WO2006016787A1 - Cantilever for atomic force microscope, and method of measuring biomolecule interaction using the same - Google Patents

Abstract

The present invention relates generally to atomic force microscopy(AFM), a cantilever for AFM, and an apparatus and a measuring method of intermolecular interaction between the biomolecules using the same.

Description

TITLE OF THE INVENTION

CANTILEVER FOR ATOMIC FORCE MICROSCOPE, AND METHOD OF MEASURING BIOMOLECULE INTERACTION USING THE SAME

BACKGROUND OF THE INVENTION

(a) Field of the Invention

The present invention relates generally to atomic force microscopy(AFM), a cantilever for AFM, and an apparatus and a measuring method of intermolecular interaction between the biomolecules using the same.

(b) Description of the Related Art

In the post-genomic era, quantitative and comprehensive studies on genome for drug discovery, as well as disease diagnosis and prevention, are fast-growing research and development areas. Growth in these sectors has already produced a strong demand for advanced biomolecular recognition probes with high sensitivity and excellent specificity (K. Wang et al., Anal Chem. 76, 5721 2004).

Out of many biomolecular recognition studies, understanding the mechanical stability (or recognition property) of complementary DNA strands is crucial for a profound understanding of numerous important biological processes, such as DNA transcription, gene expression and regulation, and DNA replication. In this respect, stretching and force- induced melting of DNA have thus been investigated using several techniques, such as optical tweezers, micro-pipette suction, and AFM (H. Clausen-Schaumann, M. Seitz, R. Krautbauer, H. E. Gaub, Curr. Opin. Chem. Biol. 4, 524 , 2000; R. Merkel, Physics Reports 346, 343, 2001; G. U. Lee, L. A. Chris, R. J. Colton, Science 266, 771, 1994).

As it is possible to measure specific interactions between individual molecules at small length scales and high sensitivity down to forces of a few piconewtons, AFM is becoming a rapidly developing technique for probing affinity and recognition properties at the molecular level (R. Krautbauer, M. Rief, H. E. Gaub, Nano Lett. 3, 493, 2003). Compared with other sensitive methods for force measurements, AFM has the advantages

i of high force resolution and high spatial resolution, and is operable under physiological conditions for investigation of specific interactions in biological processes, such as electrostatic interactions (J. Wang, A. J. Bard, Anal. Chem. 73, 2207, 2001), ligand-receptor binding (S. M. Rigby-Singleton et al, J. Chem. Soc, Perkin Trans. 2 1722, 2002), antigen- antibody interactions (F. Schwesinger et al, Proc. Natl. Acad. ScL U.S.A. 97, 9972, 2000), aptamer-protein interactions (C. Bai et al, Anal. Chem. 75, 2112, 2003), protein folding/unfolding (P. M. Williams et al, Nature 422, 446, 2003; M. S. Z. Kellermayer, S. B. Smith, H.L. Granzier, C. Bustamante, Science 276,1112, 1997), cell-cell adhesion (M. Benoit, D. Gabriel, G. Gerisch, H. E. Gaub, Nature Cell Biol. 2, 313, 2000) and DNA-DNA hybridization (C. W. Frank, Biophys. J. 16, 2922, 1999).

Although many investigations have been performed on unbinding force measurement between complementary DNA strands (H. Clausen-Schaumann, M. Seitz, R. Krautbauer, H. E. Gaub, Curr. Opin. Chem. Biol. 4, 524, 2000; R. Merkel, Physics Reports 346, 343 , 2001; G. U. Lee, L. A. Chris, R. J. Colton, Science 266, 771. 1994; R. Krautbauer, M. Rief, H. E. Gaub, Nano Lett. 3, 493, 2003), the recognition between the DNA strands during the studies at the single molecular level is problematic. The typical immobilization approach suffered from multi-point interaction, and resolving out single molecular interactions has not been an easy task. In order to avoid the unwanted interaction, surface density was reduced by mixing with an inactive surfactant, but the approach resulted in low recognition efficiency leading to less reliable analysis. Therefore, commonly practiced surface chemistry for such immobilization such as oxide-silane and gold-thiol chemistry ( T. Hugel, M. Seitz, Macromol. Rapid. Commun. 22, 989, 2001; W. K. Zhang, X. Zhang, Prog. Polym. Sci. 28, 1271, 2003) has yet to be optimized to retrieve invaluable fundamental information on single DNA-DNA interaction during the force measurement with AFM.

The above information disclosed in this section is only for the enhancement of understanding of the background of the invention, and therefore it may contain information that does not form the prior art that is already known in this country to a person of ordinary skill in the art. SUMMARY OF THE INVENTION

An object of the invention is to provide a cantilever for atomic force microscopy

(AFM) comprising a cantilever body having a fixed end and a free end, the free end having a surface region being chemically modified by a dendron in which a plurality of termini of the branched region of the dendron are bound to the surface, and a terminus of the linear region of the dendron is functionalized.

Another object of the present invention is to provide the cantilever for AFM where the dendrons are spaced at regular intervals between about 0.1 nm and about 100 nm between the linear functionalized groups. In particular, the dendrons may be spaced at regular intervals of about 10 nm.

A further object of the present invention is to provide a method for manufacturing the cantilever, comprising (i) functionalizing the surface region of the cantilever so that it will react with the termini of the dendrons; and (ii) contacting the dendrons to the surface region so that the termini and the surface form a bond. An object of the present invention is to provide a method for manufacturing the cantilever, wherein a probe nucleotide is fixed to the terminus of the linear region of dendrons, comprising the steps of i) removing protecting group from the terminus of the linear region of the dendrons on the surface region; and ii) contacting the probe nucleotide or a linker molecule linked to the probe nucleotide to the terminus of the linear region of the dendrons on the substrate so that the probe nucleotide or the linker molecule and the terminus form a bond, wherein the linker molecule is a homo-bifunctional or hetero- bifunctional linker.

The present invention also provides an apparatus for measuring an interaction between one probe nucleotide and one target nucleotide by atomic force microscopy, the apparatus comprising:

a cantilever having a fixed end and a free end, the free end having a surface region being chemically modified by a dendron in which a plurality of termini of the branched region of the dendron is bound to the surface, and a terminus of the linear region of the dendron is attached to the probe nucleotide; a substrate immobilized by a target nucleotide; a controller for adjusting the relative position and orientation of the cantilever and target nucleotide substrate to cause an interaction between the probe nucleotide immobilized on the dendron-modified surface region of the cantilever and the target nucleotide immobilized on a substrate; and a detector for measuring a physical parameter associated with the interaction between the probe nucleotide and the sample nucleic acid.

In an embodiment, the substrate to be immobilized by the target nucleotide can be adopted by any kind of the surface modification method in the art. Preferably, the substrate has a dendron-modified surface. A further object of the present invention is to provide a method of assaying a target nucleotide for interaction with a probe nucleotide, the method comprising the steps of:

(a) providing a cantilever having a fixed end and a free end, the free end having a surface region being chemically modified by dendrons in which a plurality of termini of the branched region of the dendrons are bound to the surface, and a substrate; (b) chemically modifying the substrate to immobilize a target nucleotide thereon;

(c) chemically modifying the dendron-modified surface region of the cantilever to immobilize a probe nucleotide;

(d) coupling the substrate and the cantilever to an apparatus that includes a controller for adjusting the relative position and orientation of the substrate and the cantilever to cause an interaction between the probe nucleotide immobilized on the dendron-modified surface region of the cantilever and the target nucleotide immobilized on the substrate of the sample support member,

(e) controlling the relative position and orientation of the cantilever and the substrate to cause an interaction between the probe nucleotide and the target nucleotide; and

(f) measuring a physical parameter associated with the interaction between the probe nucleotide and the target nucleotide.

In the above, the terminus of the branched region may be functional ized with -COZ, -NHR, -OR', or -PR"3, wherein Z may be a leaving group, wherein R may be an alkyl, wherein R' may be alkyl, aryl, or ether, and R" may be H, alkyl, alkoxy, or O. In particular, COZ may be ester, activated ester, acid halide, activated amide, or CO-imidazoyl ; R may be C1-C4 alkyl, and R¹ may be C1-C4 alkyl. Further, in the substrate described above, the polymer may be a dendron. Still further, the linear region of the polymer may include a spacer region. Also the spacer region may be connected to the branched region via a first functional group. Such first functional group may be without limitation -NH2, -OH, -PH3, - COOH, -CHO, or -SH. Still further, the spacer region may comprise a linker region covalently bound to the first functional group.

In the substrate and AFM cantilever, preferably AFM tip, the linker region may comprise a substituted or unsubstituted alkyl, alkenyl, alkynyl, cycloalkyl, aryl, ether, polyether, ester, or aminoalkyl group. Still further, the spacer region may comprise a second functional group. The second functional group may include without limitation, -NH2, -OH, -PH3, -COOH, -CHO, or -SH. The second functional group may be located at the terminus of the linear region. Also, a protecting group may be bound to the terminus of the linear region. Such protecting group may be acid labile or base labile. In another embodiment of the invention, in the AFM cantilever as described above, a probe Nucleotide and/or a target nucleotide may be bound to the terminus of the linear region of the dendron. In particular, the target nucleotide and the probe nucleotide may be DNA, RNA, PNA, nucleotide analog, or a combination thereof. Further, the distance between the nucleotides bound to the linear region of the dendron may be from about 0.1 to about 100 nm.

In yet another embodiment of the invention, the substrate described above may be made of semiconductor, synthetic organic metal, synthetic semiconductor, metal, alloy, plastic, silicon, silicate, glass, or ceramic. In particular, the substrate may be without limitation a slide, particle, bead, micro-well, or porous material. . These and other objects of the invention will be more fully understood from the following description of the invention, the referenced drawings attached hereto and the claims appended hereto.

BRIEF DESCRIPTION OF THE DRAWINGS FIG. IA a schematic view of a bio-AFM, and FIG. IB and 1C are photographs of the bio-AFM.

FIG.2A is a schematic drawing of a cantilever for AFM, and FIG.2B shows an enlarged view of the tip of AFM cantilever in accordance with the exemplary embodiment of the present invention, FIG.2C shows a variety of commercially available AFM tip.

FIG.3 is a schematic drawing of the interface between the probe tip of AFM and substrate target for measuring binding and unbinding forces with the AFM methodology.

FIG.4A is a histogram showing the force distribution for a complementary 30-base pair with relatively narrow spacing at a retraction velocity of 110 nm/s, and FIG.4B to FIG.4C are direct measurements of single unbinding force of complementary 30 base pairs with a retraction velocity of 540 nm/s.

FIG.5A is a histogram showing for a complementary 30-base pair with relatively broad spacing at a retraction velocity of 110 nm/s, and FIG.5B to FIG.5C are measurements of binding force of a complementary 30 base pair at a retract velocity of 110 nm/s. FIG.6A and FIG.6B are a histogram showing the binding force distributions on complementary DNA duplexes, and FIG. 6C is a histogram showing the unbinding force distributions on complementary DNA duplexes.

FIG.7 is a histogram showing the binding force distributions for single base mismatched DNA duplexes. FIG.8 is a histogram showing the binding force distributions on double base mismatched DNA duplexes.

DETAILED DESCRIPTION

In the present application, "a" and "an" are used to refer to both single and a plurality of objects.

The term "dendrimer" is characterized by a core, at least one interior branched layer, and a surface branched layer (see Petar et al, Pages 641-645, In Chem. in Britain, August 1994). A "dendron" is a species of dendrimer having branches emanating from a focal point, which is or can be joined to a core, either directly or through a linking moiety to form a dendrimer. Many dendrimers include two or more dendrons joined to a common core. However, the term "dendrimer" may be used broadly to encompass a single dendron. As used herein, "hyperbranched" or "branched" as it is used to describe a macromolecule or a dendron structure is meant to refer to a plurality of polymers having a plurality of termini which are able to bind covalently or ionically to a substrate. In one embodiment, the macromolecule containing the branched or hyperbranched structure is "pre-made" and is then attached to a substrate.

As used herein, "immobilized" means insolubilized or comprising, attached to or operatively associated with an insoluble, partially insoluble, colloidal, particulate, dispersed, suspended and/or dehydrated substance or a molecule or solid phase comprising or attached to a solid support. As used herein, "linker molecule" and "linker" when used in reference to a molecule that joins the branched portion of a size-controlled macromolecule such as a branched/linear polymer to a protecting group or a ligand. Linkers may include, for instance and without limitation, spacer molecules, for instance selected molecules capable of attaching a ligand to a dendron. As used herein, "low density" refers to about 0.01 to about 0.5 probe/nm2, preferably about 0.05 to about 0.2, more preferably about 0.075 to about 0.15, and most preferably about 0.1 probe/nm2.

As used herein, "regular intervals" refers to the spacing between the tips of the size- controlled macromolecules, which is a distance from about 1 nm to about 100 nm so as to allow room for interaction between the target-specific ligand and the target substantially without steric hindrance. Thus, the layer of macromolecules on a substrate is not too dense for specific molecular interactions to occur.

As used herein, "solid support" refers to a composition comprising an immobilization matrix such as, but not limited to, insolubilized substance, solid phase, surface, substrate, layer, coating, woven or nonwoven fiber, matrix, crystal, membrane, insoluble polymer, plastic, glass, biological or biocompatible or bioerodible or biodegradable polymer or matrix, microparticle or nanoparticle. Solid supports include, for example and without limitation, monolayers, layers, commercial membranes, resins, matrices, fibers, separation media, chromatography supports, polymers, plastics, glass, mica, gold, beads, microspheres, nanospheres, silicon, gallium arsenide, organic and inorganic metals, semiconductors, insulators, microstructures and nanostructures. Microstructures and nanostructures may include, without limitation, microminiaturized, nanometer- scale and supramolecular probes, tips, bars, pegs, plugs, rods, sleeves, wires, filaments, and tubes.

As used herein, "spacer molecule" refers to one or more nucleotide and/or nonnucleotide molecules, groups or spacer arms selected or designed to join two nucleotide or non-nucleotide molecules and preferably to alter or adjust the distance between the two nucleotide or non-nucleotide molecules.

By controlling the spacing between immobilized DNA strands on the surfaces of both an AFM tip and a substrate, unbinding and binding forces of a single oligonucleotide were measured. It was observed that the recognition efficiency could be improved, and multiple and/or secondary interaction was eliminated with appropriate choice of the spacing. In particular, histograms of unbinding force of DNA duplexes with 20, 30, 40, and 50 base pairs became sharp and represented the force of single duplex. Surprisingly, binding events were also observed, and the corresponding force coincided with the unbinding force. Also, linear increases of both forces were observed with the increase of DNA strand length, and the force measurement was sensitive enough to discriminate a single point mutation.

The present invention provides a cantilever for atomic force microscopy (AFM) comprising a cantilever body having a fixed end and a free end, the free end having a surface region being chemically modified by a dendron in which a plurality of termini of the branched region of the dendron are bound to the surface, and a terminus of the linear region of the dendron is functionalized.

In an embodiment of the present invention, at least a tapered protrusion is provided in the vicinity of the free end of the cantilever, and the protrusion is pyramidal or conical. Numerous analogous structures of the probe tip are shown in Fig.2C. Thus, the surface region of the free end of the cantilever is brought into contact with or into proximity with a particular protrusion so that interactions between a target nucleotide and a probe nucleotide can be measured.

All types of cantilevers for AFM can be used in the present invention, and they are not specifically limited. The cantilever of the present invention can be used for all type of AFM such as apparatus shown in FIG. IB and 1C. Fig. IA shows an example of a general atomic force microscope, and Fig. 2A is a cantilever for AFM. The AFM of the present invention can be illustrated in reference to FIG. IA. The AFM system 10 includes a base 15, frame 20 having an opening on its central position fixed to the base 15, and tube-like piezoelectric actuator 55 fixed to the base 15. The tube-like piezoelectric actuator 55 is deflectable in the vertical direction indicated by an arrow V2, i.e., in the direction of thickness of the cantilever by applying a voltage to the piezoelectric actuator from a controller CO through wiring lines. In reference to Fig. 2A, the cantilever 50 has a structure such that a piezoelectric actuator 25 is formed on one side of a substrate 95. An exemplary embodiment of the cantilever, the cantilever 50 includes a cantilever base 90 which has an electrode 10 formed on a insulating layer 110 laminated on rectangular substrate 95.

The cantilever may be constructed of any material known in the art for use in AFM cantilevers, including Si, SiO₂, Si₃N₄, Si₃N₄Ox, Al, or piezoelectric materials. The chemical composition of the cantilever is not critical and is preferably a material that can be easily microfabricated and that has the requisite mechanical properties for use in AFM measurements. Likewise, the cantilever may be in any size and shape known in the art for AFM cantilevers. The size of the cantilever preferably ranges from about 5 microns to about 1000 microns in length, from about 1 micron to about 100 microns in width, and from about 0.04 microns to about 5 microns in thickness. Typical AFM cantilevers are about 100 microns in length, about 20 microns in width and about 0.3 microns in thickness. The fixed end of the cantilever may be adapted so that the cantilever fits or interfaces with a cantilever-holding portion of a conventional AFM.

The surface region of the free end of the cantilever may be modified for treatment with dendron for example, with siliane agents such as GPDES or TPU.

The apparatus and methods of the present invention are not limited to use with cantilever-based AFM instruments.

Polymers such as that in Chemical Formula 1 may be referred to in describing the invention's polymer.

Chemical Formula 1

Various R, T, W, L, and X group variables are noted in chemical formula 1. The polymer may comprise any branched or hyperbranched, symmetrical or asymmetrical polymer. The branched termini of the polymer binds to the substrate preferably by a plurality of termini. The linear end of the polymer may end with a functional group to which a protecting group or a target nucleotide may be attached. The distance between the probes among the plurality of polymers on a substrate may be from about 0.1 nm to about

100 nm, preferably about 1 nm to about 100 nm, more preferably about 2 nm to about 70 nm, even more preferably about 2 nm to about 60 nm, and most preferably about 2 nm to about 50 nm.

R-Groups

In Formula I, the polymer generally includes a branched section, wherein a plurality of the ends are functionalized to bind to a substrate. Within this branched section, the first generation group of branches Rx (Rl, R2, R3) is connected to a second generation group of branches R_xx (RI l, R12, R13, R21, R22, R23, R31, R32, R33) by a functional group, W. The second gene ration group of branches is connected to a third generation group of branches Rxxx (Rl I l, R112, Rl 13, R121, R122, R123, R131, R132, R133, R211, R212, R213, R221, R222, R223, R231, R232, R233, R311, R312, R313, R321, R322, R323, R331, R332, R333) by a functional group W. And a further fourth generation may be connected to the third generation branches in like fashion. The terminal R group is functional ized so that it is capable of binding to the substrate.

The R groups of all generations may be the same or different. Typically, the R group may be a repeating unit, a linear or branched organic moiety, such as but not limited to alkyl, alkenyl, alkynyl, cycloalkyl, aryl, ether, polyether, ester, aminoalkyl, and so on. However, it is also understood that not all of the R groups need to be the same repeating unit. Nor do all valence positions for the R group need be filled with a repeating unit. For instance, in the first generation branch, R_x, Rj, R₂, R₃ all of the R groups at this branch level may be the same repeating units. Or, Ri may be a repeating unit, and R₂ and R₃ may be H or any other chemical entity. Or, R₂ may be a repeating unit, and Ri and R₃ may be H or any other chemical entity. Likewise, for the second and third generation branches, any R group may be a repeating unit, H or any other chemical entity.

Thus, a variety of shapes of polymers may be made in this way, for instance, if Ri, R₁₁, Riπ, Rn₂ and Rn₃ are the same repeating units, and all other R groups are H's or any number of small neutral molecule or atom, then a fairly long and thin polymer having a branch with three functional group termini for Rm, Rn₂ and Rn₃ is made. A variety of other optional chemical configurations are possible. Thus, it is possible to obtain from about 3 to about 81 termini having a functional group capable of binding to a substrate. A preferable number of termini may be from about 3 to about 75, from about 3 to about 70, from about 3 to about 65, from about 3 to about 60, from about 3 to about 55, from about 3 to about 50, from about 3 to about 45, from about 3 to about 40, from about 3 to about 35, from about 3 to about 30, from about 3 to about 27, from about 3 to about 25, from about 3 to about 21, from about 3 to about 18, from about 3 to about 15, from about 3 to about 12, from about 3 to about 9, or from about 3 to about 6. T-Terminal Group Terminal groups, T, are functional groups that are sufficiently reactive to undergo addition or substitution reactions. Examples of such functional groups include without limitation, amino, hydroxyl, mercapto, carboxyl, alkenyl, allyl, vinyl, amido, halo, urea, oxiranyl, aziridinyl, oxazolinyl, imidazolinyl, sulfonato, phosphonato, isocyanato, isothiocyanato, silanyl, and halogenyl.

W-Functional Group

In Formula I, W may be any functional group that may link a polymer to another (or any other divalent organic) moiety, such as but not limited to ether, ester, amide, ketone, urea, urethane, imide, carbonate, carboxylic acid anhydride, carbodiimide, imine, azo group, amidine, thiocarbonyl, organic sulphide, disulfide, polysulfide, organic sulphoxide, sulphite, organic sulphone, sulphonamide, sulphonate, organic sulphate, amine, organic phosphorous group, alkylen, alkyleneoxide, alkyleneamine and so on.

L-Spacer or Linker Group

In Chemical Formula 1, the linear portion of the polymer may include a spacer domain comprised of a linker region optionally interspersed with functional groups. The linker region may be comprised of a variety of polymers. The length of the linker may be determined by a variety of factors, including the number of branched functional groups binding to the substrate, strength of the binding to the substrate, the type of R group that is used, in particular, the type of repeating unit that is used, and the type of the protecting group or target nucleotide that is to be attached at the apex of the linear portion of the polymer. Therefore, it is understood that the linker is not to be limited to any particular type of polymer or to any particular length.

However, as a general guideline, the length of the linker may be from about 0.5 nm to about 20 nm, preferably, about 0.5 nm to about 10 nm, and most preferably about 0.5 nm to about 5 nm.

The chemical construct of the linker may include without limitation, a linear or branched organic moiety, such as but not limited to substituted or unsubstituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl, ether, polyether, ester, aminoalkyl, polyalkenylglcol and so on. The linker may further include functional groups such as those described above, and as such is not limited to any particular structure. The linker group functional ized at the tip may comprise a protective group.

X-Protecting Group The choice of protecting group depends on numerous factors such as the desirability of acid- or base-lability. Therefore, the invention is not limited to any particular protecting group so long as it serves the function of preventing the reaction of the functional group with another chemical entity, and that it is capable of being stripped under desired specified conditions. A list of commercially available protecting groups may be found in the Sigma-Aldrich (2003) Catalog, the contents of which as it relates to the disclosure of protective groups is incorporated by reference herein in its entirety.

The polymer may be deprotected, either in succession or in a single operation. Removal of the polypeptide and deprotection can be accomplished in a single operation by treating the substrate-bound polypeptide with a cleavage reagent, for example thianisole, water, ethanedithiol and trifluoroacetic acid.

In general, in one aspect of the invention, the protecting groups used in the present invention may be those that are used in the sequential addition of one or more amino acids or suitably protected amino acids to a growing peptide chain. Normally, either the amino or carboxyl group of the first amino acid is protected by a suitable protecting group.

In a particularly preferred method, the amino function is protected by an acid or base sensitive group. Such protecting groups should have the properties of being stable to the conditions of linkage formation, while being readily removable without destruction of the growing branched/linear polymer. Such suitable protecting groups may be without limitation 9-fiuorenylmethyloxycarbonyl (Fmoc), t-butyloxycarbonyl (Boc), benzyloxycarbonyl (Cbz), biphenylisopropyl-oxycarbonyl, t-amyloxycarbonyl, isobornyloxycarbonyl, (a, a)-dimethyl-3, 5-dimethoxybenzyloxycarbonyl, o- nitrophenylsulfenyl, 2-cyano-t-butyloxycarbonyl, and the like. Particularly preferred protecting groups also include 2,2, 5,7, 8- pentamethylchroman-6-sulfonyl (pmc), p-toluenesulfonyl, 4- methoxybenzenesulfonyl, adamantyloxycarbonyl, benzyl, o- bromobenzyloxycarbonyl, 2, 6-dichlorobenzyl, isopropyl, t-butyl (t-Bu), cyclohexyl, cyclophenyl and acetyl (Ac), 1 -butyl, benzyl and tetrahydropyranyl, benzyl, p- toluenesulfonyl and 2, 4-dinitrophenyl. In the addition method, the branched termini of the linear/branched polymer is attached to a suitable solid support. Suitable solid supports useful for the above synthesis are those materials which are inert to the reagents and reaction conditions of the stepwise condensation-deprotection reactions, as well as insoluble in the media used.

The removal of a protecting group such as Fmoc from the linear tip of the branched/linear polymer may be accomplished by treatment with a secondary amine, preferably piperidine. The protected portion may be introduced in about 3-fold molar excess and the coupling may be preferably carried out in DMF. The coupling agent may be without limitation O-benzotriazol-1-yl-N, N, N', N'- tetramethyluroniumhexafluorophosphate (HBTU, 1 equiv. ) and 1 -hydroxy- benzotriazole (HOBT, 1 equiv.).

The polymer may be deprotected, either in succession or in a single operation. Removal of the polypeptide and deprotection can be accomplished in a single operation by treating the substrate-bound polypeptide with a cleavage reagent, for example thianisole, water, ethanedithiol and trifluoroacetic acid.

The substrate may be any solid surface to which the branched/linear polymer may bind through either covalent or ionic bond. The substrate may be functional ized so that binding may occur between the branched termini of the branched/linear polymer. The surface of the substrate may be a variety of surfaces according to the needs of the practitioner in the art. Preferably, the substrate may be a glass slide. Other substrates may include membrane filters such as but not limited to nitrocellulose or nylon. The substrate may be hydrophilic or polar, and may possess negative or positive charge before or after coating.

The type of dendron and its preparation method is specifically disclosed in WO2005/026191, which is incorporated herein by reference.

Reaction scheme 1 shows the synthesis of a dendron. Various starting materials, intermediate compounds, and dendron compounds can be used, wherein "X" may be any protecting group, including anthracenemethyl (A), Boc, Fmoc, Ns and so forth.

Reaction scheme 1

A second generation branch dendron having surface reactive functional groups at the branch termini may be used, which self assembles and provides appropriate spacing among themselves. Previous studies showed that multiple ionic attractions between cations on a glass substrate and anionic carboxylates at the dendron's termini successfully generated a well-behaved monolayer, and guaranteed an inter-ligand space of over 24 A (Hong et al., Langmuir 19,2357-2365 (2003) ). To facilitate deprotection and increase the deprotected apex amine's reactivity, the structure was modified. Also, covalent bond formation between the dendron's carboxylic acid groups and the surface hydroxyl groups is as effective as ionic attraction, while also providing enhanced thermal stability. Moreover, an oligoetheral interlayer was effective for suppressing non-specific oligonucleotide binding.

The hydroxylated substrate was prepared by using a previously reported method (Maskis et al., Nucleic Acids Res. 20,1679-1684 (1992) ). Substrates including oxidized silicon wafer, fused silica, and glass slide, were modified with (3-glycidoxypropyl) methyldiethoxysilane (GPDES) and ethylene glycol (EG). The dendron was introduced to the above substrates through a coupling reaction between the dendron's carboxylic acid group and the substrate's hydroxyl group using l-[3-(dimethylamino)propyl]-3- ethylcarbodiimide hydrochloride (EDC) or 1-3-dicyclohexylcarbodiimide (DCC) in the presence of 4-dimethylaminopyridine (DMAP) (Boden et al., J. Org. Chem. 50,2394-2395 (1985); Dhaon et al., J. Org. Chem. 47,1962-1965 (1982) ). The increase in thickness after dendron introduction was 11 ± 2 A, which was comparable to the previous value observed for the ionic bonding (Hong et al., Langmuir 19,2357-2365 (2003) ).

After modification with di (N-succinimidyl) carbonate (DSC) according to a previously established method (Beier et al., Nucleic Acids Res. 27, 1970-1977 (1999)), probe oligonucleotides were immobilized onto the activated surface of glass slide by spotting 50 mM sodium bicarbonate buffer (10% dimethylsulfoxide (DMSO), pH 8.5) solution of the appropriate amine-tethered oligonucleotide (20, uM) using a Microsys 5100 Microarrayer (Cartesian Technologies, Inc.) in a class 10,000 clean room. Typically, for substrates with a reactive amine surface group, a thiol- tethered oligonucleotide and a heterobifunctional linker such as succinimidyl 4-maIeimido butyrate (SMB) or sulphosuccinimidyl-4- (N-maleimidomethyl) cyclohexane-1-carboxylate (SSMCC) are employed (Oh et al., Langmuir 18,1764-1769 (2002); Frutos et al., Langmuir 16,2192-2197 (2000)). In contrast, because the dendron-modified surface guarantees a certain distance among the amine functional groups, use of homobifunctional linkers such as DSC is not problematic. As a result, an amine-tethered oligonucleotide can be utilized for spotting. Unless cost effectiveness is important, use of easily oxidized thiol-tethered oligonucleotide should be avoided, although it is possible that such thiol-tethered oligonucleotides may be useful under certain conditions. To improve the recognition efficiency between complementary DNA strands at the single molecular level, DNA oligomers was immobilized onto a nanoscale-controlled dendron surface. The surface seemed to be ideal to increase the efficiency since the mesospacing existing in the dendron relieved the immobilized DNA from the steric hindrance (B. J. Hong, S. J. Oh, T. O. Youn, S. H. Kwon, J. W. Park, Langmuir 21, 4257, 2005). Either glycidylpropyldiethoxymethylsilane (or GPDES) or N-(3- (triethoxysilyl)propyl)-O-polyethyleneoxide urethane (or TPU) was employed to generate a sublayer, and the dendron (9-anthrylmethyl N-({[tris({2-[({tris[(2- carboxyethoxy)methyl]methyl}amino)carbonyl]ethoxy}methyl)methyl]amino}carbonyl)pro pylcarbamate) (or 9-acid) was immobilized onto them. Previously, mesospacing between the dendrons on the GPDES-modified surface was 32 A on average (B. J. Hong, S. J. Oh, T. O. Youn, S. H. Kwon, J. W. Park, Langmuir 21, 4257, 2005). In the case of TPU, an absorption peak observed at 257 nm arising from the anthracene moiety of the pristine dendron was one half of that in the GPDES case. Therefore it is suggested that the spacing of the dendron is larger than 32 A in the TPU case. After deprotection of the anthracene protecting group, the amine group was activated with di(N-succinimidyl)carbonate, and eventually an amine tethering oligonucleotide was immobilized. To understand the effect of the spacing, the two types of modification were employed for the substrate, while spacing on AFM tip was fixed with use of 9-acid/TPU. Since estimation of the spring constant was believed to give a typical error of 10-20 %, the force was measured under various conditions with an identical tip (Fig. 3). For example, force curves were obtained for a complementary 30-base DNA (Table 1) immobilized on 9- acid/GPDES substrate at various loading rates in the range between 110 nm/s and 540 nm/s. The perfectly matched and internal mismatched oligomer sequences are shown in Table 1, where the underlined parts are mismatched sites.

TABLE 1

The present invention is further explained in more detail with reference to the following examples. These examples, however, should not be interpreted as limiting the scope of the present invention in any manner.

EXAMPLES

Numbering scheme is used for compounds throughout the Examples such as compound 1, compound 2, 1, II, III, IV, V and so on. It is to be understood however, that the compound numbering scheme is consistent with and is confined to the particular Example section to which it is recited. For instance, compound 1 as recited in Example 2 may not necessarily be the same compound 1 as found in Example 3.

EXAMPLE 1 - Methods For Making Microarray Using Size-Controlled Macromolecule In Example 1, designations I, II, III, IV, and V refer to various compounds and intermediate compounds as shown in Figure 2. EXAMPLE 1.1 -Materials.

The silane coupling reagents, (3-glycidoxypropyl)methyldiethoxysilane (GPDES) and (3-aminopropyl)diethoxymethylsilane (APDES), were purchased from Gelest, Inc. and all other chemicals were of reagent grade from Sigma-Aldrich. Reaction solvents for the silylation are anhydrous ones in Sure/Seal bottles from Aldrich. All washing solvents for the substrates are of HPLC grade from Mallinckrodt Laboratory Chemicals. The UV grade fused silica plates (30 mm x 10 mm x 1.5 mm) were purchased from CVI Laser Corporation. The polished prime Si(IOO) wafers (dopant, phosphorus; resistivity, 1.5-2.1 Ω'cm) were purchased from MEMC Electronic Materials, Inc. Glass slides (2.5 x 7.5 cm) were purchased from Corning Co. All of the oligonucleotides were purchased from Metabion. Ultrapure water (18 M Ω/cm) was obtained from a Milli-Q purification system (Millipore).

EXAMPLE 1.2 -Instruments. The film thickness was measured with a spectroscopic ellipsometer (J. A. Woollam

Co. Model M-44). UV-vis spectra were recorded on a Hewlett-Packard diodearray 8453 spectrophotometer. Tapping mode AFM experiments were performed with a Nanoscope Ilia AFM (Digital Instruments) equipped with an "E" type scanner. EXAMPLE 1.3 - Cleaning the substrates. Substrates such as oxidized silicon wafer, fused silica, and glass slide, were immersed into Piranha solution (cone. H₂SO₄:30% H₂O₂ = 7:3 (v/v)) and the reaction bottle containing the solution and the substrates was sonicated for an hour. (Caution: Piranha solution can oxidize organic materials explosively. Avoid contact with oxidizable materials.) The plates were washed and rinsed thoroughly with a copious amount of deionized water after the sonication. The clean substrates were dried in a vacuum chamber (30-40 mTorr) for the next steps.

EXAMPLE 1.4 - Preparing the hydroxylated substrates. The above clean substrates were soaked in 160 ml toluene solution with 1.0 ml (3- glycidoxypropyl)methyldiethoxysilane (GPDES) for 1O h. After the self-assembly, the substrates were washed with toluene briefly, placed in an oven, and heated at 110⁰C for 30 min. The plates were sonicated in toluene, toluene-methanol (1: 1 (v/v)), and methanol in a sequential manner for 3 min at each washing step. The washed plates were dried in a vacuum chamber (30-40 mTorr). GPDES-modified substrates were soaked in a neat ethylene glycol (EG) solution with two or three drops of 95 % sulfuric acid at 80 - 100 °C for 8 h. After cooling, the substrates were sonicated in ethanol and methanol in a sequential manner each for 3 min. The washed plates were dried in a vacuum chamber (30-40 mTorr). EXAMPLE 1.5 -Preparing the dendron-modified substrates. The above hydroxylated substrates were immersed into a methylene chloride solution dissolving the dendron (1.2 mM) and a coupling agent, l-[-3- (dimethylamino)propyl]-3- ethylcarbodiimide hydrochloride (EDC) or 1,3- dicyclohexylcarbodiimide (DCC) (11 mM) in the presence of 4-dimethylaminopyridine (DMAP) (0.82 mM). After 3 days at room temperature, the plates were sonicated in methanol, water, and methanol in a sequential manner each for 3 min. The washed plates were dried in a vacuum chamber (30-40 mTorr) for the next step.

EXAMPLE 1.6 -Preparing the NHS-modified substrates.

The dendron-modified substrates were immersed into a methylene chloride solution with 1.0 M trifluoroacetic acid (TFA). After 3 h, they were again soaked in a methylene chloride solution with 20% (v/v) diisopropylethylamine (DIPEA) for 10 min. The plates were sonicated in methylene chloride and methanol each for 3 min. After being dried in a vacuum chamber, the deprotected substrates were incubated in the acetonitrile solution with di(N-succinimidyl)carbonate (DSC) (25 mM) and DIPEA (1.0 mM). After 4 h reaction under nitrogen atmosphere, the plates were placed in a stirred dimethylformamide solution for 30 min and washed briefly with methanol. The washed plates were dried in a vacuum chamber (30-40 mTorr) for the next step.

EXAMPLE 1.7 - Arraying oligonucleotides on the NHS-modified substrates. Probe oligonucleotides in 50 mM NaHCO3 buffer (pH 8.5) were spotted side by side in a 4 by 4 format on the NHS-modified substrate. The microarray was incubated in a humidity chamber (80 % humidity) for 12 h to give the amine-tethered DNA sufficient reaction time. Slides were then stirred in a hybridization buffer solution (2x SSPE buffer (pH 7.4) containing 7.0 mM sodium dodecylsulfate) at 37 ⁰C for 1 h and in boiling water for 5 min to remove non-specifically bound oligonucleotides. Finally, the DNA- functionalized microarray was dried under a stream of nitrogen for the next step. For a fair comparison, different kinds of probes were spotted in a single plate. EXAMPLE 1.8 - Hybridization.

Hybridization was performed in the hybridization buffer solution containing a target oligonucleotide (1.0 nM) tagged with a Cy3 fluorescent dye at 50 ⁰C for 1 h using a GeneTACTM HybStation (Genomic Solutions, Inc.). The microarray was rinsed with the hybridization buffer solution in order to remove excess target oligonucleotide and dried with nitrogen. The fluorescence signal on each spot was measured with a ScanArray Lite (GSI Lumonics) and analyzed by Imagene 4.0 (Biodiscovery).

EXAMPLE 1.9 - Synthesis of the dendron EXAMPLE 1.9.1 - Preparation of 9-anthryImethyl N-(3- carboxylpropyl)carbamate (I) - Compound I.

4-Aminobutyric acid (0.50 g, 4.8 mmol, 1.0 equiv) and triethylamine (TEA) (1.0 ml, 7.3 mmol, 1.5 equiv) were dissolved in N,N-dimethylformamide (DMF) and stirred at 50 ⁰C. 9-Anthrylmethyl p-nitrophenyl carbonate (1.81 g, 4.8 mmol, 1.0 equiv) was slowly added while stirring. After stirring at 50 ⁰C for 2 h, the solution was evaporated to dryness, and the solution was basified with 0.50 N sodium hydroxide (NaOH) solution. The aqueous solution was washed with ethyl acetate (EA), stirred in an ice bath and acidified with dilute hydrochloric acid (HCI). After the product was extracted with EA, the organic solution was dried with anhydrous MgSO₄, filtered and evaporated. The total weight of the resulting yellow powder was 1.06 g and the yield was 65 %.

¹HNMR(CDCl₃) δ 11.00-9.00(br, CH₂COOH, 1 Η), 8.41 (s, C₁₄H₉CH₂, 1 H), 8.31 (d, C₄H₉CH₂, 2H), 7.97 (d, C₁₄H₉CH₂, 2H), 7.51 (t, Ci₄H₉CH₂, 2H), 7.46(t, C₁₄H₉CH₂, 2H), 6.08(s, C₁₄H₉CH₂O, 2Η), 5.01 (t, OCONHCH₂, 1 H), 3.23(q, NHCH₂CH₂, 2H), 2.34(t, CH₂CH₂COOH, 2H), 1.77(m, CH₂CH₂CH₂, 2H). ¹³C NMR(CDC13) δ 178.5(CH₂COOH), 157.9(OCONH), 132.1 (Ci₄H₉CH₂), 131.7(Ci₄H₉CH₂), 129.7(Ci₄H₉CH₂), 129.7(Ci₄H₉CH₂), 127.3(Ci₄H₉CH₂), 126.8(Ci₄H₉CH₂), 125.8( Ci₄H₉CH₂), 124.6( Ci₄H₉CH₂), 60.2(Ci₄H₉CH₂), 41.0(NHCH₂CH₂), 31.7(CH₂CH₂COOH)^O(CH₂CH₂CH₂).

EXAMPLE 1.9.2 - Preparation of 9-anthrylmethyI N-{[(tris{[2- (methoxycarbonyl)ethoxy]methyl}methyl) amino]carbonyl}propylcarbonate (II) — Compound II.

9-Anthrylmethyl N-(3-carboxylpropyl)carbamate (0.65 g, 1.93 mmol, 1.5 equiv), 1- [3-(dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride (EDC) (0.37 g, 1.93 mmol, 1.5 equiv), and 1-hydroxybenzotriazole hydrate (HOBT) (0.261 g, 1.93 mmol, 1.5 equiv) were dissolved in acetonitrile and stirred at room temperature. Tris{[(methoxycarbonyl)ethoxy] methyl} aminomethane (0.49 g, 1.29 mmol, 1.0 equiv) dissolved in acetonitrile was added with stirring, After stirring at room temperature for 12 h, the acetonitrile was evaporated. The crude product was dissolved in EA and washed with 1.0 N HCl and saturated sodium bicarbonate solution. After being dried with anhydrous MgSO₄, filtered, and evaporated, the crude product was loaded in a column packed with silica gel. Purification by column chromatography (eluent: ethyl acetate:hexane = 5:1 (v/v)) resulted in a viscous yellow liquid. The total weight of the yellow liquid was 0.67 g, and the yield was 74 %.

¹HNMR(CDCl₃) δ 8.43(s, C^H₉CH₂, 1 H), 8.36(d, C₁₄H₉CH₂, 2H), 7.99 (d, Ci₄H₉CH₂, 2H), 7.53(t,

Ci₄H₉CH₂, 2H), 7.47(t, Ci₄H₉CH₂, 2H), 6.15(s, CONHC, 1Η), 6.08(s, Ci₄H₉CH₂O, 2Η),

5.44(t, OCONHCH₂₅I H), 3.63-3.55(m, CH₂OCH₂CH₂COOCH₃, 21 Η), 3.27(q, NHCH₂CH₂, 2H), 2.46(t, CH₂CH₂COOCH₃, 6H), 2.46(t, CH₂CH₂CONH, 2H), 1.81 (m,

CH₂CH₂CH₂, 2H).

¹³C NMR(CDCl₃)

5173.2(CH₂CONH), 172.7(CH₂COOCH₃), 157.4(OCONH), 132.9(Ci₄H₉CH₂),

131.5(Ci₄H₉CH₂), 129.5(Ci₄H₉CH₂), 129.4(C₁₄H₉CH₂), 127.5(Ci₄H₉CH₂), 127.0(Ci₄H₉CH₂), 125.6(Ci₄H₉CH₂), 124.7(Ci₄H₉CH₂), 69.6(NHCCH₂O), 67.2(Ci₄H₉CH₂), 60.1 (OCH₂CH₂), 59.4(NHCCH₂), 52.1(OCH₃), 40.8(NHCH₂CH₂), 35.1 (OCH₂CH₂), 34.7(CH₂CH₂CONH), 26.3(CH₂CH₂CH₂).

Anal. Calcd for C₃₆H₄₆N₂Oi₂ 0.5 H₂O: C 61.18, H 6.65, N 4.03; Found: C61.09, H 6.69, N 3.96. EXAMPLE 1.9.3 - Preparation of 9-anthrylmethyl N-[({tris[(2- carboxyethoxy)methyl]methyl}amino) carbonyl]propylcarbamate (III) - Compound III.

9-Anthrylmethyl N-{[(tris{[2-

(methoxycarbonyl)ethoxy]methyl}methyl)amino]carbonyl}propyl- carbonate (0.67 g, 0.93 mmol) was dissolved in acetone (30 ml) and 0.20 N NaOH (30 ml, 6 mmol). After being stirred at room temperature for 1 d, the acetone was evaporated. The aqueous solution was washed with EA, stirred in an ice bath and acidified with dilute HCl. After the product was extracted with EA, the organic solution was dried with anhydrous MgSO₄, filtered and evaporated. Solidification in acetone and ether solution at -20 ⁰C resulted in a yellow powder. The total weight of the final pale yellow powder was 0.54 g with a yield of 88%.

¹HNMR(CDCl₃) δ 11.00-9.00(br, CH₂COOH; 3Η}, 8.61(s, Ci₄H₉CH₂, 1H}, 8.47(d, Ci₄H₉CH₂, 2H), 8.11 (d, Ci₄H₉CH₂, 2H), 7.60(t, Ci₄H₉CH₂, 2H}, 7.52(t, Cj₄H₉CH₂, 2H), 6.63(s, CONHC, 1 Η), 6.36(t, OCONHCH₂, 1 Η), 6.12(s, Ci₄H₉CH₂O, 2Η). 3.40-363(m, CH₂OCH₂CH₂COOH, 12H), 3.20(q, NHCH₂CH₂, 2H), 2.52(t, CH₂CH₂COOH, 6H), 2.17(t, CH₂CH₂CONH, 2H), 1.75(m, CH₂CH₂CH₂, 2H). ¹³C NMR(CDCl₃) δ 172.2(CH₂COOH), 172.0(CH₂CONH), 156.7(OCONH), 131.2(Ci₄H₉CH₂), 130.7(Ci₄H₉CH₂), 128.6(C₁₄H₉CH₂), 128.4(Ci₄H₉CH₂), 127.3(Ci₄H₉CH₂),

126.2(Ci₄H₉CH₂), 124.8(Ci₄H₉CH₂), 124.0(Ci₄H₉CH₂), 68.6(NHCCH₂O), 66.5(Ci₄H₉CH₂), 59.5(OCH₂CH₂), 58.0(NHCCH₂), 40.0(NHCH₂CH₂), 34.0(OCH₂CH₂),

33.5(CH₂CH₂CONH)^S-S(CH₂CH₂CH₂).

Anal. Calcd for C₃₃H₄₀N₂Oi₂ - 1-5 H₂O: C 57.97, H 6.34, N 4.10; Found: C 57.89, H 6.21, N 4.09.

EXAMPLE 1.9.4 - Preparation of 9-anthrylmethyl N-[({tris[(2-{[(tris{[2- (methoxycarbonyl)ethoxy]methyl}

(methyl)amino]carbonyl}ethoxy)methyl]methyl}amino)carbonyl]propylcarbamate (IV) - Compound IV.

9-Anthrylmethyl N-[({tris[(2-carboxyethoxy)methyl]methyl}amino)carbonyl] propylcarbamate (0.54 g, 0.82 mmol, 1.0 equiv), EDC (0.55 g, 2.87 mmol, 3.5 equiv), and HOBT (0.39 g, 2.89 mmol, 3.5 equiv) were dissolved in acetonitrile and stirred at room temperature. Tris{[(methoxycarbonyl)ethoxy] methyl} aminomethane (0.96 g, 2.53 mmol, 3.1 equiv) dissolved in acetonitrile was added with stirring. After stirring at room temperature for 36 h, the acetonitrile was evaporated. The crude product was dissolved in EA and washed with 1.0 N HCl and saturated sodium bicarbonate solution. After drying with anhydrous MgSO₄, filtered, and evaporated, the crude product was loaded in a column packed with silica gel. Column purification (eluent: ethyl acetate: methanol = 20:1 (v/v)) resulted in a viscous yellow liquid. The total weight of the yellow liquid was 1.26 g with an 88% yield.

¹HNMR(CDCl₃) δ 8.47(s, C₁₄H₉CH₂, 1 H), 8.39(d, C₁₄H₉CH₂, 2H), 8.02 (d, C₁₄H₉CH₂, 2H), 7.53(t,

Ci₄H₉CH₂, 2H), 7.47(t, Ci₄H₉CH₂, 2H), 6.60(s, CH₂CH₂CH₂CONHC, 1 Η), 6.13(s, OCH₂CH₂CONHC, 3Η), 6.11 (s, C₁₄H₉CH₂O, 2Η), 5.79(t, OCONHCH₂,! H), 3.65-3.60(m, CH₂OCH₂CH₂CONH, CH₂OCH₂CH₂COOCH₃, 75Η), 3.29(q, NHCH₂CH₂, 2H), 2.50(t, CH₂CH₂COOCH₃, 18H), 2.36(t, OCH₂CH₂CONH, 6H), 2.27(t, CH₂CH₂CH₂CONH, 2H), 1.85(m, CH₂CH₂CH₂, 2H). ¹³C NMR(CDCl₃) δ 173.3(OCH₂CH₂CONH), 172.5(CH₂CH₂CH₂CONH), 171.6(CH₂COOCH₃),

157.2(OCONH), 131.8(Ci₄H₉CH₂), 131.5(Ci₄H₉CH₂), 129.4(Ci₄H₉CH₂), 129.3(Ci₄H₉CH₂), 127 .6(Ci₄H₉CH₂), 127.0(Ci₄H₉CH₂), 125.6(Ci₄H₉CH₂), 124.7(Ci₄H₉CH₂), 69.5(NHCCH₂OCH₂CH₂COOCH₃), 67.9(NHCCH₂OCH₂CH₂CONH), 67.2(CI₄H₉CH₂), 60.3(OCH₂CH₂CONH), 60.2(OCH₂CH₂COOCH₃), 59.2(NHCCH₂OCH₂CH₂COOCH₃, NHCCH₂OCH₂CH₂CONH), 52.1(OCH₃), 41.0(NHCH₂CH₂), 37.6(OCH₂CH₂CONH), 35.1(OCH₂CH₂COOCH₃), 34.7(CH₂CH₂CH₂CONH), 26.3(CH₂CH₂CH₂).

Anal. Calcd for C₈iH₁₂iN₅O₃₆ ^• H₂O: C 55.31, H 7.05, N 3.98; Found: C 55.05, H 7.08, N 4.04.

MALDI- TOF-MS: 1763.2 (MNa+), 1779.2 (MK+). EXAMPLE 1.9.5 - Preparation of 9-anthrylmethyl N-({[tris({2-[({tris[(2- carboxyethoxy)methyl] methyl} atnino)carbonyl] ethoxy} methyl)methyl] amino}carbonyl)propylcarbamate (V) - Compound V.

9-Anthrylmethyl N-[({tris[(2-{[(tris{[2- (methoxycarbonyl)ethoxy] methyl } methyl)am ino] carbonyl } ethoxy)methyl]methyl}amino)carbonyl]propylcarbamate (0.60 g, 0.34 mmol) was dissolved in acetone (30 ml) and 0.20 NNaOH (30 ml). After stirring at room temperature for 1 d, the acetone was evaporated. The aqueous solution was washed with EA, stirred in an ice bath and acidified with dilute HCI. After the product was extracted with EA, the organic solution was dried with anhydrous MgSO₄, filtered and evaporated. The total weight of the final yellow powder was 0.37 g and the yield was 68 %. ¹H NMR(DMSO) δ 13.00-11.00(br, CH₂COOH 9Η), 8.66(s, C_]4H₉CH2, 1 H), 8.42(d, Ci₄H₉CH₂,

2H), 8.13 (d, Ci₄H₉Cm, 2Η), 7.62(t, Cj₄H₉CH₂, 2H), 7.54(t, Ci₄H₉CH₂, 2H), 7.12(t, OCONHCH₂, IH), 7.10(s, OCH₂CH₂CONHC, 3Η), 7.06(s, CH₂CH₂CH₂CONHC, 1 Η),

6.06(s, Ci₄H₉CH₂O, 2Η), 3.57-3.55(m, CH₂OCH₂CH₂CONH, CH₂OCH₂CH₂COOH, 48H), 3.02(q, NHCH₂CH₂, 2H), 2.42(t, CH₂CH₂COOH, 18H), 2.32(t, OCH₂CH₂CONH, 6H), 2.1 l(t, CH₂CH₂CH₂CONH, 2H), 1.60(m, CH₂CH₂CH₂, 2H).

¹³C NMR(DMSO) δ 172.8(CH₂COOH), 172.2(CH₂CH₂CH₂CONH), 170.5(OCH₂CH₂CONH), 156.5(OCONH), 131.0(C₁₄H₉CH₂), 130.6(C₁₄H₉CH₂), 129.0(C₁₄H₉CH₂), 128.7(Ci₄H₉CH₂), 127.6(C₁₄H₉CH₂), 126.7(Ci₄H₉CH₂), 125.4(Ci₄H₉CH₂), 124.3(Ci₄H₉CH₂),

68.3(NHCCH₂OCH₂CH₂COOH), 67.4(NHCCH₂OCH₂CH₂CONH), 66.8(CI₄H₉CH₂), 59.8(OCH₂CH₂COOH), 59.6(OCH₂CH₂CONH), 57.9(NHCCH₂OCH₂CH₂CONH), 55.9(NHCCH₂OCH₂CH₂COOH), 36.4(NHCH₂CH₂), 34.6(OCH₂CH₂COOH), 30.8(OCH₂CH₂CONH), 29.7(CH₂CH₂CH₂CONH), 25.9(CH₂CH₂CH₂).

PREPARATION EXAMPLE 2 - Methods of producing alternative starting material dendron macromolecule - Fmoc-Spacer-[9]-acid

In Example 2, various indicated compounds are referred to as compound 1, 2 and so forth. First, a spacer, 6-azidohexylamine (1) from 1,6-dibromohexane was synthesized according to Lee, J. W.; Jun, S. L; Kim, K. Tetrahedron Lett., 2001, 42, 2709.

NaN₃ Triphenylphosphine

(1)

This spacer was attached to repeating unit (2) through unsymmetric urea formation and made N₃-spacer-[3]ester (3). The repeating unit was synthesized by condensation of TRIS with acrylate, which had been reported in Cardona, C. M.; Gawley, R. E. J. Org. Chem. 2002, 67, 141.

(2)

Formic Acid

This triester was transformed to N₃-spacer-[3]acid (4) through hydrolysis and coupled with triester (2) under peptide coupling conditions, which led to N₃-spacer-[9]ester. After reduction of azide to amine and protection of amine with Fmoc group, hydrolysis of nonaester afforded Fmoc-spacer-[9]acid (5).

iV-(6-AzidohexyI)-N'-tris{[2-(«'e/'/'-butoxycarbonyI)ethoxy]methyl}-methyIurea

(3). Triphosgene (1.3 g, 4.3 mmol) was dissolved in anhydrous CH₂Cl₂ (20 mL). A mixture of 6-azidohexylamine (1) (1.6 g, 12 mmol) and N,N-diisopropylethylamine (DlEA, 2.4 mL, 13.8 mmol) in anhydrous CH₂Cl₂ (35 mL) was added dropwise to the stirred solution of triphosgene over a period of 7h using a syringe pump. After further stirring for 2h, a solution of (2) (6.4 g, 13 mmol) and DIEA (2.7 mL, 15.2 mmol) in anhydrous CH₂Cl₂ (20 mL) was added. The reaction mixture was stirred for 4 h at room temperature under nitrogen, and washed with 0.5 M HCl and brine. The organic layer was then dried over anhydrous MgSO₄, and the solvent was removed by evacuation. Purification with column chromatography (silica, 1:1 EtOAc/hexane) yielded colorless oil (3.0 g, 40 %).

¹R NMR (CDCl₃, 300 MHz): δ 1.45 (s, (CH₃)₃C, 27Η); 1.36-1.58 (m, CH₂CH₂CH₂CH₂, 8H); 2.46 (t, CH₂CH₂O, J= 6.4 Hz, 6H), 3.13 (m, CONHCH₂, 2Η), 3.26 (t, N₃CH₂, J= 6.9 Hz, 2H), 3.64-3.76 (m, CCH₂O and CH₂CH₂O, 12Η); 5.00 (t, CH₂NHCO, J=6.7 Hz, IH), 5.29 (s, CONHC, 1Η). ¹³C NMR (CDCl₃, 75 MHz): δ 26.52, 26.54, 28.81, 30.26 (CH₂CH₂CH₂CH₂);

28.14((CHs)₃C); 36.20 (CH₂CH₂O); 39.86 (CONHCH₂); 51.40 (N₃CH₂); 58.81 (CCH₂O); 67.16 (CH₂CH₂O); 69.23 (CCH₂O); 80.58 ((CH₃)₃Q; 157.96 (NHCONH); 171.26 (COO/- Bu).

FAB-MS: 674.26 (M⁺). iV-(6-Azidohexyl)-N'-tris{[2-carboxyethoxy]methyl}methylurea (4). N₃-spacer-

[3]ester (3) (0.36 g, 0.56 mmol) was stirred in 6.6mL of 96 % formic acid for 24 h. The formic acid was then removed at reduced pressure at 50 ⁰C to produce colorless oil in a quantitative yield.

¹H NMR (CD₃COCD₃, 300 MHz): δ 1.34-1.60 (m, CH₂CH₂CH₂CH₂, 8H); 2.53 (t, CH₂CH₂O, J= 6.4 Hz, 6H), 3.07 (t, CONHCH₂, J= 6.9 Hz, 2H), 3.32 (t, N₃CH₂, J = 6.9 Hz, 2H), 3.67-3.73 (m, CCH₂O and CH₂CH₂O, 12Η).

¹³C NMR (CD₃COCD₃, 75 MHz): δ 27.21, 29.54, 31.02 (CH₂CH₂CH₂CH₂); 35.42 (CH₂CH₂O); 40.27 (CONHCH₂); 52.00 (N₃CH₂); 59.74 (CCH₂O); 67.85 (CH₂CH₂O); 70.96 (CCH₂O); 158.96 (NHCONH); 173.42 (COOH). FAB-MS: 506.19 (MH⁺). 7V-(6-Azidohexyl)-iV'-tris[(2-{[(tris{[2-(/ert-butoxycarbonyl)ethoxy]- methyl}methyl)amino]carbonyl}ethoxy)raethyl]methylurea (4.1).

The HOBt (0.20 g, 1.5 mmol), DIEA (0.30 niL, 1.8 mmol), and EDC (0.33 g, 1.8 mmol) were added to (4) (0.25 g, 0.50 mmol) in 5.0 mL of dry acetonitrile. Then, the amine (2) (1.14 g, 2.3 mmol) dissolved in 2.5 mL of dry acetonitrile was added, and the reaction mixture was stirred under N₂ for 48 h. After removal of the solvent at reduced pressure, the residue was dissolved in MC and washed with 0.5 M HCl and brine. The organic layer was then dried over MgSO₄, the solvent was removed in vacuo, and column chromatography

(SiO2, 2:1 EtOAc/hexane) yielded a colorless oil (0.67 g, 70%). ¹R NMR (CDCl₃, 300 MHz): δ 1.45 (s, (CH₃)₃C, 81Η); 1.36-1.58 (m,

CH₂CH₂CH₂CH₂, 8Η); 2.40-2.47 (m, CH₂CH₂O gen. 1 & 2, 24H), 3.13 (m, CONHCH₂,

2Η), 3.26 (t, N₃CH₂, 6.9 Hz, 2H), 3.62-3.69 (m, CCH₂O gen. 1 & 2, CH₂CH₂O gen. 1 & 2,

48Η); 5.36 (t, CH₂NHCO, J=6.7 Hz, IH), 5.68 (br, CONHC, 1Η), 6.28 (br, amide NH,

3H). ¹³C NMR (CDCl₃, 75 MHz): δ 26.59, 26.69, 28.91, 30.54 (CH₂CH₂CH₂CH₂);

28.22 ((CHs)₃C); 36.20 (CH₂CH₂O gen. 2); 37.43 (CH₂CH₂O gen. 1); 39.81 (CONHCH₂);

51.47 (N₃CH₂); 58.93 (CCH₂O gen. 1); 59.89 (CCH₂O gen. 2); 67.15 (CH₂CH₂O gen. 2);

67.68 (CH₂CH₂O gen. 1); 69.23 (CCH₂O gen. 2); 70.12 (CCH₂O gen. 1); 80.57 ((CH₃)₃Q;

158.25 (NHCONH); 171.01 (COOt-Bu) 171.41 (CONH amides). MALDI-MS: 1989.8 (MNa⁺), 2005.8 (MK⁺).

^-(ό-AminohexyO-N'-tris^-H^ristP-^ert-butoxycarbonyOethoxy]- methyl}methyl)amino]carbonyl}ethoxy)methyl]methylurea (4.2).

Nona-tert-butyl ester (4.1) (0.37 g, 0.20 mmol) was stirred with 10 % Pd/C (37.0 mg) in ethanol (20.0 mL) under H₂ at room temperature for 12 h. After checking completion of the reaction with TLC, the mixture was filtered with a 0.2 /an Millipore filter.

After the filter paper was rinsed with CH₂Cl₂, the combined solvent was removed in vacuo, and colorless oil was recovered.

^-{β^-fluorenylmethoxycarbonyOaminohexylJ-N'-tris^-II^rislP-^er/- butoxycarbonyl)ethoxy]methyl}methyl)amino]carbonyl}ethoxy)methyl]methylurea (4.3). The amine (4.2) (0.33 g, 0.17 mmol) and DIEA (33 μL, 0.19 mmol) were dissolved in 5.0 mL Of CH₂Cl₂, and stirred for 30 min under nitrogen atmosphere. 9-Fluorenylmethyl chloro formate (48 mg, 0.19 mmol) in 2.0 mL of CH₂Cl₂ was added, and the reaction mixture was stirred for 3 h at room temperature. The solvent was removed under reduced pressure and washed with 0.5 M HCl and brine. The residue was purified with column chromatography (silica, EtOAc) to yield colorless oil (0.18 g, 64 %).

¹H NMR (CDCl₃, 300 MHz): δ 1.45(s, (CH₃)₃C, 81Η); 1.23-1.58 (m, CH₂CH₂CH₂CH₂, 8H); 2.37-2.47 (m, CH₂CH₂O gen. 1 & 2, 24H); 3.10-3.22 (m, CONHCH₂, 4Η); 3.62- 3.70 (m, CCH₂O gen. 1 & 2, CH₂CH₂O gen. 1 & 2, 48Η); 4.22 (t, CH(fluorenyl)-CH₂, J=7Λ Hz, IH); 4.36 (d, fluorenyl-CH₂, J=7.1 Hz, 2H); 5.27-5.35 (m, CH₂NHCO, 2Η); 5.67 (br, CONHC, 1Η); 6.25 (br, amide, 3Η); 7.28 -7.77 (fluorenyl, 8H).

¹³C NMR (CDCl₃, 75 MHz): δ 26.85, 27.02, 30.27, 30.88 (CH₂CH₂CH₂CH₂); 28.49 ((CH₃)SC); 36.48 (CH₂CH₂O gen. 2); 37.73 (CH₂CH₂O gen. 1); 40.03, 41.34 (CONHCH₂); 47.68 (CH(fluorenyl)-CH₂); 59.22 (CCH₂O gen. 1); 60.16 (CCH₂O gen. 2); 66.87 (fluorenyl-GH₂); 67.43 (CH₂CH₂O gen. 2); 67.98 (CH₂CH₂O gen. 1); 69.52 (CCH₂O gen. 2); 70.42 (CCH₂O gen.l); 80.84 ((CH₃)₃Q; 120.28, 125.52, 127.38, 127.98, 141.65, 144.48 (fluorenyl); 156.88 (OCONH); 158.52 (NHCONH); 171.27 (COOt-Bu) 171.65(amide CONH).

MALDI-MS : 2186.8 (MNa⁺), 2002.8 (MK⁺). iV-{6-(9-fluorenylmethoxycarbonyI)aminohexyl}-iV'-tris[(2-{[(tris{[2- carboxyethoxy]methyl}methyl)amino]carbonyl}ethoxy)methyl]-methylurea (5). Nona- tert-butyl ester having a protecting group (4.3) (0.12 g, 72 mmol) was stirred in 10 mL of 96 % formic acid for 18 h. The formic acid was then removed at reduced pressure at 50 ⁰C to produce colorless oil in a quantitative yield. ¹H NMR (CD₃COCD₃, 300 MHz): δ 1.23-1.51 (m, CH₂CH₂CH₂CH₂, 8H); 2.44-

2.58 (m, CH₂CH₂O gen. 1 & 2, 24H); 3.15-3.18 (m, CONHCH₂, 4Η); 3.61-3.75 (m, CCH₂O gen. 1 & 2, CH₂CH₂O gen. 1 & 2, 48Η); 4.23 (t, CH(fluorenyl)-CH₂, J=7.0 Hz, IH); 4.35 (d, fluorenyl-CH₂, J=7.0 Hz, 2H); 5.85, 6.09 (br, CH₂NHCO, 2Η); 6.57 (br, CONHC, 1Η); 6.88 (br, amide NH, 3H); 7.31-7.88 (fluorenyl, 8H). ¹³C NMR (CD₃COCD₃, 75 MHz): δ 27.21, 27.33, 30.69, 30.98 (CH₂CH₂CH₂CH₂);

35.31 (CH₂CH₂O gen. 2); 37.83 (CH₂CH₂O gen. 1); 40.56, 41.54 (CONHCH₂); 48.10 (CH(fluorenyl)-CH₂); 59.93 (CCH₂O gen. 1); 61.10 (CCH₂O gen. 2); 66.86 (fluorenyl- CH₂); 67.81 (CH₂CH₂O gen. 2); 68.37 (CH₂CH₂O gen. 1); 69.80 (CCH₂O gen. 2); 70.83 (CCH₂O gen.1); 120.84, 126.13, 127.98, 128.56, 142.10, 145.16 (fluorenyl); 157.50 (OCONH); 159.82 (NHCONH); 173.20 (amide CONH); 173.93 (COOH).

EXAMPLE 3 - Additional Dendron Compounds

It is to be noted that while a particular protecting group may be shown with a macromolecule, the compounds are not limited to the specific protecting groups shown. Moreover, while various chains and spacers are depicted indicating an exact molecular structure, modifications are possible according to accepted chemical modification methods to achieve the function of a density controlled, preferably low density, array on a substrate surface. As a point of reference for the short-hand description of the compounds, the left most letter(s) indicates the protecting group; the numeral in brackets indicates the number of branched termini; and the right most chemical entity indicates the chemistry on the branched termini. For example, "A-[27]-acid" indicates anthrylmethyl protecting group; 27 termini, and acid groups at the termini.

A-[27]-acid

Boc-[l]-acid

BocHNT ^^ XOOH

Boc-[3]-ester

Boc-[3]-acid

Boc-[9]-ester

Boc-[9]-acid

Ns-[9]-ester

Ns- [9] -acid

Fmoc-[9]-ester (R=/-butyl)

Fmoc-[9]-acid

AE-[l]-acid

AE-[3]-acid

AE-[9]-acid

A- [6] -acid

A-[8]-Acid

A-[12]-Acid

A-[16]-Acid

A-[18]-Acid

G. R. Newkome J Org. Chem. 1985, 50, 2003

J. -J. Lee Macromolecules 1994, 27, 4632

L. J. Twyman Tetrahedron Lett. 1994, 35, 4423

D. A. Tomalia Polym. J. 1985, 77, 117

E. Buhleier. Synthesis 1978, 155

A. W. van der Made J. Chem. Soc, Chem. Commiin. 1992, 1400

G. R. Newkome Angew. Chem. Int. Ed. Engl. 1991, 30, 1176

G. R. Newkome Angew. Chem. Int. Ed. Engl. 1991, 30, 1176

K. L. Wooley J Chem. Soc, Perkin Trans.1 1991, 1059

EXAMPLE 3.1 - Preparation Methods 1. A-[3]-OEt (3)

Compound 1 reacted with NaC(CO₂Et)₃ 2 in C₆H₆/DMF at 8O⁰C.

2. A-[3]-OMe (5)

A-[S]-OEt 3 was reduced with LiAlH₄ or LiBH₄ in ether, reacted with chloroacetic acid in the presence of t-BuOK/t-BUOH, and esterified with MeOH.

3. A-[3]-OTs (7)

5 6 7

Reduction of A-[3]-0Me 5 with LiAlH₄ in ether yields triol compound 6, which is tosylated to compound 7. 4. A-[9]-OEt (8)

A-[3]-OTs 7 was treated with NaC(CO₂Et)₃ in C₆H₆-DMF to afford the desired nonaester (compound 8) 5. A-[27]-OH (9)

A-[9]-0Et 8 was treated with tris(hydroxymethyl)aminomethane and K₂CO₃ in DMSO at 70 ⁰C. EXAMPLE 3.2 l. Boc-[2]-OMe (3)

Compound 1 was reacted with methyl acrylate 2 in methanol solvent at temperature below 50 ⁰C. Excess reagents and solvent were removed under high vacuum at temperature below 55 ⁰C.

2. Boc-[4]-NH₂ (5)

Boc-[2]-OMe 3 was reacted with large excesses of ethylenediamine (EDA) 4 in methanol solvent at temperature below 50 ⁰C. Excess reagents and solvent were removed under high vacuum at temperature below 55 ⁰C. 3. Boc-[8]-OMe (6)

Boc-[4]-NH₂ 5 was reacted with methyl acrylate 2 in methanol solvent at temperature below 50 ⁰C. Excess reagents and solvent were removed under high vacuum at temperature below 55 ⁰C. EXAMPLE 3.3 1. Boc-[2]-OH (3)

Compound 1, l-[3-(dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride

(EDC), and 1-hydroxybenzotriazole hydrate (HOBT) were dissolved in acetonitrile and stirred at room temperature. L-glutamic acid-diethyl ester (H₂NCH(CO₂Et)CH₂CH₂CO₂Et) dissolved in acetonitrile was added with stirring, After stirring at room temperature for 12 h, the acetonitrile was evaporated. The crude product was dissolved in EA and washed with 1.0 N HCl and saturated sodium bicarbonate solution. After being dried with anhydrous MgSO₄, filtered, and evaporated, the crude product was loaded in a column packed with silica gel. Purification by column chromatography (eluent: ethyl acetate : haxane) resulted in a viscous yellow liquid. Compound 2 was hydrolyzed by NaOH solution. After being stirred at room temperature for 1 d, the organic liquid was evaporated. The aqueous solution was washed with EA, stirred in an ice bath and acidified with dilute HCl. After the product was extracted with EA, the organic solution was dried with anhydrous MgSO₄, filtered and evaporated.

2. Boc-[4]-OH (3)

Compound 3, l-[3-(dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride (EDC), and 1-hydroxybenzotriazole hydrate (HOBT) were dissolved in acetonitrile and stirred at room temperature. L-glutamic acid-diethyl ester (H₂NCH(CO₂Et)CH₂CH₂CO₂Et) dissolved in acetonitrile was added with stirring, After stirring at room temperature for 12 h, the acetonitrile was evaporated. The crude product was dissolved in EA and washed with 1.0 N HCl and saturated sodium bicarbonate solution. After being dried with anhydrous MgSO₄, filtered, and evaporated, the crude product was loaded in a column packed with silica gel. Purification by column chromatography (eluent: ethyl acetate : haxane) resulted in a viscous yellow liquid.

Compound 4 was hydrolyzed by NaOH solution. After being stirred at room temperature for 1 d, the organic liquid was evaporated. The aqueous solution was washed with EA, stirred in an ice bath and acidified with dilute HCl. After the product was extracted with EA, the organic solution was dried with anhydrous MgSO₄, filtered and evaporated.

3. Boc-[8]-OH (3)

Compound 5, l-[3-(dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride

(EDC), and 1-hydroxybenzotriazole hydrate (HOBT) were dissolved in acetonitrile and stirred at room temperature. L-glutamic acid-diethyl ester (H₂NCH(CO₂Et)CH₂CH₂CO₂Et) dissolved in acetonitrile was added with stirring, After stirring at room temperature for 12 h, the acetonitrile was evaporated. The crude product was dissolved in EA and washed with 1.0 N HCl and saturated sodium bicarbonate solution. After being dried with anhydrous MgSO₄, filtered, and evaporated, the crude product was loaded in a column packed with silica gel. Purification by column chromatography (eluent: ethyl acetate : haxane) resulted in a viscous yellow liquid.

Compound 6 was hydrolyzed by NaOH solution. After being stirred at room temperature for 1 d, the organic liquid was evaporated. The aqueous solution was washed with EA, stirred in an ice bath and acidified with dilute HCl. After the product was extracted with EA, the organic solution was dried with anhydrous MgSO₄, filtered and evaporated.

EXAMPLE 3.4 1. Boc-[2]-CN (3)

Compound 1 was dissolved at room temp, in acrylonitrile. Glacial acetic acid was added and the solution is heated under reflux for 24 h. Excess acrylonitrile was distilled off under vacuum, the residue was extracted with chloroform, and added to concentrated ammonia solution. The organic phase was separated, washed with water, and dried with sodium sulfate.

2. Boc-[2]-NH₂ (4)

Boc-[2]-CN 3 was dissolved in methanol and cobalt(II) chloride hexahydrate was added. Sodium borohydride was added in portions. The resultant mixture was stirred for 2 h at room temp, and then cautiously acidified with concentrated hydrochloric acid. The solvent was removed under vacuum and concentrated. The organic phase was separated, washed with water, and dried with sodium sulfate.

3. Boc-[4]-CN (5)

Boc-[2]-NH₂ 4 was dissolved at room temp, in acrylonitrile. Glacial acetic acid was added and the solution is heated under reflux for 24 h. Excess acrylonitrile was distilled off under vacuum, the residue was extracted with chloroform, and added to concentrated ammonia solution. The organic phase was separated, washed with water, and dried with sodium sulfate.

4. Boc-[4]-NH₂ (6)

Boc-[4]-CN 5 was dissolved in methanol and cobalt(II) chloride hexahydrate was added. Sodium borohydride was added in portions. The resultant mixture was stirred for 2 h at room temp, and then cautiously acidified with concentrated hydrochloric acid. The solvent was removed under vacuum and concentrated. The organic phase was separated, washed with water, and dried with sodium sulfate.

5. Boc-[8]-CN (7)

Boc-[4]-NH₂ 6 was dissolved at room temp, in acrylonitrile. Glacial acetic acid was added and the solution is heated under reflux for 24 h. Excess acrylonitrile was distilled off under vacuum, the residue was extracted with chloroform, and added to concentrated ammonia solution. The organic phase was separated, washed with water, and dried with sodium sulfate.

6. Boc-[8]-NH₂ (8)

Boc-[8]-CN 7 was dissolved in methanol and cobalt(II) chloride hexahydrate was added. Sodium borohydride was added in portions. The resultant mixture was stirred for 2 h at room temp, and then cautiously acidified with concentrated hydrochloric acid. The solvent was removed under vacuum and concentrated. The organic phase was separated, washed with water, and dried with sodium sulfate.

7. Boc-[16]-CN (9)

Boc-[8]-NH₂ 8 was dissolved at room temp, in acrylonitrile. Glacial acetic acid was added and the solution is heated under reflux for 24 h. Excess acrylonitrile was distilled off under vacuum, the residue was extracted with chloroform, and added to concentrated ammonia solution. The organic phase was separated, washed with water, and dried with sodium sulfate.

7. Boc-[16]-NH₂ (10)

10 Boc-[16]-CN 9 was dissolved in methanol and cobalt(II) chloride hexahydrate was added. Sodium borohydride was added in portions. The resultant mixture was stirred for 2 h at room temp, and then cautiously acidified with concentrated hydrochloric acid. The solvent was removed under vacuum and concentrated. The organic phase was separated, washed with water, and dried with sodium sulfate.

EXAMPLE 3.5

1. A-[3]-Alkene (3)

A-[I]-SiCl₃ 1 was refluxed with 10% excess of allylmagnesium bromide in diethyl ether for 4 h, and cooled to 0 ⁰C and hydrolyzed with 10 % aqueous NH₄Cl. The organic layer was washed with water, dried MgSO₄ and concentrated.

2. A-[3]-SiCI₃ (4)

3HSiCl₃ + Pt catalyst

A mixture of A-[3]-Alkene 3, HSiCl₃, and a common platinum-based hydrosilylation catalyst, e.g. H2PtC16 in propan-2-ol (Speier's catalyst) or platinum divinylsiloxane complecx (Karstedt's catalyst), was stirred for 24 h at room temp. When the reaction was completed, excess HSiCl₃ was removed under vacuum. 3. A-[9]-Alkene (5)

4 2 5

A-[3]-SiCl₃ 4 was refluxed with 10% excess of allylmagnesium bromide in diethyl ether for 4 h, and cooled to 0 ⁰C and hydrolyzed with 10 % aqueous NH₄Cl. The organic layer was washed with water, dried MgSO₄ and concentrated.

4. A-[9]-SiCl₃ (6)

+ 3HSiCI₃ + Pt catalyst

A mixture of A-[9]-Alkene 5, HSiCl₃, and a common platinum-based hydrosilylation catalyst, e.g. H2PtC16 in propan-2-ol (Speier's catalyst) or platinum divinylsiloxane complecx (Karstedt's catalyst), was stirred for 24 h at room temp. When the reaction was completed, excess HSiCl₃ was removed under vacuum.

EXAMPLE 3.6

1. [l]-acid-[3]-triol (3)

(a) The triol 1 was cyanoethylated affording the nitrile compound 2. Acrylonitrile, nBu₃SnH, and azobisisobutyronitrile was added in PhCH₃ including compound 1 at HO⁰C. (b) The nitirle compound 2 was hydrolyzed to give compound 3 with carboxylic acid cleanly in such condition as KOH, EtOH/H₂O, H₂O₂, Δ.

2. A-[3]-triol (5)

(c) [l]-acid-[3]-triol was linked with compound 4 through an amide coupling , 15 reaction using l-[3-(dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride (EDC) and 1-hydroxybenzotriazole hydrate (HOBT). 3. A-[3]-tribromide (6)

20 (d)The alcohol was used to synthesize tribromide by bromination with HBiVH₂SO₄ at 100 ⁰C.

4. [l]-CN-[3]-OBzl (8)

(e) The triol 1 was treated with benzyl chloride to give trisether using Me₂SO and KOH. (f) The trisether 8 was cyanoethylated affording the nitrile compound 9. Acrylonitrile, nBu₃SnH, and azobisisobutyronitrile was added in PhCH₃ including compound 8 at HO⁰C.

5. [l]-OH-[3]-OBzl (11)

10 11

(g) The nitirle compound 9 was hydrolyzed to give compound 10 with carboxylic acid cleanly in such condition as KOH, EtOH/H₂O, H₂O₂, Δ. (h) The compound 10 with a carboxylic acid was proceeded with excess 1.0 M BH₃-THF solution to converse the acid into alcohol.

6. [l]-Alkyne-[3]-OBzl (13)

11 12 13

(i) The alcohol was transformed into chloride (CH₂Cl₂) with excess SOCl₂ and a catalytic amount of pyridine, (j) The chloride was reacted with lithium acetylide ethylenediamine complex in dimethylsulphoxide at 4O⁰C.

7. A-[3]-Alkyne-[9]-OBzl (14)

13 14

(k) The A-[3]-0Bzl 6 was alkylated with 4 equivalents of terminal alkyne building block 13, hexamethylphosphoric rtriamide (HMPA), lithium diisopropylamide (LDA), and tetramethylethylenediamine (TMED) at 0-40⁰C for 1.5 h. EXAMPLE 3.7 1. A-[9]-0H (15)

14 15

A-[3]-Alkyne-[9]-OBzl 14 was reduced and deprotected with Pd-C/H to produce

A-[9]-0H 15 in EtOH and THF solution including 10% Pd-C/H at 6O⁰C for 4d.

2. A-[27]-COOH (17)

15 13

16 17

The alcohol was smoothly converted into the nonabromide employing SOBr₂ in CH₂Cl₂ at 4O⁰C for 12 h. And then the nonabromide compound was alkylated with 12 equivalents of [l]-Alkyne-[3]-OBzl 13 to give 49% of A-[9]-Alkyne-[27]- OBzI 16. A-[9]- Alkyne-[27]- OBzI 16 were reduced and deprotected in one step with Pd-C/H in EtOH and THF solution including 10% Pd-C/H at 60⁰C for 4d yielding 89% of A-[27]-OH. A-[27]- OH was oxidized by RuO₄ treating with NH₄OH or (CH₃)₄NOH to achieve 85% of A-[27]- COOH 17.

EXAMPLE 3.8

1) [Gl]-(OMe)₂ (3)

A mixture of compound 1 (1.05 mol equiv.), 3,5-dimethoxybenzyl bromide (1.00 mol equiv. 2), potassium carbonate (1.1 mol equiv.) and 18-C-6 (0.2 mol equiv.) in dry acetone was heated at reflux under nitrogen for 48h. The mixture was cooled and evaporated to dryness, and the residue was partitioned between CH₂Cl₂ and water. The aqueous layer was extracted with CH₂Cl₂ (3 x), and the combined organic layers were dried and evaporated to dryness. The crude product was purified by flash chromatography with EtOAc-CH₂Cl₂ as eluent to give compound 3.

2) [Gl]-(OH)₂ (4)

Methyl ether group of compound 3 was deprotected by BBr₃ in EtOAc solution for 1 h, and the crude product was purified by flash chromatography with MeOH-EtOAc as eluent to give compound 4. 3) [G2]-(OMe)₄ (5)

4 2 5

A mixture Of [Gl]-(OH)₂ (1.00 mol equiv. 4), 3,5-dimethoxybenzyl bromide (2.00 mol equiv. 2), potassium carbonate (2.1 mol equiv.) and 18-C-6 (0.2 mol equiv.) in dry acetone was heated at reflux under nitrogen for 48h. The mixture was cooled and evaporated to dryness, and the residue was partitioned between CH₂Cl₂ and water. The aqueous layer was extracted with CH₂Cl₂ (3 x), and the combined organic layers were dried and evaporated to dryness. The crude product was purified by flash chromatography with EtOAc-CH₂Cl₂ as eluent to give compound 5.

4) [G2]-(OH)₄ (6)

Methyl ether group of compound 5 was deprotected by BBr₃ in EtOAc solution for 1 h, and the crude product was purified by flash chromatography with MeOH-EtOAc as eluent to give compound 4. 5) [G3]-(OMe)₈ (7)

A mixture of [G2]-(OH)₄ (1.00 mol equiv. 6), 3,5-dimethoxybenzyl bromide (4.00 mol equiv. 2), potassium carbonate (4.1 mol equiv.) and 18-c-ό (0.2 mol equiv.) in dry acetone was heated at reflux under nitrogen for 48h. The mixture was cooled and evaporated to dryness, and the residue was partitioned between CH₂Cl₂ and water. The aqueous layer was extracted with CH₂Cl₂ (3 x), and the combined organic layers were dried and evaporated to dryness. The crude product was purified by flash chromatography with EtOAc-CH₂Cl₂ as eluent to give compound 7.

6) [G3]-(OH)₈ (8)

Methyl ether group of compound 7 was deprotected by BBr₃ in EtOAc solution for 1 h, and the crude product was purified by flash chromatography with MeOH-EtOAc as eluent to give compound 8.

EXAMPLE 4 - Assembly of the Dendron on a Substrate

TMAC (N-trimethoxysilylpropyl-N,N,N-trimethylammonium chloride) was self- assembled on oxide glass instead of APDES. The dendrimer layer on TMAC layer did not need to cap the residual amine.

Aminosilylation with TMAC. Clean substrates (slide glass) were placed into a solution of TMAC (2mL) and acetone (10OmL) for 5 h. After the self-assembly, the substrates were taken out of the flask, washed with acetone. The substrates were placed in an oven, and heated at 110 ⁰C for 40 min. After immersion in acetone, the substrates were sonicated for 3 min. The washed substrate was placed in a Teflon vessel, and placed in a glass container with a big screw cap lined with an O-ring, and eventually the container was evacuated (30-40 mTorr) to dry the substrate.

Structure of TMAC (N-trimethoxysilylpropyl-N,N,N-trimethyIammoniuin chloride).

Self-assembly of the Fmoc-spacer-[9]acid was performed in same condition to the case of CBz-[9]acid with exception of capping of the residual amines by acetic anhydride

Self-Assembly of the Fmoc-spacer-[9]acid (5). A certain amount of the Fmoc- spacer-[9]acid (5) was dissolved in a mixed solvent (DMF:deionized water = 1:1 (v/v)) to make a solution of 20 mL. The solution was added into a Teflon vessel, and subsequently pieces of the above prepared aminosilylated slide glass were placed in the solution. While allowing the flask at room temperature to self-assemble, each piece of the substrate was taken out of the solution after 1 day. Right after being taken out, the plate was washed with a copious amount of deionized water. Each substrate was sonicated for 3 min in deionized water, a mixture of deionized water-methanol (1:1 (v/v)), and methanol in a sequential manner. After sonication, the substrates were placed in a Teflon vessel, and placed in a glass container with a big screw cap lined with an O-ring, and eventually the container was evacuated (30-40 mTorr) to dry the substrate.

Deprotection of Fmoc from the Self-Assembled Fmoc-spacer-[9]acid (5).

Teflon vessels containing 5 % piperidine in DMF were prepared. The self-assembled substrates were immersed in the vessels, and stirred for 20 min. Each substrate was sonicated for 3 min in acetone, and MeOH in a sequential manner and evacuated in a vacuum chamber (30-40 mTorr).

EXAMPLE 5: Preperation of Dendron-modified AFM tip and Substrate Materials The silane coupling agent N-(3-(triethoxysilyl)propyl)-O-polyethyleneoxide urethane (TPU) was purchased from Gelest Inc. All other chemicals are of reagent grade from Sigma-Aldrich. The UV-grade fused silica plates were purchased from CVI Laser Co. The polished prime Si(IOO) wafers (dopant, phosphorus; resistivity, 1.5-2.1 Ω-cm) were purchased from MEMC Electronic Materials Inc. Deionized water (18 MΩ-cm) was obtained by passing distilled water through a Barnstead E-pure 3-Module system. Thickness was measured with a variable angle ellipsometer (Model M-44) from J. A. Woolam Co. UV-vis spectra were recorded with a Hewlett-Packard diode array 8453 spectrophotometer.

1) Cleaning the Substrates. Fused silica plates and silicon wafers were sonicated in Piranha solution (concentrated H₂SO₄:30 % H₂O₂ = 7:3 (v/v)) for 4 h (Caution: Piranha solution can oxidize organic materials explosively. Avoid contact with oxidizable materials.). The plates and the wafers were washed and rinsed thoroughly with deionized water after the sonication. Subsequently, the substrates were immersed in a mixture of deionized water, concentrated ammonia solution, and 30 % hydrogen peroxide (5:1:1 (v/v/v)) contained in a Teflon beaker. The beaker was placed in a water bath and heated at 80 ⁰C for 10 min_; The substrates were taken out of the solution and rinsed thoroughly with deionized water. Again, the substrates were placed in a Teflon beaker containing a mixture of deionized water, concentrated hydrochloric acid, and 30 % hydrogen peroxide (6:1:1 (v/v/v)). The beaker was heated at 80 ⁰C for 10 min. The substrates were taken out of the solution and washed and rinsed thoroughly with a copious amount of deionized water. The clean substrates were dried in a vacuum chamber (30-40 mTorr) for about 20 min and used immediately in the following steps.

2) Cleaning the Tip. The standard V-shaped silicon nitride cantilevers (MLCT- AUNM) with pyramidal tips (Veeco Instrument; k = 10 pN/nm) were first activated by dipping in 10 % nitric acid and heating at 80 ⁰C for 20 min. The cantilevers were taken out of the solution and washed and rinsed thoroughly with a copious amount of deionized water. The clean cantilevers were dried in a vacuum chamber (30-40 mTorr) for about 20 min and used immediately in the following steps. 3) Aminosilylation. Clean fused silica, silicon wafer, and cantilevers were immersed into anhydrous toluene (20 mL) containing the coupling agent (0.20 mL) under nitrogen atmosphere, and placed in the solution for 6 h. After silylation, the substrates and cantilevers were washed with toluene, baked for 30 min at 110 ⁰C. The substrates were immersed in toluene, toluene-methanol (1:1 (v/v)), and methanol in a sequential manner, and they were sonicated for 3 min in each washing solution. The cantilevers rinsed thoroughly with toluene and methanol in a sequential manner. Finally the substrates and cantilevers were dried under vacuum (30-40 mTorr).

4) Preparation of Dendron Modified Surface. The above hydroxylated substrates and cantilevers were immersed into a methylene chloride solution with a small amount of DMF dissolving the dendron (1.0 mM) and a coupling agent, 1,3-dicyclohexylcarbodiimide (DCC) (9.9 mM) in the presence of 4-dimethylaminopyridine (DMAP) (0.90 mM) for 12-24 h. The dendron (9-anthrylmethyl N-({[tris({2-[({tris[(2- carboxyethoxy)methyl]methyl}amino)carbonyl]ethoxy}methyl)methyl]amino}carbonyl)pro pylcarbamate) used in this work was prepared in this group. After reaction, the substrates were immersed in methylene chloride, methanol, and water in a sequential manner, and they were sonicated for 3 min at each washing step. The cantilevers were rinsed thoroughly with methylene chloride, methanol, and water in a sequential manner. Finally the substrates and cantilevers were washed with methanol, and dried under vacuum (30-40 mTorr).

EXAMPLE 6: IMMOBILIZATION OF OLIGONUCLEOTIDES 1) Deprotection of Carboanthrylmethoxy Group from the Dendron Surface.

The dendron modified substrates and cantilevers were immersed into a methylene chloride solution with 1.0 M trifluoroacetic acid (TFA), and they were stirred for 3 h. After the reaction, they were soaked in a methylene chloride solution with 20 % (v/v) diisopropylethylamine (DIPEA) for 10 min. The substrates were sonicated in methylene chloride and methanol each for 3 min and the cantilevers were rinsed thoroughly with methylene chloride and methanol in a sequential manner. The substrates and cantilevers were dried under vacuum (30-40 mTorr).

2) Preparing the NHS-Modified Substrates. The above deprotected substrates and cantilevers were immersed into an acetonitrile solution with di(N- succinimidyl)carbonate (DSC) (25 mM) and DIPEA (1.0 mM) for 4 h under nitrogen atmosphere. After the reaction, the substrates and cantilevers were placed in stirred dimethylformamide for 30 min and washed with methanol. The substrates and cantilevers were dried under vacuum (30-40 mTorr).

3) Immobilization of Oligonucleotides on the Dendron modified Substrates.

The above NHS-modified substrates and cantilevers were soaked in an oligonucleotide (20 μM) in 25 mM NaHCO₃ buffer (pH 8.5) with 5.0 mM MgCl₂ for 12 h. After the reaction, the substrates and cantilevers were stirred in a hybridization buffer solution (2x SSPE buffer (pH 7.4) containing 7.0 mM sodium dodecylsulfate) at 37 ⁰C for 1 h and in boiling water for 5 min to remove non-specifically bound oligonucleotide. Finally the substrates and cantilevers were dried under vacuum (30-40 mTorr). The oligonucleotides to be immobilized are shown in Table 1.

EXMPEL 7: AFM Force Measurements

7-1: sample preparation

To understand effect of the spacing, the two types of the modification (9- acid/GPDES substrate and 9-acid/TPU substrate) were employed for the substrate by using the two silane agents such as GPDES and TPU, while spacing on AFM tip was fixed with use of 9-acid/TPU. The surface modification of the substrate was performed according to

Example 5. The oligonucleotides as shown in SEQ ID NOs: 1 to 4 were immobilized on the

9-acid/TPU substrate, respectively according to Example 6. The 30 bp complementary

DNA as represented by SEQ ID NO: 2 was immobilized on the 9-acid/GPDES substrate.

The oligonucleotides as shown in SEQ ID NOs: 5 to 20 were immobilized on the 9- acid/TPU type of AFM tip, respectively.

Table 2

In the example, 9-acid dedron is (9-anthrylmethyl N-({[tris({2-[({tris[(2- carboxyethoxy)methyl]methyl}amino)carbonyl]ethoxy}methyl)methyl]amino}carbonyl)pro pylcarbamate), and 27- acid dedron is described in Example 3.

7-2: AFM force measurement

All force measurements were performed with a NanoWizard AFM (JPK Instrument). The spring constant, k_c, of each individual AFM tip was calibrated in solution before each experiment by thermal fluctuation method available via a NanoWizard software. The spring constant varied between 12 and 15 pN/nm. All measurements were carried out in a fresh PBS buffer (pH 7.4) at room temperature. The loading rate of force measurements varied between 110 nm/s and 540 nm/s. At each experimental condition, force curves were recorded more than one hundred times at a spot, and at least more than 5 spots were examined. In these measurements, both binding and unbinding force curves were recorded. To calculate distance that the tip actually moved, the cantilever displacement was subtracted from the piezo displacement. The cantilever displacement was obtained by dividing the force by the cantilever spring constant.

7-3: Unbinding force for 9-acid/GPDES substrate immobilized by a complementary 30-base pair DNA Using the oligonucleode as shown in SEQ ID NO: 2 immobilized on 9- acid/GPDES substrate, and the oligonucleode as shown in SEQ ID NO: 6 immobilized on 9-acid/TPU AFM tip, AFM force measurement was performed at various loading rate in the range between 110 nm/s and 540 nm/s according to AFM measurement of example 7-2 to obtain unbinding force distribution (FIG.4A) at a retraction rate of 110 nm/s, and force distance curve (FIG.4B) and unbinding force distribution (FIG.4C) at a retraction rate of 540 nm/s.

A large unbinding force, attributable to an interaction of multiple oligonucleotides, was observed at 540 nm/s retraction rate (FIG.4B). Also, the histogram is rather broad (the maximum half-width is 15 pN.) and unresolved(FIG.4C). However, at 110 nm/s retraction rate the histogram (Fig. 4A) was resolved into three peaks, and each peak was sharp (the maximum half-width is 3 pN for the first peak.). Exact interpretation of the behavior is not straightforward, but the first peak at 37 pN is very likely to be from single DNA-DNA interaction (vide infra) and the other two (46 pN and 55 pN) represent unbinding events with the secondary interaction in addition to the single one.

FIG.4A is a histogram showing the force distribution of a complementary 30-base pair when relatively narrow spacing (realized with a dendron on the GPDES surbstrate). FIG.4B is a direct measurement of single unbinding force of complementary 30 base pairs with a retraction velocity of 540 nm/s. FIG.4B is a force versus distance curve measured between complementary 30 base pairs with a retraction velocity of 540 nm/s. Much larger force (blue curve), attributable to interactions of multiple oligonucleotides, can be observed at 540 nm/s retraction rate (For comparison, unbinding force (red curve) observed in 110 nm/s retraction rate is displayed.). FIG.4C shows the probability distribution of unbinding force with a retraction velocity of 540 nm/s. The histogram shows the observed force distribution with relatively narrow spacing (realized with the dendron on the GPDES surface). The maximum of the distribution is found by a Gaussian fit to be 68 ± 13 pN, and the distribution curve is not resolved to show single interaction.

7-4: Binding force and unbinding for 9-acid/TPU substrate immobilized by a complementary 30-base pair DNA

Using the oligonucleode as shown in SEQ ID NO: 2 immobilized on 9-acid/TPU substrate, and the oligonucleode as shown in SEQ ID NO: 6 immobilized on 9-acid/TPU AFM tip, AFM force measurement was performed at a retraction rate of 110 nm/s according to AFM measurement of example 7-2 to obtain unbinding force distribution (FIG.5A), binding force vs distance curve (FIG.5B), and binding force distribution curve (FIG.5C).

When the DNA was immobilized on 9-acid/TPU surface, the unbinding force histogram (Fig.5A) showed only one peak at 37 ± 2 pN, and the narrowness of the peak was not tarnished. Disappearance of the minor peaks at 46 pN and 55 pN confirms that these peaks represent events associated with the secondary interaction. For analysis of the above two cases, only unusual curves were discarded, and more than 90 % of measurements were included in the plot. While the curves are frequently indented for 9-aicd/GPDES case, none of the curves for 9-acid/TPU showed any indentation. Thus, it is possible to measure single DNA-DNA interaction by modifying the substrate surface with TPU as a silane agent, because of the sufficient spacing.

The binding force curves were observed every time when the tip approached the dendron-modified surface (Fig.5B). In this particular process, again 9-acid/TPU-modified surface produced single dip force curves, while 9-acid/GPDES case frequently showed double- or multiple-dipped force curves. Because the behavior was so consistent and reproducible, not a single datum had to be discarded to generate the histogram. As in the histogram for the unbinding event, the peak is narrow (the maximum half-width is 3 pN.), and the value of 39 pN is pretty close to that of the unbinding case. It is intriguing to find that such unprecedented binding process can be observed when the spacing between DNAs was controlled properly.

Moreover, it was found that the binding force behavior is less dependent on the loading rate. In other word, the same histogram (Fig.5C) was obtained at any loading rate between 70 nm/s and 540 nm/s. The particular experiment was repeated many times using different tips and samples, and the above binding behavior and the histogram were consistently reproduced.

7-5: Unbinding force for 27-acid and TPU modified substrate for examining single strand interaction Previously, unbinding force of 48 pN for other complementary 30-base DNA was recorded even at a slower retraction rate (T. Strunz, K. Oroszlan, R. Schafer, H.-J. Gϋntherodt, Proc. Natl. Acad. ScL U.S.A. 96, 11277, 1999). It is interesting to observe a smaller unbinding force even with DNA with the same GC content.

In order to examine whether these interactions are from a single strand or multiple strands, a higher generation dendron, 27-acid, was employed. The third generation dendron is expected to provide spacing around 10 nm. Spacing on the substrate was increased with a combination of 27-acid and TPU, while AFM tip was modified with 9-acid/TPU. It was interesting to note the histogram was exactly same as that of 9-acid/TPU case. The AFM tip was modified with 27-acid/TPU, and observed again the same histogram. The only difference is a reduced chance of observing the unbinding. For the last case, about 50 % of the retraction events did not show the unbinding phenomenon at all. This change seems reasonable, because too big spacing between the oligonucleotides reduces chance of the hybridization. This behavior showed clearly spacing generated from 9-acid/TPU was already large enough for realization of single strand interaction.

7-6: Binding force and unbinding force for complementary DNA duplexes Prior to testing other oligonucleotides, the accuracy of the force measurement was tested in the above condition. Samples from different batches were prepared, and the cantilevers were calibrated. The inventors found that the variation was within 10-15 %. The value suggests that reproducible and precise control of the surface allows minimal error: the value never goes beyond the error associated with spring constant calibration. With 9- acid/TPU-modified surface, binding and unbinding events of DNA duplexes of 20, 30, 40, and 50 base pairs (Table 1) were performed at the 110 nm/s loading rate. Force-distance curves were obtained on each duplex during the approach and retract cycles.

As previously mentioned above, binding and unbinding histograms were almost the same, and average force values were identical. The binding force histogram, and the unbinding force histogram of complementary DNA duplexes with 20, 30, 40 and 50 base pairs, were shown in Fig.6A, and FIG.6C, respectively.

In the histogram as shown in FIG.6A, non-overlapped peaks, and clear increment of the force with the length of DNA were seen. The values are 29 pN, 39 pN, 50 pN, and 59 pN for 20, 30, 40, and 50 base pairs. Coincidentally the increment of the force is roughly 10 pN at each increase of 10 DNA bases. For verification, the forces of non-complementary DNA strands were measured. In all cases, force curves were mostly not detected, and with a low probability, a tiny force of 10 pN was recorded.

In FIG.6B for force-piezo displacement curve of complementary DNA duplexes with 20, 30, 40 and 50 base pairs was obtained by calculating from the binding force distribution of FIG 4. The observed distance that the tip moved towards the surface to relieve the strain upon the binding event was retrieved from the force-piezo displacement curve and the value was plotted. In the particular situation, distances of 2.4 nm, 3.2 nm, 3.6 nm, and 4.2 nm were recorded for 20-mer, 30-mer, 40-mer, and 50-mer cases. Because the peaks are quite narrow, and the distance increases almost linearly with the DNA length, the parameter should be diagnostic for analyzing the interaction DNA length in unknown samples. 7-7: Binding force distribution for mismatched DNA duplexes

To further probe this recognition phenomenon, interaction force curves were recorded for the single base and double base mismatched pairs (Table 1). Using the oligonucleodes as shown in SEQ ID NO: 5 to 8 immobilized on 9-acid/TPU substrate for single base mismatched DNA, the oligonucleodes as shown in SEQ ID NO: 9 to 12 immobilized on 9-acid/TPU substrate for double base mismatched DNA, and the oligonucleode as shown in SEQ ID NO:1 to 4 immobilized on 9-acid/TPU AFM tip, AFM force measurements were performed at a retraction rate of 110 nm/s according to AFM measurement of example 7-2 to obtain binding force distribution for single base mismatched DNA duplexs (FIG.7), and binding force distribution for double base mismatched DNA duplexs (FIG.8).

As expected, it was observed that the introduction of the mismatch decreased binding and unbinding forces. As shown in FIG.7 for single base mismatched pairs, binding force of 27 pN, 37 pN, 43 pN, and 50 pN was observed for 20-mer, 30-mer, 40-mer, and 50-mer, respectively. As shown in FIG.8 for double base mismatched pairs, binding force of 24 pN, 32 pN, 40 pN, and 45 pN was observed for 20-mer, 30-mer, 40-mer, and 50-mer, respectively.

As in the previous case for complementary DNA duplex, binding and unbinding forces were identical. However, for single base mismatch cases, there were only marginal decrease (2 pN) for both 20 mer and 30 mer. Meanwhile, substantial decrease (> 7 pN) was observed for 40 mer and 50 mer. The result shows that use of DNA longer than 40 mer guarantees reliable detection of single point mutation. As expected, larger reduction of the force was observed for the double base mismatched pairs. For examples, decrease of 5 pN was observed for 20 mer, while 14 pN was observed for 50 mer. It is worthwhile to note the capability of picoforce AFM for detecting a single point mutation at the single molecular level.

While this invention has been described in connection with what is presently considered to be practical exemplary embodiments, it is to be understood that the invention is not limited to the disclosed embodiments, but, on the contrary, is intended to cover various modifications and equivalent arrangements included within the spirit and scope of the appended claims.

Claims

WHAT IS CLAIMED IS:

1. A cantilever for atomic force microscopy (AFM) comprising a cantilever body having a fixed end and a free end, the free end having a surface region being chemically modified by a dendron in which a plurality of termini of the branched region of the dendron are bound to the surface, and a terminus of the linear region of the dendron is functionalized.

2. The cantilever according to claim 1, wherein at least one tapered protrusion is provided in the vicinity of the free end.

^■3. The cantilever according to Claim 2, wherein the protrusion is pyramidal or conical.

4. The cantilever according to Claim 1, wherein the dendrons are spaced at regular intervals between about 0.1 nm and about 100 nm among the linear functionalized groups.

5. The cantilever according to Claim 4, wherein the dendrons are spaced at regular interval of about 10 nm.

6. The cantilever according to Claim 1, wherein the terminus of the branched region is functionalized with -COZ, -NHR₅-OR', or -PR"3, wherein Z is a leaving group, wherein R is an alkyl, wherein R' is alkyl, aryl, or ether, and R" is H, alkyl, or alkoxy.

7. The cantilever according to claim 6, wherein COZ is acid, ester, activated ester, acid halide, activated amide, or CO-imidazoyl.

8. The cantilever according to claim 1, wherein the linear region comprises a spacer region. 9. The cantilever according to claim 8, wherein the spacer region is connected to the branched region via a first functional group.

10. The cantilever according to claim 9, wherein the functional group is -NH2, -

OH, -PH3, -COOH, -CHO or -SH.

;11. The cantilever according to claim 8, wherein the spacer region comprises a linker region covalently bound to the first functional group.

12. The cantilever according to claim 11, wherein the linker region comprises a substituted or unsubstituted alkyl, alkenyl, alkynyl, cycloalkyl, aryl, ether, polyether, ester, or aminoalkyl group.

13. The cantilever according to claim 8, wherein the spacer region comprises a second functional group.

14. The cantilever according to claim 13, wherein the second functional group is -NH2, -OH, -PH3, -COOH, -CHO or -SH.

15. The cantilever according to claim 13, wherein the second functional group is located at the terminus of the linear region.

16. The cantilever according to claim 1, wherein a protecting group is bound to the terminus of the linear region.

17. The cantilever according to claim 16, wherein the protecting group is acid labile or base labile.

18. The cantilever according to claim 1, wherein a probe nucleotide is bound to the terminus of the linear region of the dendron.

19. The cantilever according to claim 18, wherein the probe nucleotide is at a low density ranging about 0.01 probe/nm2 to about 0.5 probe/nm2.

20. The cantilever according to claim 18, wherein the probe nucleotide is DNA, RNA, oligonucleotide, cDNA, nucleotide analog or a combination thereof.

21. A cantilever according to claim 18, wherein the distance between the probe nucleotides bound to the linear region of the dendron is from about 0.1 to about 100 nm.

22. A method for manufacturing a cantilever according to any one of claims 1 to

20, comprising (i) functionalizing the surface region of the cantilever so that it will react with the termini of the dendrons; and (ii) contacting the dentrons to the surface region so that the termini and the surface form a bond.

23. The method for manufacturing the cantilever according to claim 22, wherein a probe nucleotide is fixed to the terminus of the linear region of dendrons, comprising the steps of i) removing protecting group from the terminus of the linear region of the dendrons on the surface region; and ii) contacting the probe nucleotide or a linker molecule linked to the probe nucleotide to the terminus of the linear region of the dendrons on the substrate so that the probe nucleotide or the linker molecule and the terminus form a bond, wherein the linker molecule is a homobifunctional or heterobifunctional linker.

24. An apparatus for measuring an interaction between one probe nucleotide and one target nucleotide by AFM, the apparatus comprising: a cantilever having a fixed end and a free end, the free end having a surface region being chemically modified by a dendron in which a plurality of termini of the branched region of the dendrons are bound to the surface, and a terminus of the linear region of the denderon is attached to the probe nucleotide according to any one of claims 1 to 20; a substrate to which the target nucleotide is immobilized; a controller for adjusting the relative position and orientation of the cantilever and target nucleotide substrate to cause an interaction between the probe nucleotide immobilized on the dendron-modified surface region of the cantilever and the target nucleotide immobilized on the substrate; and a detector for measuring a physical parameter associated with the interaction between the probe nucleotide and the target nucleotide.

25. The apparatus according to claim 24, wherein the substrate is modified by dendrons to which the target nucleotide is immobilized. ,

26. A method of assaying a target nucleotide for interaction with a probe nucleotide, the method comprising steps of:

(a) providing a cantilever having a fixed end and a free end, the free end having a surface region being chemically modified by a dendron in which a plurality of termini of the branched region of the dendrons are bound to the surface according to any one of claims i to 20;

(b) immobilizing a target nucleotide on a substrate;

(c) chemically modifying the dendron-modified surface region of the cantilever to immobilize a probe nucleotide;

(d) coupling the substrate and the cantilever to apparatus that includes a controller for adjusting the relative position and orientation of the substrate and the cantilever to cause an interaction between the probe nucleotide immobilized on the dendron-modified surface region of the cantilever and the target nucleotide immobilized on the substrate of the sample support member,

(e) controlling the relative position and orientation of the cantilever and the substrate to cause an interaction between a probe nucleotide and the target nucleotide; and

(f) measuring a physical parameter associated with the interaction between the probe nucleotide and the target nucleotide.

27. The method according to claim 26, wherein the probe nucleotide is a single strand of DNA or RNA, and target nucleotide is complimentary strands or base mismatched strands of DNA or RNA.

28. The method according to claim 26, wherein in step (b), the substrate is chemically modified by dendron to immobilize a target nucleotide thereon;