Protein-DNA chimeras for nano assembly

ACS Nano

Volumn 8, Issue 7, 2014, Pages 6551-6555

  Pippig, Diana A ^a   Baumann, Fabian ^a   Strackharn, Mathias ^a,c   Aschenbrenner, Daniela ^a,b   Gaub, Hermann E ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b Munich Center for Integrated Protein Science   (Germany)

^c SCANLAB AG   (Germany)

Author keywords

AFM; patterning; protein DNA chimera; single molecule cut paste; single molecule fluorescence; spatial arrangement

Indexed keywords

AMINO ACIDS; DNA; FLUORESCENCE; MOLECULES; PROTEINS;

AFM; PATTERNING; PROTEIN-DNA CHIMERA; SINGLE-MOLECULE; SINGLE-MOLECULE FLUORESCENCES; SPATIAL ARRANGEMENTS;

SCAFFOLDS (BIOLOGY);

BACTERIAL PROTEIN; COENZYME A; DNA; GREEN FLUORESCENT PROTEIN; IMMOBILIZED PROTEIN; NANOMATERIAL; PHOSPHOPANTETHEINYL TRANSFERASE; PHOSPHOTRANSFERASE;

CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; METABOLISM; STAINING; SURFACE PROPERTY;

BACTERIAL PROTEINS; COENZYME A; DNA; GREEN FLUORESCENT PROTEINS; IMMOBILIZED PROTEINS; MODELS, MOLECULAR; NANOSTRUCTURES; NUCLEIC ACID CONFORMATION; STAINING AND LABELING; SURFACE PROPERTIES; TRANSFERASES (OTHER SUBSTITUTED PHOSPHATE GROUPS);

EID: 84904751083     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn501644w     Document Type: Article

References (32)

1. Kufer, S. K.; Puchner, E. M.; Gumpp, H.; Liedl, T.; Gaub, H. E. Single-Molecule Cut-and-Paste Surface Assembly Science 2008, 319, 594-596
2. Puchner, E. M.; Kufer, S. K.; Strackharn, M.; Stahl, S. W.; Gaub, H. E. Nanoparticle Self-Assembly on a DNA-Scaffold Written by Single-Molecule Cut-and-Paste Nano Lett. 2008, 8, 3692-3695
3. Rief, M.; Clausen-Schaumann, H.; Gaub, H. E. Sequence-Dependent Mechanics of Single DNA Molecules Nat. Struct. Biol. 1999, 6, 346-349
4. Morfill, J.; Kuhner, F.; Blank, K.; Lugmaier, R. A.; Sedlmair, J.; Gaub, H. E. B-S Transition in Short Oligonucleotides Biophys. J. 2007, 93, 2400-2409
5. Morfill, J.; Blank, K.; Zahnd, C.; Luginbuhl, B.; Kuhner, F.; Gottschalk, K. E.; Pluckthun, A.; Gaub, H. E. Affinity-Matured Recombinant Antibody Fragments Analyzed by Single-Molecule Force Spectroscopy Biophys. J. 2007, 93, 3583-3590
6. Dudko, O. K.; Hummer, G.; Szabo, A. Intrinsic Rates and Activation Free Energies from Single-Molecule Pulling Experiments Phys. Rev. Lett. 2006, 96, 108101
7. Strackharn, M.; Stahl, S. W.; Puchner, E. M.; Gaub, H. E. Functional Assembly of Aptamer Binding Sites by Single-Molecule Cut-and-Paste Nano Lett. 2012, 12, 2425-2428
8. Strackharn, M.; Stahl, S. W.; Severin, P. M.; Nicolaus, T.; Gaub, H. E. Peptide-Antibody Complex as Handle for Single-Molecule Cut & Paste ChemPhysChem 2012, 13, 914-917
9. Strackharn, M.; Pippig, D. A.; Meyer, P.; Stahl, S. W.; Gaub, H. E. Nanoscale Arrangement of Proteins by Single-Molecule Cut-and-Paste J. Am. Chem. Soc. 2012, 134, 15193-15196
10. Akter, F.; Mie, M.; Grimm, S.; Nygren, P. A.; Kobatake, E. Detection of Antigens Using a Protein-DNA Chimera Developed by Enzymatic Covalent Bonding with Phix Gene A Anal. Chem. 2012, 84, 5040-5046
11. Burbulis, I.; Yamaguchi, K.; Gordon, A.; Carlson, R.; Brent, R. Using Protein-DNA Chimeras To Detect and Count Small Numbers of Molecules Nat. Methods 2005, 2, 31-37
12. Cecconi, C.; Shank, E. A.; Dahlquist, F. W.; Marqusee, S.; Bustamante, C. Protein-DNA Chimeras for Single Molecule Mechanical Folding Studies with the Optical Tweezers Eur. Biophys. J. 2008, 37, 729-738
13. Rothemund, P. W. Folding DNA To Create Nanoscale Shapes and Patterns Nature 2006, 440, 297-302
14. Kolb, H. C.; Finn, M. G.; Sharpless, K. B. Click Chemistry: Diverse Chemical Function from a Few Good Reactions Angew. Chem., Int. Ed. 2001, 40, 2004-2021
15. van Dongen, S. F.; Teeuwen, R. L.; Nallani, M.; van Berkel, S. S.; Cornelissen, J. J.; Nolte, R. J.; van Hest, J. C. Single-Step Azide Introduction in Proteins via an Aqueous Diazo Transfer Bioconjugate Chem. 2009, 20, 20-23
16. Wang, L.; Schultz, P. G. Expanding the Genetic Code Angew. Chem., Int. Ed. 2004, 44, 34-66
17. Wang, L.; Brock, A.; Herberich, B.; Schultz, P. G. Expanding the Genetic Code of Escherichia coli Science 2001, 292, 498-500
18. Cellitti, S. E.; Jones, D. H.; Lagpacan, L.; Hao, X. S.; Zhang, Q.; Hu, H. Y.; Brittain, S. M.; Brinker, A.; Caldwell, J.; Bursulaya, B. et al. In Vivo Incorporation of Unnatural Amino Acids To Probe Structure, Dynamics, and Ligand Binding in a Large Protein by Nuclear Magnetic Resonance Spectroscopy J. Am. Chem. Soc. 2008, 130, 9268-9281
19. Lallana, E.; Riguera, R.; Fernandez-Megia, E. Reliable and Efficient Procedures for the Conjugation of Biomolecules through Huisgen Azide-Alkyne Cycloadditions Angew. Chem., Int. Ed. 2011, 50, 8794-8804
20. Los, G. V.; Encell, L. P.; McDougall, M. G.; Hartzell, D. D.; Karassina, N.; Zimprich, C.; Wood, M. G.; Learish, R.; Ohana, R. F.; Urh, M. et al. Halotag: A Novel Protein Labeling Technology for Cell Imaging and Protein Analysis ACS Chem. Biol. 2008, 3, 373-382
21. Popa, I.; Berkovich, R.; Alegre-Cebollada, J.; Badilla, C. L.; Rivas-Pardo, J. A.; Taniguchi, Y.; Kawakami, M.; Fernandez, J. M. Nanomechanics of Halotag Tethers J. Am. Chem. Soc. 2013, 135, 12762-12771
22. Keppler, A.; Kindermann, M.; Gendreizig, S.; Pick, H.; Vogel, H.; Johnsson, K. Labeling of Fusion Proteins of O6-Alkylguanine-DNA Alkyltransferase with Small Molecules in Vivo and in Vitro Methods 2004, 32, 437-444
23. Yin, J.; Straight, P. D.; McLoughlin, S. M.; Zhou, Z.; Lin, A. J.; Golan, D. E.; Kelleher, N. L.; Kolter, R.; Walsh, C. T. Genetically Encoded Short Peptide Tag for Versatile Protein Labeling by Sfp Phosphopantetheinyl Transferase Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 15815-15820
24. Maillard, R. A.; Chistol, G.; Sen, M.; Righini, M.; Tan, J.; Kaiser, C. M.; Hodges, C.; Martin, A.; Bustamante, C. Clpx(P) Generates Mechanical Force to Unfold and Translocate Its Protein Substrates Cell 2011, 145, 459-469
25. Yin, J.; Lin, A. J.; Golan, D. E.; Walsh, C. T. Site-Specific Protein Labeling by Sfp Phosphopantetheinyl Transferase Nat. Protoc. 2006, 1, 280-285
26. Wong, L. S.; Thirlway, J.; Micklefield, J. Direct Site-Selective Covalent Protein Immobilization Catalyzed by a Phosphopantetheinyl Transferase J. Am. Chem. Soc. 2008, 130, 12456-12464
27. Wong, L. S.; Karthikeyan, C. V.; Eichelsdoerfer, D. J.; Micklefield, J.; Mirkin, C. A. A Methodology for Preparing Nanostructured Biomolecular Interfaces with High Enzymatic Activity Nanoscale 2012, 4, 659-666
28. Limmer, K.; Pippig, D. A.; Aschenbrenner, D.; Gaub, H. E. A Force-Based, Parallel Assay for the Quantification of Protein-DNA Interactions PLoS One 2014, 9 e89626
29. Kufer, S. K.; Strackharn, M.; Stahl, S. W.; Gumpp, H.; Puchner, E. M.; Gaub, H. E. Optically Monitoring the Mechanical Assembly of Single Molecules Nat. Nanotechnol. 2009, 4, 45-49
30. Kinkhabwala, A. A.; Yu, Z. F.; Fan, S. H.; Moerner, W. E. Fluorescence Correlation Spectroscopy at High Concentrations Using Gold Bowtie Nanoantennas Chem. Phys. 2012, 406, 3-8
31. Heucke, S. F.; Baumann, F.; Acuna, G. P.; Severin, P. M.; Stahl, S. W.; Strackharn, M.; Stein, I. H.; Altpeter, P.; Tinnefeld, P.; Gaub, H. E. Placing Individual Molecules in the Center of Nanoapertures Nano Lett. 2014, 14, 391-395
32. Heucke, S. F.; Puchner, E. M.; Stahl, S. W.; Holleitner, A. W.; Gaub, H. E.; Tinnefeld, P. Nanoapertures for AFM-Based Single-Molecule Force Spectroscopy Int. J. Nanotechnol. 2013, 10, 607-619