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Publication numberUS20030148380 A1
Publication typeApplication
Application numberUS 10/155,883
Publication dateAug 7, 2003
Filing dateMay 24, 2002
Priority dateJun 5, 2001
Also published asUS8372949, US20080242552
Publication number10155883, 155883, US 2003/0148380 A1, US 2003/148380 A1, US 20030148380 A1, US 20030148380A1, US 2003148380 A1, US 2003148380A1, US-A1-20030148380, US-A1-2003148380, US2003/0148380A1, US2003/148380A1, US20030148380 A1, US20030148380A1, US2003148380 A1, US2003148380A1
InventorsAngela Belcher
Original AssigneeBelcher Angela M.
Export CitationBiBTeX, EndNote, RefMan
External Links: USPTO, USPTO Assignment, Espacenet
Using semiconductors comprised of crystal binding peptides for selective recognition of amino acid oligomers
US 20030148380 A1
Abstract
The present invention includes methods for selective binding of inorganic materials and the compositions that made up of the selecting agent and the target materials. One form of the present invention is a method for selecting crystal-binding peptides with binding specificity including the steps of contacting one or more amino acid oligomers with one or more single-crystals of a semiconductor material so that the oligomers may bind to the crystal and eluting the bound amino acid oligomers from the single-crystals.
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Claims(62)
What is claimed is:
1. A method for selecting crystal-binding peptides with binding specificity comprising the steps of:
contacting one or more amino acid oligomers with one or more single-crystals of a semiconductor material so that the oligomers may bind to the crystal; and
eluting the bound amino acid oligomers from the single-crystals.
2. The method recited in claim 1, further comprising the step of contacting the eluted amino acid oligomers with one or more semiconductor crystals, and repeating the eluting step.
3. The method recited in claim 1, wherein the nucleic acid sequence underlying eluted oligomers is amplified.
4. The method recited in claim 3, wherein the amplification is accomplished using a polymerase chain reaction.
5. The method recited in claim 1, further comprising the step of determining the sequence of the eluted amino acid oligomers.
6. The method recited in claim 1, wherein the semiconductor material is chosen from the group consisting of gallium arsenide, indium phosphide, gallium nitride, zinc sulfide, cadmium sulfide, aluminum arsenide, gallium stibinide, aluminum gallium arsenide, aluminum stibinide, cadmium selenide, zinc selenide, cadmium telluride, zinc selenide, indium arsenide, aluminum arsenide and silicon.
7. The method recited in claim 1, wherein the semiconductor material is chosen from the group consisting of a Group II-Group V semiconductor and a Group III-Group VI semiconductor.
8. The method recited in claim 1, wherein the one or more amino acid oligomers that are contacted with the single-crystal further comprise a phage-display library.
9. The method recited in claim 1, wherein the one or more amino acid oligomers that are contacted with the single-crystal further comprise an antibody expression library.
10. The method recited in claim 1, wherein the one or more amino acid oligomers that are contacted with the single-crystal further comprise a bacterial expression library.
11. The method recited in claim 1, where the amino acid oligomers are about 12 amino acids in length.
12. The method recited in claim 1, wherein the one or more amino acid oligomers that are contacted with the single crystal further comprise a library of random amino acid sequences.
13. The method recited in claim 12, where the amino acid oligomers are about 12 amino acids in length.
14. The method recited in claim 12, wherein the amino acid oligomers are about 7 amino acids in length.
15. The method recited in claim 12, wherein the amino acid oligomers are between about 7 to 15 amino acids in length, and disulfide constrained.
16. The method recited in claim 1, wherein the eluting is done at high stringency.
17. The method recited in claim 1, wherein the eluting is done at moderate stringency.
18. The method recited in claim 1, wherein the eluting is done at low stringency.
19. An amino acid sequence for the binding GaAs (100) chosen from the group consisting of Seq. ID Nos. 1 through 11, inclusive.
20. A method for selecting amino acid sequences with binding specificity comprising the steps of:
contacting one or more amino acid oligomers with one or more single-crystals of a magnetic, mineral or optical material so that the oligomers may bind to the crystal; and
eluting the bound amino acid oligomers from the single-crystals.
21. The method recited in claim 20, further comprising the step of contacting the eluted amino acid oligomers with one or more single-crystals of a magnetic material, and repeating the eluting step.
22. The method recited in claim 20, wherein nucleic acid sequence underlying the eluted oligomers is amplified.
23. The method recited in claim 22, wherein the amplification is accomplished using a polymerase chain reaction.
24. The method recited in claim 20, further comprising the step of determining the sequence of the eluted amino acid oligomers.
25. The method recited in claim 20, wherein the magnetic, mineral or optical material is chosen from the group consisting of FePd, cobalt, manganese, lithium niobate, iron oxides and calcium carbonate.
26. The method recited in claim 20, wherein the one or more amino acid oligomers that are contacted with the single-crystal further comprise a phage-display library.
27. The method recited in claim 26, where the amino acid oligomers are about 12 amino acids in length.
28. The method recited in claim 20, wherein the one or more amino acid oligomers that are contacted with the single crystal further comprise a library of random amino acid sequences.
29. The method recited in claim 28, where the amino acid oligomers are about 12 amino acids in length.
30. The method recited in claim 28, wherein the amino acid oligomers are between about 7 and 15 amino acids in length.
31. The method recited in claim 28, wherein the amino acid oligomers are 7 amino acids in length, and disulfide constrained.
32. The method recited in claim 20, wherein the eluting is done at moderate stringency.
33. The method recited in claim 20, wherein the eluting is done at low stringency.
34. A method for selecting crystal-bonding amino acids comprising the steps of:
contacting one or more amino acid oligomers with one or more crystals of a target material so that the oligomers may bind to the crystal; and
eluting the bound amino acid oligomers from the crystals.
35. The method recited in claim 34, further comprising the step of contacting the eluted amino acid oligomers with one or more semiconductor crystals, and repeating the eluting step.
36. The method recited in claim 34, wherein nucleic acid sequence underlying the eluted oligomers is amplified.
37. The method recited in claim 36, wherein the amplification is accomplished using a polymerase chain reaction.
38. The method recited in claim 34, further comprising the step of determining the sequence of the eluted amino acid oligomers.
39. The method recited in claim 34, wherein the semiconductor material is chosen from the group consisting of gallium arsenide, indium phosphide, gallium nitride, zinc sulfide, cadmium sulfide, aluminum arsenide, gallium stibinide, aluminum gallium arsenide, aluminum stibinide, aluminum arsenide, cadmium selenide, zinc selenide, cadmium telluride, zinc selenide, indium arsenide and silicon.
40. The method recited in claim 34, wherein the semiconductor material is chosen from the group consisting of a Group III-Group V semiconductor and a Group II-Group VI semiconductor.
41. The method recited in claim 34, wherein the one or more amino acid oligomers that are contacted with the single-crystal further comprise a phage-display library.
42. The method recited in claim 41, where the amino acid oligomers are about 12 amino acids in length.
43. The method recited in claim 20, wherein the one or more amino acid oligomers that are contacted with the single crystal further comprise a library of random amino acid sequences.
44. The method recited in claim 43, where the amino acid oligomers are about 12 amino acids in length.
45. The method recited in claim 43, wherein the amino acid oligomers are about 7 to 15 amino acids in length.
46. The method recited in claim 43, wherein the amino acid oligomers are 7 amino acids in length, and disulfide constrained.
47. An amino acid sequence for the binding GaAs (100) chosen from the group consisting of Seq. ID Nos. 1 to 11.
48. A specificity structure comprising:
one or more single crystals of gallium arsenide; and
a selective binding amino acid sequence.
49. The specificity structure recited in claim 48, wherein the selective binding amino acid sequence is chosen from the group consisting of Seq. ID Nos. 1,2,3,4,5,6,7,8,9,10, 11 and 117.
50. A specificity structure comprising:
one or more single crystals of cadmium sulfide; and
a selective binding amino acid sequence.
51. The specificity structure recited in claim 50, wherein the selective binding amino acid sequence is chosen from the group consisting of Seq. ID Nos. 12 through 82.
52. A specificity structure comprising:
one or more single crystals of zinc sulfide; and
a selective binding amino acid sequence.
53. The specificity structure recited in claim 52, wherein the selective binding amino acid sequence is chosen from the group consisting of Seq. ID Nos. 83 through 116.
54. A specificity structure comprising:
one or more single crystals of lead sulfide; and
a selective binding amino acid sequence.
55. The specificity structure recited in claim 54, wherein the selective binding amino acid sequence is chosen from the group consisting of Seq. ID Nos. 118 through 158.
56. A crystal binding amino acid oligomers comprising the sequence motif (ser/tyr/thr)-(arg/asp/ser)-Xaa-(ser/asn/glu/arg/thr)-Xaa-Xaa-(ser/thr/glu/asp)-(ser/thr/tyr).
57. A crystal binding amino acid oligomers comprising the sequence motif Xaa-Xaa-(ser/tyr/thr)-(arg/asp/ser)-Xaa -(ser/asn/glu/arg/thr)-Xaa-Xaa-(ser/thr/glu/asp)-(ser/thr/tyr) -(ser/thr/his)-Xaa-Xaa.
58. A method of determining a binding motif comprising the steps:
contacting a binding library with one or more crystals of a target material to allow components of the library to bind via a binding region to the crystals;
eluting off bound components; and
sequencing the eluted components.
59. The method recited in claim 58, wherein the library is comprised of peptides.
60. The method recited in claim 58, wherein the library is a phage display library.
61. The method recited in claim 58, wherein the library is an antibody display library.
62. The method recited in claim 58, wherein the library is comprised of chimeric proteins with protein cleavage sites adjacent to the binding region.
Description
FIELD OF THE INVENTION

[0001] The present invention is directed to the selective recognition of inorganic materials in general and specifically toward surface recognition of single crystals of semiconductor and magnetic materials using small organic molecules.

BACKGROUND OF THE INVENTION

[0002] In biological systems, organic molecules exert a remarkable level of control over the nucleation and mineral phase of inorganic materials such as calcium carbonate and silica, and over the assembly of crystallites and other nanoscale building blocks into complex structures required for biological function.

[0003] Materials produced by biological processes are typically soft, and consist of a surprisingly simple collection of molecular building blocks (i.e., lipids, peptides, and nucleic acids) arranged in astoundingly complex architectures. Unlike the semiconductor industry, which relies on a serial lithographic processing approach for constructing the smallest features on an integrated circuit, living organisms execute their architectural “blueprints” using mostly non-covalent forces acting simultaneously upon many molecular components. Furthermore, these structures can often elegantly rearrange between two or more usable forms without changing any of the molecular constituents.

[0004] The use of “biological” materials to process the next generation of microelectronic devices provides a possible solution to resolving the limitations of traditional processing methods. The critical factors in this approach are identifying the appropriate compatibilities and combinations of biological-inorganic materials, and the synthesis of the appropriate building blocks.

SUMMARY OF THE INVENTION

[0005] The ability to direct the assembly of nanoscale components into controlled and sophisticated structures has motivated intense efforts to develop assembly methods that mimic or exploit the recognition capabilities and interactions found in biological systems. Of particular value would be methods that could be applied to materials with interesting electronic or optical properties, but natural evolution has not selected for interactions between biomolecules and such materials.

[0006] The present invention is based on recognition that biological systems efficiently and accurately assemble nanoscale building blocks into complex and functionally sophisticated structures with high perfection, controlled size and compositional uniformity.

[0007] The present invention includes methods for selective binding of inorganic materials and the compositions that are made up of the selecting agent and the target materials. One form of the present invention is a method for selecting crystal-binding peptides with binding specificity and includes the steps of contacting one or more amino acid oligomers with one or more single-crystals of a semiconductor material so that the oligomers may bind to the crystal and eluting the bound amino acid oligomers from the single-crystals.

[0008] Another form of the present invention is a method for selecting crystal-binding peptides with binding specificity and includes the steps of contacting one or more amino acid oligomers with one or more crystals of a semiconductor, such as a Group III-V or II-VI material; or a magnetic material, such an iron oxide, so that the oligomers may bind to the crystal and eluting the bound amino acid oligomers from the single-crystals.

[0009] Another form of the present invention is a peptide sequence for the binding GaAs (100) chosen from the group consisting of Seq. ID Nos. 1 through 11.

[0010] Still another form of the present invention is a method for selecting polymeric organic molecules, lipids or nucleic acids with binding specificity. A method of the present invention begins by contacting one or more oligomers with one or more single-crystals of a magnetic material so that the oligomers may bind to the crystal and eluting the bound peptide oligomers from the single-crystals. The sequence of the organic polymer is then determined by direct or indirect sequencing.

[0011] Another form of the present invention is a method for selecting crystal-bonding amino acids including the steps of contacting one or more amino acid oligomers with one or more crystals of a target material so that the oligomers may bind to the crystal and eluting the bound amino acid oligomers from the crystals.

[0012] Another form of the present invention is a specificity structure made up of one or more single crystals of gallium arsenide, indium phosphide, mercury cadmium telluride, zinc sulfide, cadmium sulfide, aluminum-gallium-arsenide, zinc selenide, cadmium selenide, cadmium telluride, zinc telluride, aluminum arsenide, indium arsenide and the like and a selective binding amino acid sequence.

[0013] Another form of the present invention is a crystal binding amino acid oligomer made up of the sequence motif (ser/tyr/thr)-(arg/asp/ser)-Xaa-(ser/asn/glu/arg/thr)-Xaa-Xaa-ser/thr/glu/asp)-(ser/thr/tyr) (SEQ. ID NO. 159) or Xaa-Xaa-(ser/tyr/thr)-(arg/asp/ser)-Xaa-(ser/asn/glu/arg/thr)-Xaa-Xaa-(ser/thr/glu/asp)-(ser/thr/tyr)-(ser/thr/his)-Xaa-Xaa (SEQ. ID NO 160).

[0014] The motifs and other polymers referred to in the descriptions of various embodiments of the present invention may be free molecules, e.g. amino acid oligomers, or they may be part of a chimera, such as a phage display.BRIEF

DESCRIPTION OF THE DRAWINGS

[0015] For a more complete understanding of the features and advantages of the present invention, reference is now made to the detailed description of the invention along with the accompanying figures in which corresponding numerals in the different figures refer to corresponding parts and in which:

[0016]FIG. 1 depicts selected random amino acid sequences in accordance with the present invention;

[0017]FIG. 2 depicts XPS spectra of structures in accordance with the present invention;

[0018]FIG. 3 depicts phage recognition of heterostructures in accordance with the present invention; and

[0019] FIGS. 4-8 depict specific amino acid sequences in accordance with the present invention.

DETAILED DESCRIPTION OF THE INVENTION

[0020] Although making and using various embodiments of the present invention are discussed in detail below, it should be appreciated that the present invention provides many applicable inventive concepts that can be embodied in a wide variety of specific contexts. The specific embodiments discussed herein are merely illustrative of specific ways to make and use the invention, and do not delimit the scope of the invention.

[0021] The facility with which biological systems assemble immensely complicated structure on an exceedingly minute scale has motivated a great deal of interest in the desire to identify non-biological systems that can behave in a similar fashion. Of particular value would be methods that could be applied to materials with interesting electronic or optical properties, but natural evolution has not selected for interactions between biomolecules and such materials.

[0022] The present invention is based on recognition that biological systems efficiently and accurately assemble nanoscale building blocks into complex and functionally sophisticated structures with high perfection, controlled size and compositional uniformity.

[0023] One method of providing a random organic polymer pool is using a Phage-display library, based on a combinatorial library of random peptides containing between 7 and 12 amino acids fused to the pIII coat protein of M13 coliphage, provided different peptides that were reacted with crystalline semiconductor structures. Five copies of the pIII coat protein are located on one end of the phage particle, accounting for 10-16 nm of the particle. The phage-display approach provided a physical linkage between the peptide substrate interaction and the DNA that encodes that interaction. The examples described here used as examples, five different single-crystal semiconductors: GaAs (100), GaAs (111)A, GaAs(111)B, InP(100) and Si(100). These substrates allowed for systematic evaluation of the peptide substrate interactions and confirmation of the general utility of the methodology of the present invention for different crystalline structures.

[0024] Protein sequences that successfully bound to the specific crystal were eluted from the surface, amplified by, e.g., a million-fold, and reacted against the substrate under more stringent conditions. This procedure was repeated five times to select the phage in the library with the most specific binding. After, e.g., the third, fourth and fifth rounds of phage selection, crystal-specific phage were isolated and their DNA sequenced. Peptide binding has been identified that is selective for the crystal composition (for example, binding to GaAs but not to Si) and crystalline face (for example, binding to (100) GaAs, but not to (111)B GaAs).

[0025] Twenty clones selected from GaAs(100) were analyzed to determine epitope binding domains to the GaAs surface. The partial peptide sequences of the modified pIII or pVIII protein are shown in FIG. 1, revealing similar amino-acid sequences among peptides exposed to GaAs. With increasing number of exposures to a GaAs surface, the number of uncharged polar and Lewis-base functional groups increased. Phage clones from third, fourth and fifth round sequencing contained on average 30%, 40% and 44% polar functional groups, respectively, while the fraction of Lewis-base functional groups increased at the same time from 41% to 48% to 55%. The observed increase in Lewis bases, which should constitute only 34% of the functional groups in random 12-mer peptides from our library, suggests that interactions between Lewis bases on the peptides and Lewis-acid sites on the GaAs surface may mediate the selective binding exhibited by these clones.

[0026] The expected structure of the modified 12-mers selected from the library may be an extended conformation, which seems likely for small peptides, making the peptide much longer than the unit cell (5.65 A°) of GaAs. Therefore, only small binding domains would be necessary for the peptide to recognize a GaAs crystal. These short peptide domains, highlighted in FIG. 1, contain serine- and threonine-rich regions in addition to the presence of amine Lewis bases, such as asparagine and glutamine. To determine the exact binding sequence, the surfaces have been screened with shorter libraries, including 7-mer and disulphide constrained 7-mer libraries. Using these shorter libraries that reduce the size and flexibility of the binding domain, fewer peptide-surface interactions are allowed, yielding the expected increase in the strength of interactions between generations of selection.

[0027] Phage, tagged with streptavidin-labelled 20-nm colloidal gold particles bound to the phage through a biotinylated antibody to the M13 coat protein, were used for quantitative assessment of specific binding. X-ray photoelectron spectroscopy (XPS) elemental composition determination was performed, monitoring the phage substrate interaction through the intensity of the gold 4f-electron signal (FIG. 2a-c). Without the presence of the G1-3 phage, the antibody and the gold streptavidin did not bind to the GaAs(100)substrate. The gold-streptavidin binding was, therefore, specific to the phage and an indicator of the phage binding to the substrate. Using XPS it was also found that the G1-3 clone isolated from GaAs(100) bound specifically to GaAs(100) but not to Si(100) (see FIG. 2a). In complementary fashion the S1 clone, screened against the (100) Si surface, showed poor binding to the (100) GaAs surface.

[0028] Some GaAs clones also bound the surface of InP (100), another zinc-blende structure. The basis of the selective binding, whether it is chemical, structural or electronic, is still under investigation. In addition, the presence of native oxide on the substrate surface may alter the selectivity of peptide binding.

[0029] The preferential binding of the G1-3 clone to GaAs(100), over the (111)A (gallium terminated) or (111)B (arsenic terminated) face of GaAs was demonstrated (FIG. 2b, c). The G1-3 clone surface concentration was greater on the (100) surface, which was used for its selection, than on the gallium-rich (111)A or arsenic-rich (111)B surfaces. These different surfaces are known to exhibit different chemical reactivities, and it is not surprising that there is selectivity demonstrated in the phage binding to the various crystal faces. Although the bulk termination of both 111 surfaces give the same geometric structure, the differences between having Ga or As atoms outermost in the surface bilayer become more apparent when comparing surface reconstructions. The composition of the oxides of the various GaAs surfaces is also expected to be different, and this in turn may affect the nature of the peptide binding.

[0030] The intensity of Ga 2 p electrons against the binding energy from substrates that were exposed to the G1-3 phage clone is plotted in 2 c. As expected from the results in FIG. 2b, the Ga 2 p intensities observed on the GaAs (100), (111)A and (111)B surfaces are inversely proportional to the gold concentrations. The decrease in Ga 2 p intensity on surfaces with higher gold-strptavidin concentrations was due to the increase in surface coverage by the phage. XPS is a surface technique with a sampling depth of approximately 30 angstroms; therefore, as the thickness of the organic layer increases, the signal from the inorganic substrate decreases. This observation was used to confirm that the intensity of gold-streptavidin was indeed due to the presence of phage containing a crystal specific bonding sequence on the surface of GaAs. Binding studies were performed that correlate with the XPS data, where equal numbers of specific phage clones were exposed to various semiconductor substrates with equal surface areas. Wild-type clones (no random peptide insert) did not bind to GaAs (no plaques were detected). For the G1-3 clone, the eluted phage population was 12 times greater from GaAs(100) than from the GaAs(111)A surface.

[0031] The G1-3, G12-3 and G7-4 clones bound to GaAs(100) and InP(100) were imaged using atomic force microscopy (AFM). The InP crystal has a zinc-blende structure, isostructural with GaAs, although the In-P bond has greater ionic character than the GaAs bond. The 10-nm width and 900-nm length of the observed phage in AFM matches the dimensions of the M13 phage observed by transmission electron microscopy (TEM), and the gold spheres bound to M13 antibodies were observed bound to the phage (data not shown). The InP surface has a high concentration of phage. These data suggest that there are many factors involved in substrate recognition, including atom size, charge, polarity and crystal structure.

[0032] The G1-3 clone (negatively stained) is seen bound to a GaAs crystalline wafer in the TEM image (not shown). The data confirms that binding was directed by the modified pIII protein of G1-3, not through non-specific interactions with the major coat protein. Therefore, peptides of the present invention may be used to direct specific peptide-semiconductor interactions in assembling nanostructures and heterostructures (FIG. 4e).

[0033] X-ray fluorescence microscopy was used to demonstrate the preferential attachment of phage to a zinc-blende surface in close proximity to a surface of differing chemical and structural composition. A nested square pattern was etched into a GaAs wafer; this pattern contained 1-μm lines of GaAs, and 4-μm SiO2 spacings in between each line (FIGS. 3a, 3 b). The G12-3 clones were interacted with the GaAs/SiO2 patterned substrate, washed to reduce non-specific binding, and tagged with an immuno-fluorescent probe, tetramethyl rhodamine (TMR). The tagged phage were found as the three red lines and the center dot, in FIG. 3b, corresponding to G12-3 binding only to GaAs. The SiO2 regions of the pattern remain unbound by phage and are dark in color. This result was not observed on a control that was not exposed to phage, but was exposed to the primary antibody and TMR (FIG. 3a). The same result was obtained using non-phage bound G12-3 peptide.

[0034] The GaAs clone G12-3 was observed to be substrate-specific for GaAs over AlGaAs (FIG. 3c). AlAs and GaAs have essentially identical lattice constraints at room temperature, 5.66 A° and 5.65 A°, respectively, and thus ternary alloys of AlxGa1-xAs can be epitaxially grown on GaAs substrates. GaAs and AlGaAs have zinc-blende crystal structures, but the G12-3 clone exhibited selectivity in binding only to GaAs. A multilayer substrate was used, consisting of alternating layers of GaAs and of Al0.98Ga0.02As. The substrate material was cleaved and subsequently reacted with the G12-3 clone.

[0035] The G12-3 clones were labeled with 20-nm gold-streptavidin nanoparticles. Examination by scanning electron microscopy (SEM) shows the alternating layers of GaAs and Al0.98Ga0.02As within the heterostructure (FIG. 3c). X-ray elemental analysis of gallium and aluminum was used to map the gold-streptavidin particles exclusively to the GaAs layers of the heterostructure, demonstrating the high degree of binding specificity for chemical composition. In FIG. 3d, a model for the discrimination of phage for semiconductor heterostructures, as seen in the fluorescence and SEM images (FIGS. 3a-c).

[0036] The present invention demonstrates the power use of phage-display libraries to identify, develop and amplify binding between organic peptide sequences and inorganic semiconductor substrates. This peptide recognition and specificity of inorganic crystals has been extended to other substrates, including GaN, ZnS, CdS, Fe3O4, Fe2O3, CdSe, ZnSe and CaCO3 using peptide libraries. Bivalent synthetic peptides with two-component recognition (FIG. 4e) are currently being designed; such peptides have the potential to direct nanoparticles to specific locations on a semiconductor structure. These organic and inorganic pairs should provide powerful building blocks for the fabrication of a new generation of complex, sophisticated electronic structures.

EXAMPLES

[0037] Peptide selection. The phage display or peptide library was contacted with the semiconductor, or other, crystals in Tris-buffered saline (TBS) containing 0.1% TWEEN-20, to reduce phage-phage interactions on the surface. After rocking for 1 h at room temperature, the surfaces were washed with 10 exposures to Tris-buffered saline, pH 7.5, and increasing TWEEN-20 concentrations from 0.1% to 0.5% (v/v). The phage were eluted from the surface by the addition of glycine-HCl (pH 2.2) 10 minute, transferred to a fresh tube and then neutralized with Tris-HCl (pH 9.1). The eluted phage were titred and binding efficiency was compared.

[0038] The phage eluted after third-round substrate exposure were mixed with their Escherichia coli ER2537 host and plated on LB XGal/IPTG plates. Since the library phage were derived from the vector M13mp19, which carries the laczA gene, phage plaques were blue in color when plated on media containing Xgal (5-bromo-4-chloro-3-indoyl-β-D-galactoside) and IPTG (isopropyl-β-D-thiogalactoside). Blue/white screening was used to select phage plaques with the random peptide insert. Plaques were picked and DNA sequenced from these plates.

[0039] Substrate preparation. Substrate orientations were confirmed by X-ray diffraction, and native oxides were removed by appropriate chemical specific etching. The following etches were tested on GaAs and InP surfaces: NH4OH:H2O 1:10, HCl:H2O 1:10, H3PO4:H2O2:H2O 3:1:50 at 1 minute and 10 minute etch times. The best element ratio and least oxide formation (using XPS) for GaAs and InP etched surfaces was achieved using HCl:H2O for 1 minute followed by a deionized water rinse for 1 minute. However, since an ammonium hydroxide etch was used for GaAs in the initial screening of the library, this etch was used for all other GaAs substrate examples. Si(100) wafers were etched in a solution of HF:H2O 1:40 for one minute, followed by a deionized water rinse. All surfaces were taken directly from the rinse solution and immediately introduced to the phage library. Surfaces of control substrates, not exposed to phage, were characterized and mapped for effectiveness of the etching process and morphology of surfaces by AFM and XPS.

[0040] Multilayer substrates of GaAs and of Al0.98Ga0.02 As were grown by molecular beam epitaxy onto (100) GaAs. The epitaxially grown layers were Si-doped (n-type) at a level of 5×10−7 cm−3.

[0041] Antibody and Gold Labeling. For the XPS, SEM and AFM examples, substrates were exposed to phage for 1 h in Tris-buffered saline then introduced to an anti-fd bacteriophage-biotin conjugate, an antibody to the pIII protein of fd phage, (1:500 in phosphate buffer, Sigma) for 30 minute and then rinsed in phosphate buffer. A streptavidin/20-nm colloidal gold label (1:200 in phosphate buffered saline (PBS), Sigma) was attached to the biotin-conjugated phage through a biotin-streptavidin interaction; the surfaces were exposed to the label for 30 minutes and then rinsed several times with PBS.

[0042] X-ray Photoelectron Spectroscopy (XPS). The following controls were done for the XPS examples to ensure that the gold signal seen in XPS was from gold bound to the phage and not non-specific antibody interaction with the GaAs surface. The prepared (100) GaAs surface was exposed to (1) antibody and the streptavidin-gold label, but without phage, (2) G1-3 phage and streptavidin-gold label, but without the antibody, and (3) streptavidin-gold label, without either G1-3 phage or antibody.

[0043] The XPS instrument used was a Physical Electronics Phi ESCA 5700 with an aluminum anode producing monochromatic 1,487-eV X-rays. All samples were introduced to the chamber immediately after gold-tagging the phage (as described above) to limit oxidation of the GaAs surfaces, and then pumped overnight at high vacuum to reduce sample outgassing in the XPS chamber.

[0044] Atomic Force Microscopy (AFM). The AFM used was a Digital Instruments Bioscope mounted on a Zeiss Axiovert 100s-2tv, operating in tip scanning mode with a G scanner. The images were taken in air using tapping mode. The AFM probes were etched silicon with 125-mm cantilevers and spring constants of 20±100 Nm −1 driven near their resonant frequency of 200±400 kHz. Scan rates were of the order of 1±5 mms −1. Images were leveled using a first-order plane to remove sample tilt.

[0045] Transmission Electron Microscopy (TEM). TEM images were taken using a Philips EM208 at 60 kV. The G1-3 phage (diluted 1:100 in TBS) were incubated with GaAs pieces (500 mm) for 30 minute, centrifuged to separate particles from unbound phage, rinsed with TBS, and resuspended in TBS. Samples were stained with 2% uranyl acetate.

[0046] Scanning Electron Microscopy (SEM). The G12-3 phage (diluted 1:100 in TBS) were incubated with a freshly cleaved hetero-structure surface for 30 minute and rinsed with TBS. The G12-3 phage were tagged with 20-nm colloidal gold. SEM and elemental mapping images were collected using the Norian detection system mounted on a Hitachi 4700 field emission scanning electron microscope at 5 kV.

[0047] Although this invention has been described in reference to illustrative embodiments, this description is not intended to be construed in a limiting sense. Various modifications and combinations of the illustrative embodiments, as well as other embodiments of the invention, will be apparent to persons skilled in the art upon reference to the description. It is therefore intended that the appended claims encompass any such modifications or embodiments.

1 95 1 12 PRT artificial sequence peptide binding sequence retrieved from phag biopanning 1 Ala Met Ala Gly Thr Thr Ser Asp Pro Ser Thr Val 1 5 10 2 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 2 Ala Ala Ser Pro Thr Gln Ser Met Ser Gln Ala Pro 1 5 10 3 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 3 His Thr His Thr Asn Asn Asp Ser Pro Asn Gln Ala 1 5 10 4 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 4 Asp Thr Gln Gly Phe His Ser Arg Ser Ser Ser Ala 1 5 10 5 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 5 Thr Ser Ser Ser Ala Leu Gln Pro Ala His Ala Trp 1 5 10 6 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 6 Ser Glu Ser Ser Pro Ile Ser Leu Asp Tyr Arg Ala 1 5 10 7 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 7 Ser Thr His Asn Tyr Gln Ile Pro Arg Pro Pro Thr 1 5 10 8 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 8 His Pro Phe Ser Asn Glu Pro Leu Gln Leu Ser Ser 1 5 10 9 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 9 Gly Thr Leu Ala Asn Gln Gln Ile Phe Leu Ser Ser 1 5 10 10 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 10 His Gly Asn Pro Leu Pro Met Thr Pro Phe Pro Gly 1 5 10 11 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 11 Arg Leu Glu Leu Ala Ile Pro Leu Gln Gly Ser Gly 1 5 10 12 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 12 Cys His Ala Ser Asn Arg Leu Ser Cys 1 5 13 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 13 Ser Met Asp Arg Ser Asp Met Thr Met Arg Leu Pro 1 5 10 14 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 14 Gly Thr Phe Thr Pro Arg Pro Thr Pro Ile Tyr Pro 1 5 10 15 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 15 Gln Met Ser Glu Asn Leu Thr Ser Gln Ile Glu Ser 1 5 10 16 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 16 Asp Met Leu Ala Arg Leu Arg Ala Thr Ala Gly Pro 1 5 10 17 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 17 Ser Gln Thr Trp Leu Leu Met Ser Pro Val Ala Thr 1 5 10 18 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 18 Ala Ser Pro Asp Gln Gln Val Gly Pro Leu Tyr Val 1 5 10 19 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 19 Leu Thr Trp Ser Pro Leu Gln Thr Val Ala Arg Phe 1 5 10 20 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 20 Gln Ile Ser Ala His Gln Met Pro Ser Arg Pro Ile 1 5 10 21 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 21 Ser Met Lys Tyr Asn Leu Ile Val Asp Ser Pro Tyr 1 5 10 22 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 22 Gln Met Pro Ile Arg Asn Gln Leu Ala Trp Pro Met 1 5 10 23 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 23 Thr Gln Asn Leu Glu Ile Arg Glu Pro Leu Thr Pro 1 5 10 24 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 24 Tyr Pro Met Ser Pro Ser Pro Tyr Pro Tyr Gln Leu 1 5 10 25 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 25 Ser Phe Met Ile Gln Pro Thr Pro Leu Pro Pro Ser 1 5 10 26 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 26 Gly Leu Ala Pro His Ile His Ser Leu Asn Glu Ala 1 5 10 27 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 27 Met Gln Phe Pro Val Thr Pro Tyr Leu Asn Ala Ser 1 5 10 28 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 28 Ser Pro Gly Asp Ser Leu Lys Lys Leu Ala Ala Ser 1 5 10 29 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 29 Gly Tyr His Met Gln Thr Leu Pro Gly Pro Val Ala 1 5 10 30 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 30 Ser Leu Thr Pro Leu Thr Thr Ser His Leu Arg Ser 1 5 10 31 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 31 Thr Leu Thr Asn Gly Pro Leu Arg Pro Phe Thr Gly 1 5 10 32 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 32 Leu Asn Thr Pro Lys Pro Phe Thr Leu Gly Gln Asn 1 5 10 33 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 33 Cys Asp Leu Gln Asn Tyr Lys Ala Cys 1 5 34 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 34 Cys Arg His Pro His Thr Arg Leu Cys 1 5 35 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 35 Cys Ala Asn Leu Lys Pro Lys Ala Cys 1 5 36 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 36 Cys Tyr Ile Asn Pro Pro Lys Val Cys 1 5 37 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 37 Cys Asn Asn Lys Val Pro Val Leu Cys 1 5 38 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 38 Cys His Ala Ser Lys Thr Pro Leu Cys 1 5 39 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 39 Cys Ala Ser Gln Leu Tyr Pro Ala Cys 1 5 40 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 40 Cys Asn Met Thr Gln Tyr Pro Ala Cys 1 5 41 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 41 Cys Phe Ala Pro Ser Gly Pro Ala Cys 1 5 42 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 42 Cys Pro Val Trp Ile Gln Ala Pro Cys 1 5 43 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 43 Cys Gln Val Ala Val Asn Pro Leu Cys 1 5 44 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 44 Cys Gln Pro Glu Ala Met Pro Ala Cys 1 5 45 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 45 Cys His Pro Thr Met Pro Leu Ala Cys 1 5 46 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 46 Cys Pro Pro Phe Ala Ala Pro Ile Cys 1 5 47 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 47 Cys Asn Lys His Gln Pro Met His Cys 1 5 48 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 48 Cys Phe Pro Met Arg Ser Asn Gln Cys 1 5 49 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 49 Cys Gln Ser Met Pro His Asn Arg Cys 1 5 50 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 50 Cys Asn Asn Pro Met His Gln Asn Cys 1 5 51 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 51 Cys His Met Ala Pro Arg Trp Gln Cys 1 5 52 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 52 His Val His Ile His Ser Arg Pro Met 1 5 53 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 53 Leu Pro Asn Met His Pro Leu Pro Leu 1 5 54 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 54 Leu Pro Leu Arg Leu Pro Pro Met Pro 1 5 55 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 55 His Ser Met Ile Gly Thr Pro Thr Thr 1 5 56 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 56 Ser Val Ser Val Gly Met Lys Pro Ser 1 5 57 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 57 Leu Asp Ala Ser Phe Met Gln Asp Trp 1 5 58 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 58 Thr Pro Pro Ser Tyr Gln Met Ala Met 1 5 59 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 59 Tyr Pro Gln Leu Val Ser Met Ser Thr 1 5 60 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 60 Gly Tyr Ser Thr Ile Asn Met Tyr Ser 1 5 61 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 61 Asp Arg Met Leu Leu Pro Phe Asn Leu 1 5 62 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 62 Ile Pro Met Thr Pro Ser Tyr Asp Ser 1 5 63 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 63 Met Tyr Ser Pro Arg Pro Pro Ala Leu 1 5 64 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 64 Gln Pro Thr Thr Asp Leu Met Ala His 1 5 65 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 65 Ala Thr His Val Gln Met Ala Trp Ala 1 5 66 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 66 Ser Met His Ala Thr Leu Thr Pro Met 1 5 67 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 67 Ser Gly Pro Ala His Gly Met Phe Ala 1 5 68 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 68 Ile Ala Asn Arg Pro Tyr Ser Ala Gln 1 5 69 7 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 69 Val Met Thr Gln Pro Thr Arg 1 5 70 7 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 70 His Met Arg Pro Leu Ser Ile 1 5 71 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 71 Leu Thr Arg Ser Pro Leu His Val Asp Gln Arg Arg 1 5 10 72 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 72 Val Ile Ser Asn His Ala Glu Ser Ser Arg Arg Leu 1 5 10 73 7 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 73 His Thr His Ile Pro Asn Gln 1 5 74 7 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 74 Leu Ala Pro Val Ser Pro Pro 1 5 75 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 75 Cys Met Thr Ala Gly Lys Asn Thr Cys 1 5 76 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 76 Cys Gln Thr Leu Trp Arg Asn Ser Cys 1 5 77 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 77 Cys Thr Ser Val His Thr Asn Thr Cys 1 5 78 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 78 Cys Pro Ser Leu Ala Met Asn Ser Cys 1 5 79 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 79 Cys Ser Asn Asn Thr Val His Ala Cys 1 5 80 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 80 Cys Leu Pro Ala Gln Gly His Val Cys 1 5 81 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 81 Cys Leu Pro Ala Gln Val His Val Cys 1 5 82 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 82 Cys Pro Pro Lys Asn Val Arg Leu Cys 1 5 83 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 83 Cys Pro His Ile Asn Ala His Ala Cys 1 5 84 9 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 84 Cys Ile Val Asn Leu Ala Arg Ala Cys 1 5 85 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 85 Thr Met Gly Phe Thr Ala Pro Arg Phe Pro His Tyr 1 5 10 86 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 86 Ala Thr Gln Ser Tyr Val Arg His Pro Ser Leu Gly 1 5 10 87 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 87 Thr Ser Thr Thr Gln Gly Ala Leu Ala Tyr Leu Phe 1 5 10 88 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 88 Asp Pro Pro Trp Ser Ala Ile Val Arg His Arg Asp 1 5 10 89 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 89 Phe Asp Asn Lys Pro Phe Leu Arg Val Ala Ser Glu 1 5 10 90 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 90 His Gln Ser His Thr Gln Gln Asn Lys Arg His Leu 1 5 10 91 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 91 Thr Ser Thr Thr Gln Gly Ala Leu Ala Tyr Leu Phe 1 5 10 92 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 92 Lys Thr Pro Ile His Thr Ser Ala Trp Glu Phe Gln 1 5 10 93 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 93 Asp Leu Phe His Leu Lys Pro Val Ser Asn Glu Lys 1 5 10 94 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 94 Lys Pro Phe Trp Thr Ser Ser Pro Asp Val Met Thr 1 5 10 95 12 PRT artificial sequence peptide binding sequence retrieved from phage biopanning 95 Pro Trp Ala Ala Thr Ser Lys Pro Pro Tyr Ser Ser 1 5 10

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Classifications
U.S. Classification435/7.1, 436/518, 435/287.2
International ClassificationG01N33/543, G01N33/68
Cooperative ClassificationG01N33/6803, G01N33/543, G01N33/68
European ClassificationG01N33/68, G01N33/543, G01N33/68A
Legal Events
DateCodeEventDescription
Jul 23, 2007ASAssignment
Owner name: BOARD OF REGENTS, THE UNIVERSITY OF TEXAS SYSTEM,
Free format text: ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNOR:BELCHER, ANGELA M.;REEL/FRAME:019589/0211
Effective date: 20020930