Scanning probe-based fabrication of 3D nanostructures via affinity templates, functional RNA, and meniscus-mediated surface remodeling

Scanning

Volumn 30, Issue 2, 2008, Pages 159-171

  Chung, Sung Wook ^a   Presley, Andrew D ^a,b   Elhadj, Selim ^a   Hok, Saphon ^a   Sang, Soo Hah ^a   Chernov, Alex A ^a   Francis, Matthew B ^b   Eaton, Bruce E ^c   Feldheim, Daniel L ^c   DeYoreo, James J ^a,d  

^a LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF COLORADO   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Affinity templates; Functional RNA; Meniscus mediated surface remodeling; Nanostructures; Scanning probe microscopy; Scanning probe nanolithography; Virus

Indexed keywords

ATOMIC FORCE MICROSCOPY; MOLECULAR DYNAMICS; RNA; SELF ASSEMBLED MONOLAYERS; SURFACE TOPOGRAPHY;

AFFINITY TEMPLATES; FUNCTIONAL RNA; MENISCUS-MEDIATED SURFACE REMODELING; SCANNING PROBE NANOLITHOGRAPHY;

NANOSTRUCTURED MATERIALS;

METAL; NANOPARTICLE; NANOWIRE; OLIGONUCLEOTIDE; RNA; WATER;

ATOMIC FORCE MICROSCOPY; COVALENT BOND; CRYSTALLIZATION; NANOTECHNOLOGY; POLYMERIZATION; PRIORITY JOURNAL; REVIEW; SCANNING PROBE MICROSCOPY; TOBACCO MOSAIC VIRUS;

EID: 42349107285     PISSN: 01610457     EISSN: None     Source Type: Journal    
DOI: 10.1002/sca.20086     Document Type: Review

References (82)

1. Abdelsalam ME, Bartlett PN, Kelf T, Baumberg J: Wetting of regularly structured gold surfaces. Langmuir 21(5), 1753-1757 (2005).
2. Bahatyrova S, Frese RN, Siebert CA, Olsen JD, van der Werf KO, et al.: The native architecture of a photosynthetic membrane. Nature 430(7003), 1058-1062 (2004).
3. Bhatnagar P, Mark SS, Kim I, Chen HY, Schmidt B, et al.: Dendrimer-scaffod-based electron-beam patterning of biomolecules. Adv Mater 18(3), 315-+ (2006).
4. Bhyravbhatla B, Watowich SJ, Caspar DLD: Refined atomic model of the four-layer aggregate of the tobacco mosaic virus coat protein at 2.4-angstrom resolution. Biophys J 74(1), 604-615 (1998).
5. Butler PJG: Self-assembly of tobacco mosaic virus: the role of an intermediate aggregate in generating both specificity and speed. Philos Trans R Soc Lond B 354(1383), 537-550 (1999).
6. Camarero JA: In Nanoscale Structure and Assembly at Solid-Fluid Interfaces, Vol. II (Eds. Liu XY, De Yoreo JJ), Kluwer Academic Publishers, Norwell, MA, 239-280 (2003).
7. Chapman HN, Barty A, Marchesini S, Noy A, Hau-Riege SR, et al.: High-resolution ab initio three-dimensional x-ray diffraction microscopy. J Opt Soc Am A 23(5), 1179-1200 (2006).
8. Chapman HN, Hau-Riege SP, Bogan MJ, Bajt S, Barty A, et al.: Femtosecond time-delay X-ray holography. Nature 448(7154), 676-U676 (2007).
9. Chatterji A, Ochoa WF, Ueno T, Lin TW, Johnson JE: A virus-based nanoblock with tunable electrostatic properties. Nano Lett 5(4), 597-602 (2005).
10. Cheung CL, Camarero JA, Woods BW, Lin TW, Johnson JE, et al.: Fabrication of assembled virus nanostructures on templates of chemoselective linkers formed by scanning probe nanolithography. J Am Chem Soc 125(23), 6848-6849 (2003).
11. Cheung CL, Chung SW, Chatterji A, Lin TW, Johnson JE, et al.: Physical controls on directed virus assembly at nanoscale chemical templates. J Am Chem Soc 128(33), 10801-10807 (2006).
12. Chung SW, Ginger DS, Morales MW, Zhang ZF, Chandrasekhar V, et al.: Top-down meets bottom-up: Dip-pen nanolithography and DNA-directed assembly of nanoscale electrical circuits. Small 1(1), 64-69 (2005).
13. Demers LM, Ginger DS, Park SJ, Li Z, Chung SW, et al.: Direct patterning of modified oligonucleotides on metals and insulators by dip-pen nanolithography. Science 296(5574), 1836-1838 (2002).
14. Demir M, Stowell MHB: A chemoselective biomolecular template for assembling diverse nanotubular materials. Nanotechnology 13(4), 541-544 (2002).
15. Douglas T, Young M: Virus particles as templates for materials synthesis. Adv Mater 11(8), 679-681 (1999).
16. Eaton BE: The joys of in vitro selection: chemically dressing oligonucleotides to satiate protein targets. Curr Opin Chem Biol 1(1), 10-16 (1997).
17. Eaton BE, Holley B: In Evolutionary Methods in Biotechnology, (Eds. Brakmann S, Schwienhorst A), Wiley-VCH, Weinheim, Germany, 87-111 (2004).
18. Eisenfuhr A, Arora PS, Sengle G, Takaoka LR, Nowick JS, et al.: A ribozyme with michaelase activity: Synthesis of the substrate precursors. Bioorg Med Chem 11(2), 235-249 (2003).
19. Elhadj S, De Yoreo JJ, Chernov AA: Solvent-mediated repair and patterning of surfaces by AFM, Nanotechnology In Press (2007).
20. Ellington AD, Szostak JW: Invitro selection of RNA molecules that bind specific ligands. Nature 346(6287), 818-822 (1990).
21. Falconnet D, Pasqui D, Park S, Eckert R, Schift H, et al.: A novel approach to produce protein nanopatterns by combining nanoimprint lithography and molecular self-assembly. Nano Lett 4(10), 1909-1914 (2004).
22. Feldheim DL, Eaton BE: Selection of biomolecules capable of mediating the formation of nanocrystals, ACS Nano 1(3), 154-159 (2007).
23. Fusz S, Eisenfuhr A, Srivatsan SG, Heckel A, Famulok M: A ribozyme for the aldol reaction. Chem Biol 12(8), 941-950 (2005).
24. Garcia-Manyes S, Verdaguer A, Gorostiza P, Sanz F: Alkali halide nanocrystal growth and etching studied by AFM and modeled by MD simulations. J Chem Phys 120(6), 2963-2971 (2004).
25. Ginger D, Zhang H, Mirkin C: The evolution of dip-pen nanolithography. Angew Chem Int Ed Engl 43(1), 30-45 (2004).
26. Gugliotti LA, Feldheim DL, Eaton BE: RNA-mediated metal-metal bond formation in the synthesis of hexagonal palladium nanoparticles. Science 304(5672), 850-852 (2004).
27. Gugliotti LA, Feldheim DL, Eaton BE: RNA-mediated control of metal nanoparticle shape. J Am Chem Soc 127(50), 17814-17818 (2005).
28. Guo LJ: Nanoimprint lithography: Methods and material requirements. Adv Mater 19(4), 495-513 (2007).
29. Gur I, Fromer NA, Chen CP, Kanaras AG, Alivisatos AP: Hybrid solar cells with prescribed nanoscale morphologies based on hyperbranched semiconductor nanocrystals. Nano Lett 7(2), 409-414 (2007).
30. Gur I, Fromer NA, Geier ML, Alivisatos AP: Air-stable all-inorganic nanocrystal solar cells processed from solution. Science 310(5747), 462-465 (2005).
31. Huang FQ, Bugg CW, Yarus M: RNA-catalyzed CoA, NAD, and FAD synthesis from phosphopantetheine, NMN, and FMN. Biochemistry 39(50), 15548-15555 (2000).
32. Huang Y, Duan XF, Cui Y, Lauhon LJ, Kim KH, et al.: Logic gates and computation from assembled nanowire building blocks. Science 294(5545), 1313-1317 (2001).
33. Huynh WU, Dittmer JJ, Alivisatos AP: Hybrid nanorod-polymer solar cells. Science 295(5564), 2425-2427 (2002).
34. Illangasekare M, Sanchez G, Nickles T, Yams M: Aminoacyl-RNA synthesis catalyzed by an RNA. Science 267(5198), 643-647 (1995).
35. Klimov E, Li W, Yang X, Hoffmann GG, Loos J: Scanning near-field and confocal Raman microscopic investigation of P3HT-PCBM systems for solar cell applications. Macromolecules 39(13), 4493-4496 (2006).
36. Klug A: The tobacco mosaic virus particle: structure and assembly. Philos Trans R Soc Lond B 354(1383), 531-535 (1999).
37. Lee SW, Mao CB, Flynn CE, Belcher AM: Ordering of quantum dots using genetically engineered viruses. Science 296(5569), 892-895 (2002a).
38. Lee KB, Park SJ, Mirkin CA, Smith JC, Mrksich M: Protein nanoarrays generated by Dip-Pen Nanolithography. Science 295(5560), 1702-1705 (2002b).
39. Lim JH, Ginger DS, Lee KB, Heo J, Nam JM, et al.: Direct-write Dip-Pen Nanolithography of proteins on modified silicon oxide surfaces. Angew Chem Int Ed Engl 42(20), 2309-2312 (2003).
40. Lohse PA, Szostak JW: Ribozyme-catalysed amino-acid transfer reactions. Nature 381(6581), 442-444 (1996).
41. Lopez GP, Biebuyck HA, Harter R, Kumar A, Whitesides GM: Fabrication and imaging of 2-dimensional patterns of proteins adsorbed on self-assembled monolayers by scanning electron-microscopy. J Am Chem Soc 115(23), 10774-10781 (1993).
42. Mao CB, Flynn CE, Hayhurst A, Sweeney R, Qi JF, et al.: Viral assembly of oriented quantum dot nanowires. Proc Natl Acad Sci USA 100(12), 6946-6951 (2003).
43. Medintz IL, Sapsford KE, Konnert JH, Chatterji A, Lin TW, et al.: Decoration of discretely immobilized cowpea mosaic virus with luminescent quantum dots. Langmuir 21(12), 5501-5510 (2005).
44. Melosh NA, Boukai A, Diana F, Gerardot B, Badolato A, et al.: Ultrahigh-density nanowire lattices and circuits. Science 300(5616), 112-115 (2003).
45. Miller RA, Presley AD, Francis MB: Self-assembling light-harvesting systems from synthetically modified tobacco mosaic virus coat proteins. J Am Chem Soc 129(11), 3104-3109 (2007).
46. Mirkin CA, Hong SH, Demers L: Dip-pen nanolithography: Controlling surface architecture on the sub-100 nanometer length scale. Chemphyschem 2(1), 37-39 (2001).
47. Murray CB, Kagan CR, Bawendi MG: Synthesis and characterization of monodisperse nanocrystals and close-packed nanocrystal assemblies. Annu Rev Mater Sci 30, 545-610 (2000).
48. Nieuwlandt D, West M, Cheng XQ, Kirshenheuter G, Eaton BE: The first example of an RNA urea synthase: selection through the enzyme active site of human neutrophile elastase. Chembiochem 4(7), 651-654 (2003).
49. Noy A, Miller AE, Klare JE, Weeks BL, Woods BW, et al.: Fabrication of luminescent nanostructures and polymer nanowires using dip-pen nanolithography. Nano Lett 2(2), 109-112 (2002).
50. Nozik AJ: Quantum dot solar cells. Physica E 14(1-2), 115-120 (2002).
51. 2) Meta-OH on gold. J Am Chem Soc 113(1), 12-20 (1991).
52. Pattanayek R, Stubbs G: Structure of the U2 strain of tobacco Mosaic-Virus refined at 3.5 angstrom resolution using X-Ray fiber diffraction. J Mol Biol 228(2), 516-528 (1992).
53. Piner RD, Zhu J, Xu F, Hong SH, Mirkin CA: "Dip-Pen" Nanolithography. Science 283(5402), 661-663 (1999).
54. Rozhok S, Sun P, Piner R, Lieberman M, Mirkin CA: AFM study of water meniscus formation between an AFM tip and NaCl substrate. J Phys Chem B 108(23), 7814-7819 (2004).
55. Salaita K, Wang YH, Fragala J, Vega RA, Liu C, et al.: Massively parallel dip-pen nanolithography with 55000-pen two-dimensional arrays. Angew Chem Int Ed Engl 45(43), 7220-7223 (2006).
56. Schaller RD, Agranovich VM, Klimov VI: High-efficiency carrier multiplication through direct photogeneration of multi-excitons via virtual single-exciton states. Nat Phys 1(3), 189-194 (2005).
57. Schaller RD, Klimov VI: High efficiency carrier multiplication in PbSe nanocrystals: Implications for solar energy conversion. Phys Rev Lett 92(18), (2004).
58. Schlick TL, Ding ZB, Kovacs EW, Francis MB: Dual-surface modification of the tobacco mosaic virus. J Am Chem Soc 127(11), 3718-3723 (2005).
59. Seelig B, Jaschke A: A small catalytic RNA motif with Diels-Alderase activity. Chem Biol 6(3), 167-176 (1999).
60. Sengle G, Eisenfuhr A, Arora PS, Nowick JS, Famulok M: Novel RNA catalysts for the Michael reaction. Chem Biol 8(5), 459-473 (2001).
61. Shindo H, Ohashi M, Tateishi O, Seo A: Atomic force microscopic observation of step movements on NaCl(001) and NaF(001) with the help of adsorbed water. J Chem Soc Faraday Trans 93(6), 1169-1174 (1997).
62. Szostak JW, Bartel D, Hager A, Das A, Lohse P: Isolation of new ribozymes form pools of random sequences. FASEB J 10(6), C1-C1 (1996).
63. Tarasow TM, Tarasow SL, Eaton BE: RNA-catalysed carbon-carbon bond formation. Nature 389(6646), 54-57 (1997).
64. Tsukiji S, Pattnaik SB, Suga H: An alcohol dehydrogenase ribozyme. Nat Struct Biol 10(9), 713-717 (2003).
65. Tuerk C, Gold L: Systematic evolution of Ligands by exponential enrichment-Rna Ligands to Bacteriophage-T4 DNA-Polymerase. Science 249(4968), 505-510 (1990).
66. Vega RA, Maspoch D, Salaita K, Mirkin CA: Nanoarrays of single virus particles. Angew Chem Int Ed Engl 44(37), 6013-6015 (2005).
67. Vlasov YA, Yao N, Norris DJ: Synthesis of photonic crystals for optical wavelengths from semiconductor quantum dots. Adv Mater 11(2), 165-169 (1999).
68. Wadu-Mesthrige K, Amro NA, Garno JC, Xu S, Liu GY: Fabrication of nanometer-sized protein patterns using atomic force microscopy and selective immobilization. Biophys J 80(4), 1891-1899 (2001).
69. Wadu-Mesthrige K, Xu S, Amro NA, Liu GY: Fabrication and imaging of nanometer-sized protein patterns. Langmuir 15(25), 8580-8583 (1999).
70. Wagner P, Hegner M, Guntherodt HJ, Semenza G: Formation and in-Situ modification of monolayers Chemisorbed on Ultraflat Template-stripped gold Surfaces. Langmuir 11(10), 3867-3875 (1995).
71. Wang Q, Lin TW, Tang L, Johnson JE, Finn MG: Icosahedral virus particles as addressable nanoscale building blocks. Angew Chem Int Ed Engl 41(3), 459-462 (2002).
72. Wecker M, Smith D, Gold L: In vitro selection of a novel catalytic RNA: Characterization of a sulfur alkylation reaction and interaction with a small peptide. RNA 2(10), 982-994 (1996).
73. Weeks BL, DeYoreo JJ: Dynamic meniscus growth at a scanning probe tip in contact with a gold substrate. J Phys Chem B 110(21), 10231-10233 (2006).
74. Weeks BL, Noy A, Miller AE, De Yoreo JJ: Effect of dissolution kinetics on feature size in dip-pen nanolithography. Phys Rev Lett 88(25), 255505 (2002).
75. Weeks BL, Vaughn MW, DeYoreo JJ: Direct imaging of meniscus formation in atomic force microscopy using environmental scanning electron microscopy. Langmuir 21(18), 8096-8098 (2005).
76. Wiegand TW, Janssen RC, Eaton BE: Selection of RNA amide syntheses. Chem Biol 4(9), 675-683 (1997).
77. Wilson C, Szostak JW: In vitro evolution of a self-alkylating ribozyme. Nature 374(6525), 777-782 (1995).
78. Xia YN, Whitesides GM: Soft lithography. Angew Chem Int Ed Engl 37(5), 551-575 (1998a).
79. Xia YN, Whitesides GM: Soft lithography. Annu Rev Mater Sci 28, 153-184 (1998b).
80. Yang PD, Kim F: Langmuir-Blodgett assembly of one-dimensional nanostructures. Chemphyschem 3(6), 503-+ (2002).
81. 2 solar cells sensitized with InAs quantum dots. J Phys Chem B 110(50), 25451-25454 (2006).
82. Zhang BL, Cech TR: Peptidyl-transferase ribozymes: trans reactions, structural characterization and ribosomal RNA-like features. Chem Biol 5(10), 539-553 (1998).