluorescent dye 4 stretched (left side) and contracted (right side) on an Au electrode 3 (corresponding to a substrate in the present invention) provided on a pedestal 2. ). The charged molecule 5 in a contracted state can be brought into an extended state by applying a predetermined potential difference between the Au electrode 3 and the counter electrode 8 by an external electric field applying device 9. As a result, the distance between the fluorescent dye 4 and the Au electrode 3 changes. At this time, when the light 11 is irradiated from the light irradiation device 10, fluorescence 12 is obtained from the charged molecule 5 in the extended state (left side).

  When the molecular detection device according to the present invention is used, the adhesion density of molecules adhering to the solid surface can be controlled, whereby the structure and behavior of molecules adhering to the solid surface in the solution can be clarified. High reliability and high sensitivity of devices using molecules attached to the surface can be realized.

  For example, if DNA or an antibody is used as a charged molecule attached to the substrate surface and its density is quantitatively controlled, the structure and behavior of the target DNA or protein in the solution can be clarified. Further, by optimizing the detection conditions through such information, it is possible to realize high reliability and high sensitivity of the device. Therefore, it is easy to determine the presence / absence and to determine the type, size, and amount of the target.

  In addition, when observing the electrical and physical properties of each molecule on the functional surface and applying it to a biosensor as MEMS or μ-TAS, these molecules are sufficiently separated (ie, steric hindrance). In this field, the technique of the present invention is very effective.

  Furthermore, in contrast to this, when it is necessary to interact with surrounding molecules, such as when attaching attached molecules to each other, exchange of charges between molecules, transfer of optical energy, etc. These molecules need to be sufficiently close to each other, but the technique of the present invention is very effective even in such a field.

  Furthermore, it is expected that the technology of the present invention can greatly contribute to the elucidation of the function of charged molecules whose behavior in an aqueous solution is unknown, leading to the discovery of new functional materials and functional surfaces.

  As the substrate according to the present invention, any of conductive materials such as metals, semiconductors such as silicon, insulators such as glass, ceramics, plastics, and sapphire can be used depending on the purpose. As the conductive material, it is conceivable to use a conductive substance itself or to provide a conductive substance layer on the surface of glass, ceramics, plastic, metal or the like. Such a conductive substance may be any material such as a single metal, an alloy, or a laminate thereof. Noble metals represented by Au are chemically stable and can be preferably used.

  Next, examples of the present invention will be described in detail.

[Example 1]
This example relates to determining the effective radius of a single-stranded oligonucleotide in an aqueous solution, and further to controlling the attachment density of the oligonucleotide attached to the substrate.

A 24-residue single-stranded oligonucleotide introduced with a thiol (—C ₆ H ₁₂ —SH) group having a C ₆ H ₁₂ alkyl chain at the 3 ′ end was synthesized, and the gold electrode polished with this thiol group at room temperature. The reaction was performed for 30 minutes to bind the single-stranded oligonucleotide to the gold electrode. The thiol group may be introduced in the middle of the single strand or at the 5 ′ end. The aqueous solution used for the reaction contained Tris buffer (2-amino-2-hydroxypropylene-1,3-diol) 10 mM and was adjusted to pH 7.4.

  NaCl was used as the electrolyte, and the ion concentration (salt concentration) of the electrolyte was changed to control the screening effect of the negatively charged oligonucleotide. The structure of the oligonucleotide is known, but the effective size in the aqueous solution is unknown, so the thiol group of the single-stranded oligonucleotide is reacted with the gold electrode in advance under the conditions of salt concentrations of 3 mM, 500 mM, and 1000 mM. The adhesion density of the oligonucleotide attached to the surface was measured.

  FIG. 5 is a graph showing the relationship between the adhesion density of a single-stranded oligonucleotide and the ion concentration of the electrolyte, and the relationship between the Debye length and the ion concentration of the electrolyte. The circles in FIG. 5 are the adhesion density obtained in the experiment. As a result of calculation so that the calculation curves obtained from the formulas (1) and (3) were superimposed on this experimental value, the effective size of the 24-residue oligonucleotide in the aqueous solution was found to have a radius of 1.9 nm.

Next, when the electrode surface controlled to 3 × 10 ¹² cm ⁻² as a desired adhesion density is obtained from this calculated curve, the salt concentration should be controlled to 50 mM from the calculated curve once obtained. I understand. In the figure, ● represents experimental values in which the oligonucleotide was attached by controlling the salt concentration to 50 mM. The condition of salt concentration with a desired adhesion density can be easily obtained from the calculation.

  In addition, the ■ marks indicate the results of an adhesion experiment when a 12-residue single-stranded oligonucleotide having a similar thiol group is used. As a result of calculation so that the calculation curves obtained from the formulas (1) and (3) are overlapped, it was found that this molecule also has an effective size similar to that of 24 residues in an aqueous solution. Both 12-residue single-stranded oligonucleotides and 24-residue single-stranded oligonucleotides are string-like molecules, but since there is no difference in the Debye length, a thiol group is modified at one end of the string-like molecule. When chemically adsorbed on the substrate, the molecular length is considered not to affect the effective size or Debye length.

  Thus, by using the present invention, it is possible not only to control the adhesion density of charged molecules such as oligonucleotides, but also to estimate the effective size of unknown molecules in aqueous solution and to obtain knowledge of the adhesion state. be able to.

[Example 2]
As a related example, using the above method, a 12-residue single-stranded oligonucleotide with a fluorescent dye attached at the tip and a thiol group on the opposite side is attached to a gold substrate with varying attachment density, The result of monitoring the fluorescence from the dye is shown in FIG. When the fluorescent dye approaches or comes into contact with the gold substrate, it is dimmed or extinguished due to a quenching effect.

  As is clear from FIG. 6, by changing the adhesion density, (1) a region where the fluorescence intensity depends only on the increase in the adhesion density without interfering with adjacent oligonucleotides due to low density, (2) adjacent The steric hindrance occurs with the oligonucleotide that is forced to stand and the oligonucleotide is forced to stand, reducing the quenching effect on the gold substrate, and increasing the fluorescence intensity significantly by increasing the adhesion density and decreasing the quenching effect. (3) Most of the oligonucleotides stand up, the quenching effect does not change, and the three regions can be observed: a high-density region in which the fluorescence intensity depends only on the increase in density.

  Therefore, by using the present invention, when the oligonucleotide is used for an application that allows free movement without being disturbed by surrounding nucleotides, the attached molecules are bound to the region (1). When the interaction with surrounding molecules is required, such as in the case of charge exchange between molecules and transfer of optical energy, etc., provision of devices with controlled adhesion density in the areas (2) and (3) Is possible.

  In addition, the invention shown to the following additional remarks can be derived from the content disclosed above.

(Appendix 1)
A method for determining an effective size of a molecule having a charge, wherein the effective size of the molecule having a charge in a solution containing an electrolyte and a molecule having a charge is estimated from a screening effect by the electrolyte.

(Appendix 2)
The effective size determination method of the molecule | numerator which has an electric charge of Additional remark 2 using the electrolyte which consists of a monovalent cation and a monovalent anion as said electrolyte.

(Appendix 3)
The effective sizing method for molecules having a charge according to appendix 2, wherein the electrolyte composed of the monovalent cation and the monovalent anion is NaCl, KCl, or a mixture thereof.

(Appendix 4)
The charged molecule is obtained by subjecting proteins, DNA, RNA, antibodies, natural or artificial single-stranded nucleotide bodies, natural or artificial double-stranded nucleotide bodies, aptamers, and antibodies to limited digestion with proteolytic enzymes. Products, organic compounds having affinity for proteins, biopolymers having affinity for proteins, complexes thereof, positively or negatively charged ionic polymers, and any combinations thereof. The effective size determination method of the molecule | numerator which has an electric charge in any one of Additional remarks 1-3 which comprises the substance chosen.

(Appendix 5)
The method for determining the effective size of a molecule having a charge according to any one of appendices 1 to 4, wherein the molecule having a charge has a thiol group.

(Appendix 6)
The method for determining the effective size of a molecule having a charge according to any one of appendices 1 to 5, wherein the molecule having a charge comprises a fluorescent dye.

(Appendix 7)
In attaching a molecule having a charge to a substrate, by coexisting an electrolyte in a solution containing the molecule, adjusting the screening effect by the electrolyte, and considering the effective size of the molecule in the solution, A method for attaching molecules having a charge to a substrate, which controls the adhesion density of the molecules.

(Appendix 8)
The effective size of the molecule having the charge in the solution containing the electrolyte and the molecule having the charge is estimated from the screening effect by the electrolyte, and the effective size is used as the effective size. A method for attaching charged molecules.

(Appendix 9)
9. The method for attaching molecules having a charge to a substrate according to appendix 7 or 8, wherein an electrolyte comprising a monovalent cation and a monovalent anion is used as the electrolyte.

(Appendix 10)
10. The method for attaching molecules having charge to a substrate according to appendix 9, wherein the electrolyte composed of a monovalent cation and a monovalent anion is NaCl, KCl, or a mixture thereof.

(Appendix 11)
An apparatus for attaching charged molecules to a substrate using the method for attaching molecules to a substrate according to any one of appendices 7 to 10, wherein the density of molecules attached to the substrate can be controlled.

(Appendix 12)
Using the method for attaching molecules to a substrate according to any one of appendixes 7 to 10, the adhesion density is controlled so that the distance between molecules to be attached to the substrate is at least twice the effective length of the molecules. Molecule detection device that uses the processed substrate as a detection part of the molecule.

(Appendix 13)
Using the method for attaching molecules to the substrate according to any one of appendices 7 to 10, the adhesion density is controlled so that the molecule-molecule distance to be attached to the substrate is less than twice the effective length of the molecule. Molecule detection device that uses the processed substrate as a detection part of the molecule.

(Appendix 14)
The charged molecule is obtained by subjecting proteins, DNA, RNA, antibodies, natural or artificial single-stranded nucleotide bodies, natural or artificial double-stranded nucleotide bodies, aptamers, and antibodies to limited digestion with proteolytic enzymes. Products, organic compounds having affinity for proteins, biopolymers having affinity for proteins, complexes thereof, positively or negatively charged ionic polymers, and any combinations thereof. 14. The molecular detection device according to appendix 12 or 13, comprising a substance to be selected.

(Appendix 15)
The molecular detection device according to any one of appendices 12 to 14, wherein the molecule having a charge has a thiol group.

(Appendix 16)
The molecular detection device according to any one of appendices 12 to 15, wherein the molecule having an electric charge comprises a fluorescent dye.

(Appendix 17)
The molecular detection device according to any one of appendices 12 to 16, wherein the substrate is made of a conductive material, a semiconductor, or an insulator.

(Appendix 18)
18. The molecular detection device according to appendix 17, wherein the substrate is made of gold or platinum.

It is a graph which shows the ion concentration dependence of Debye length when using a 1: 1 type electrolyte. It is a schematic diagram which shows the principle of the close-packed structure of the molecule | numerator adhering to a board | substrate, and the principle of adhesion density calculation. It is a schematic diagram which shows the principle of the closest packing structure of the molecule | numerator adhering to a board | substrate when the Debye length is considered, and the principle of adhesion density calculation. It is a graph which shows the ion concentration dependence of the electrolyte of the adhesion density of the adsorption molecule calculated in consideration of Debye length. It is a graph which shows the relationship between the adhesion density of a single strand oligonucleotide and the ion concentration of electrolyte, and the relationship between Debye length and the ion concentration of electrolyte. It is a graph which shows the relationship between fluorescence intensity and adhesion density. It is a schematic diagram showing an example of a molecular detection device that attaches a fluorescent dye to a charged molecule and detects this fluorescence.

Explanation of symbols

DESCRIPTION OF SYMBOLS 1 Molecule detection device 2 Base 3 Au electrode 4 Fluorescent dye 5 Charged molecule 8 Counter electrode 9 External electric field application apparatus 10 Light irradiation apparatus 11 Light 12 Fluorescence

Claims (10)

  A method for determining an effective size of a molecule having a charge, wherein the effective size of the molecule having a charge in a solution containing the electrolyte and the molecule having a charge is estimated from a screening effect by the electrolyte.   In attaching a molecule having a charge to a substrate, by coexisting an electrolyte in a solution containing the molecule, adjusting the screening effect by the electrolyte, and considering the effective size of the molecule in the solution, A method for attaching molecules having a charge to a substrate, which controls the adhesion density of the molecules.   3. The substrate according to claim 2, wherein an effective size of the molecule having a charge in a solution containing an electrolyte and a molecule having a charge is estimated from a screening effect by the electrolyte, and the effective size is used as the effective size. Of attaching molecules having the following charge.   The method for attaching molecules having a charge to a substrate according to claim 2 or 3, wherein an electrolyte comprising a monovalent cation and a monovalent anion is used as the electrolyte.   5. The method for attaching molecules having a charge to a substrate according to claim 4, wherein the electrolyte composed of a monovalent cation and a monovalent anion is NaCl, KCl, or a mixture thereof.   Using the method for attaching molecules to a substrate according to any one of claims 2 to 5, the adhesion density is adjusted so that the molecule-molecule distance to be attached to the substrate is at least twice the effective length of the molecules. A molecular detection device that uses a controlled substrate as a detection unit for the molecule.   Using the method for attaching molecules to a substrate according to any one of claims 2 to 5, the adhesion density is adjusted so that the distance between molecules to be attached to the substrate is less than twice the effective length of the molecules. A molecular detection device that uses a controlled substrate as a detection unit for the molecule.   The charged molecule is obtained by subjecting proteins, DNA, RNA, antibodies, natural or artificial single-stranded nucleotide bodies, natural or artificial double-stranded nucleotide bodies, aptamers, and antibodies to limited digestion with proteolytic enzymes. Products, organic compounds having affinity for proteins, biopolymers having affinity for proteins, complexes thereof, positively or negatively charged ionic polymers, and any combinations thereof. The molecular detection device according to claim 6 or 7, comprising a substance to be selected.   The molecular detection device according to claim 6, wherein the molecule having a charge has a thiol group.   The molecular detection device according to claim 6, wherein the molecule having an electric charge comprises a fluorescent dye.

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