Bioorthogonal noncovalent chemistry: fluorous phases in chemical biology

Current Opinion in Chemical Biology

Volumn 10, Issue 6, 2006, Pages 576-583

  Yoder, Nicholas C ^a   Yüksel, Deniz ^a   Dafik, Laila ^a   Kumar, Krishna ^a,b  

^a TUFTS UNIVERSITY   (United States)

^b TUFTS MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FLUOROCARBON; LIPID; NUCLEIC ACID; PEPTIDE DERIVATIVE;

BIOLOGY; CELL ADHESION; CHEMISTRY; ENVIRONMENT; FLUORINATION; PROTEIN MOTIF; PROTEOMICS; REVIEW;

CELL ADHESION; FLUOROCARBONS; PROTEOMICS;

EID: 33751408183     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2006.10.007     Document Type: Review

References (53)

1. Speers A.E., Adam G.C., and Cravatt B.F. Activity-based protein profiling in vivo using a copper(I)-catalyzed azide-alkyne 3 + 2 cycloaddition. J Am Chem Soc 125 (2003) 4686-4687
2. Prescher J.A., and Bertozzi C.R. Chemistry in living systems. Nat Chem Biol 1 (2005) 13-21. An excellent introduction to bioorthogonal covalent chemistry and its applications.
3. Guignet E.G., Hovius R., and Vogel H. Reversible site-selective labeling of membrane proteins in live cells. Nat Biotechnol 22 (2004) 440-444
4. Crabtree G.R., and Schreiber S.L. Three-part inventions: intracellular signalling and induced proximity. Trends Biochem Sci 21 (1996) 418-422
5. Bayle J.H., Grimley J.S., Stankunas K., Gestwicki J.E., Wandless T.J., and Crabtree G.R. Rapamycin analogs with differential binding specificity permit orthogonal control of protein activity. Chem Biol 13 (2006) 99-107
6. Chandra R.A., Douglas E.S., Mathies R.A., Bertozzi C.R., and Francis M.B. Programmable cell adhesion encoded by DNA hybridization. Angew Chem Int Ed Engl 45 (2006) 896-901. This paper gives a glimpse of the imaginative applications enabled by the combination of bioorthogonal covalent and noncovalent chemistries. Specific covalent attachment of DNA to cell-surface saccharides can be used to control cell adhesion to surfaces displaying complementary DNA.
7. Kasuya M.C.Z., Cusi R., Ishihara O., Miyagawa A., Hashimoto K., Sato T., and Hatanaka K. Fluorous-tagged compound: a viable scaffold to prime oligosaccharide synthesis by cellular enzymes. Biochem Biophys Res Commun 316 (2004) 599-604
8. Wang L., and Schultz P.G. Expanding the genetic code. Angew Chem Int Ed Engl 44 (2005) 34-66
9. Tang Y., Ghirlanda G., Petka W.A., Nakajima T., DeGrado W.F., and Tirrell D.A. Fluorinated coiled-coil proteins prepared in vivo display enhanced thermal and chemical stability. Angew Chem Int Ed Engl 40 (2001) 1494-1496
10. Keppler O.T., Horstkorte R., Pawlita M., Schmidts C., and Reutter W. Biochemical engineering of the N-acyl side chain of sialic acid: biological implications. Glycobiology 11 (2001) 11R-18R
11. Wang P., Fichera A., Kumar K., and Tirrell D.A. Alternative translations of a single RNA message: An identity switch of (2S,3R)-4,4,4-trifluorovaline between valine and isoleucine codons. Angew Chem Int Ed Engl 43 (2004) 3664-3666
12. Curran D.P. Fluorous reverse phase silica gel. A new tool for preparative separations in synthetic organic and organofluorine chemistry. Synlett (2001) 1488-1496
13. Horvath I.T., and Rabai J. Facile Catalyst Separation without Water - Fluorous Biphase Hydroformylation of Olefins. Science 266 (1994) 72-75
14. Zhang W. Fluorous tagging strategy for solution-phase synthesis of small molecules, peptides and oligosaccharides. Curr Opin Drug Discov Dev 7 (2004) 784-797
15. Pearson W.H., Berry D.A., Stoy P., Jung K.Y., and Sercel A.D. Fluorous affinity purification of oligonucleotides. J Org Chem 70 (2005) 7114-7122
16. Beller C., and Bannwarth W. Noncovalent attachment of nucleotides by fluorous fluorous interactions: Application to a simple purification principle for synthetic DNA fragments. Helv Chim Acta 88 (2005) 171-179
17. Manzoni L. Rapid synthesis of oligosaccharides using an anomeric fluorous silyl protecting group. Chem Commun (2003) 2930-2931
18. Miura T., Goto K.T., Hosaka D., and Inazu T. Oligosaccharide synthesis on a fluorous support. Angew Chem Int Ed Engl 42 (2003) 2047-2051
19. Palmacci E.R., Hewitt M.C., and Seeberger P.H. "Cap-Tag"-novel methods for the rapid purification of oligosaccharides prepared by automated solid-phase synthesis. Angew Chem Int Ed Engl 40 (2001) 4433-4437
20. Mizuno M., Goto K., Miura T., Matsuura T., and Inazu T. Peptide synthesis on fluorous support. Tetrahedron Lett 45 (2004) 3425-3428
21. de Visser P.C., van Helden M., Filippov D.V., van der Marel G.A., Drijfhout J.W., van Boom J.H., Noort D., and Overkleeft H.S. A novel, base-labile fluorous amine protecting group: synthesis and use as a tag in the purification of synthetic peptides. Tetrahedron Lett 44 (2003) 9013-9016
22. Filippov D.V., van Zoelen D.J., Oldfield S.P., van der Marel G.A., Overkleeft H.S., Drijfhout J.W., and van Boom J.H. Use of benzyloxycarbonyl (Z)-based fluorophilic tagging reagents in the purification of synthetic peptides. Tetrahedron Lett 43 (2002) 7809-7812
23. Montanari V., and Kumar K. A fluorous capping strategy for Fmoc-based automated and manual solid-phase peptide synthesis. Eur Org J Chem (2006) 874-877
24. Montanari V., and Kumar K. Just add water: a new fluorous capping reagent for facile purification of peptides synthesized on the solid phase. J Am Chem Soc 126 (2004) 9528-9529. Demonstrates practical application of fluorous capping reagents in the purification of peptides synthesized on solid-phase.
25. Brittain S.M., Ficarro S.B., Brock A., and Peters E.C. Enrichment and analysis of peptide subsets using fluorous affinity tags and mass spectrometry. Nat Biotechnol 23 (2005) 463-468. Practical application of fluorous 'affinity' purification to proteomics. This paper demonstrates that fluorous tagging can specifically recover peptides from complex mixtures, in this case whole cell protein extracts.
26. Ko K.S., Jaipuri F.A., and Pohl N.L. Fluorous-based carbohydrate microarrays. J Am Chem Soc 127 (2005) 13162-13163
27. Orner B.P., Derda R., Lewis R.L., Thomson J.A., and Kiessling L.L. Arrays for the combinatorial exploration of cell adhesion. J Am Chem Soc 126 (2004) 10808-10809
28. Stenger D.A., Georger J.H., Dulcey C.S., Hickman J.J., Rudolph A.S., Nielsen T.B., McCort S.M., and Calvert J.M. Coplanar molecular assemblies of aminoalkylsilane and perfluorinated alkylsilane - characterization and geometric definition of mammalian-cell adhesion and growth. J Am Chem Soc 114 (1992) 8435-8442
29. Mrksich M., and Whitesides G.M. Using self-assembled monolayers to understand the interactions of man-made surfaces with proteins and cells. Annu Rev Biophys Biomolec Struct 25 (1996) 55-78
30. Bilgiçer B., Fichera A., and Kumar K. A coiled coil with a fluorous core. J Am Chem Soc 123 (2001) 4393-4399
31. Bilgiçer B., Xing X., and Kumar K. Programmed self-sorting of coiled coils with leucine and hexafluoroleucine cores. J Am Chem Soc 123 (2001) 11815-11816
32. Lee K.H., Lee H.Y., Slutsky M.M., Anderson J.T., and Marsh E.N.G. Fluorous effect in proteins: De novo design and characterization of a four-alpha-helix bundle protein containing hexafluoroleucine. Biochemistry 43 (2004) 16277-16284
33. Yoder N.C., and Kumar K. Fluorinated amino acids in protein design and engineering. Chem Soc Rev 31 (2002) 335-341
34. Bilgiçer B., and Kumar K. Synthesis and thermodynamic characterization of self-sorting coiled coils. Tetrahedron 58 (2002) 4105-4112
35. Bowie J.U. Solving the membrane protein folding problem. Nature 438 (2005) 581-589
36. Naarmann N., Bilgiçer B., Meng H., Kumar K., and Steinem C. Fluorinated interfaces drive self-association of transmembrane alpha helices in lipid bilayers. Angew Chem Int Ed Engl 45 (2006) 2588-2591. This study demonstrates that simultaneous use of fluorinated interfaces and hydrogen bonding fuels a stronger affinity between helical transmembrane peptides.
37. Bilgiçer B., and Kumar K. De novo design of defined helical bundles in membrane environments. Proc Natl Acad Sci USA 101 (2004) 15324-15329. This paper shows that fluorination of peptide side-chains can be used to self-assemble oligomeric helical peptides using a simple and flexible design paradigm.
38. Drews J. Drug discovery: A historical perspective. Science 287 (2000) 1960-1964
39. Yeaman M.R., and Yount N.Y. Mechanisms of antimicrobial peptide action and resistance. Pharmacol Rev 55 (2003) 27-55
40. Ishikawa Y., Kuwahara H., and Kunitake T. Self-Assembly of Bilayer-Membranes in Organic-Solvents by Novel Amphiphilic Compounds. J Am Chem Soc 111 (1989) 8530-8531
41. Elbert R., Folda T., and Ringsdorf H. Saturated and polymerizable amphiphiles with fluorocarbon chains - investigation in monolayers and liposomes. J Am Chem Soc 106 (1984) 7687-7692
42. Kunitake T., Tawaki S., and Nakashima N. Excimer formation and phase-separation of hydrocarbon and fluorocarbon bilayer-membranes. Bull Chem Soc Jpn 56 (1983) 3235-3242
43. Ringsdorf H., Schlarb B., and Venzmer J. Molecular architecture and function of polymeric oriented systems - models for the study of organization, surface recognition, and dynamics of biomembranes. Angew Chem Int Ed Engl 27 (1988) 113-158
44. Buschl R., Folda T., and Ringsdorf H. Polymeric monolayers and liposomes as models for biomembranes. Makromol Chem Suppl 6 (1984) 245-258
45. Riess J.G., and Krafft M.P. Fluorinated phosphocholine-based amphiphiles as components of fluorocarbon emulsions and fluorinated vesicles. Chem Phys Lipids 75 (1995) 1-14
46. Gege C., Schneider M.F., Schumacher G., Limozin L., Rothe U., Bendas G., Tanaka M., and Schmidt R.R. Functional microdomains of glycolipids with partially fluorinated membrane anchors: Impact on cell adhesion. ChemPhysChem 5 (2004) 216-224. Provides evidence for the clustering of fluorinated glycolipid analogs in various monolayer and bilayer contexts, suggesting that this may be a general strategy for clustering of ligands at surfaces.
47. Schumacher G., Bakowsky U., Gege C., Schmidt R.R., Rothe U., and Bendas G. Lessons learned from clustering of fluorinated glycolipids on selectin ligand function in cell rolling. Biochemistry 45 (2006) 2894-2903
48. Kool E.T. Hydrogen bonding, base stacking, and steric effects in DNA replication. Annu Rev Biophys Biomolec Struct 30 (2001) 1-22
49. Lai J.S., and Kool E.T. Selective pairing of polyfluorinated DNA bases. J Am Chem Soc 126 (2004) 3040-3041
50. Henry A.A., Olsen A.G., Matsuda S., Yu C.Z., Geierstanger B.H., and Romesberg F.E. Efforts to expand the genetic alphabet: identification of a replicable unnatural DNA self-pair. J Am Chem Soc 126 (2004) 6923-6931
51. Hwang G.T., and Romesberg F.E. Substituent effects on the pairing and polymerase recognition of simple unnatural base pairs. Nucleic Acids Res 34 (2006) 2037-2045
52. Patrick C.R., and Prosser G.S. Molecular complex of benzene and hexafluorobenzene. Nature 187 (1960) 1021
53. Coates G.W., Dunn A.R., Henling L.M., Dougherty D.A., and Grubbs R.H. Phenyl-perfluorophenyl stacking interactions: a new strategy for supermolecule construction. Angew Chem Int Ed Engl 36 (1997) 248-251