Oligonucleotide-Based Systems for Input-Controlled and Non-Covalently Regulated Protein-Binding

Overview

Journal Supramol Chem

Date 2013 Nov 5

PMID 24187478

Citations 5

Authors

Cooper Battle

Xiaozhu Chu

Janarthanan Jayawickramarajah

Affiliations

Soon will be listed here.

Abstract

Supramolecular chemists continuously take inspiration from complex biological systems to develop functional molecules involved in molecular recognition and self-assembly. In this regard, "smart" synthetic molecules that emulate allosteric proteins are both exciting and challenging, since many allosteric proteins can be considered as molecular switches that bind to other protein targets in a non-covalent fashion, and importantly, are capable of having their output activity controlled by prior binding to input molecules. This review discusses the foundations and passage toward the development of non-covalently operated oligonucleotide-based systems with protein-binding capacity that can be precisely regulated in an input-controlled manner.

Citing Articles

Chemically programmable bacterial probes for the recognition of cell surface proteins.

Prasad P, Eizenshtadt N, Goliand I, Fellus-Alyagor L, Oren R, Golani O Mater Today Bio. 2023; 20:100669.

PMID: 37334185 PMC: 10275978. DOI: 10.1016/j.mtbio.2023.100669.

Decorating bacteria with self-assembled synthetic receptors.

Lahav-Mankovski N, Prasad P, Oppenheimer-Low N, Raviv G, Dadosh T, Unger T Nat Commun. 2020; 11(1):1299.

PMID: 32157077 PMC: 7064574. DOI: 10.1038/s41467-020-14336-7.

Nucleic Acid Templated Reactions for Chemical Biology.

Pisa M, Seitz O ChemMedChem. 2017; 12(12):872-882.

PMID: 28480997 PMC: 5488204. DOI: 10.1002/cmdc.201700266.

Mimicking the Function of Signaling Proteins: Toward Artificial Signal Transduction Therapy.

Peri-Naor R, Motiei L, Margulies D J Vis Exp. 2016; (115).

PMID: 27768030 PMC: 5092080. DOI: 10.3791/54396.

Bile Acid Conjugated DNA Chimera that Conditionally Inhibits Carbonic Anhydrase-II in the Presence of MicroRNA-21.

Chu X, Battle C, Zhang N, Aryal G, Mottamal M, Jayawickramarajah J Bioconjug Chem. 2015; 26(8):1606-12.

PMID: 26191606 PMC: 4709253. DOI: 10.1021/acs.bioconjchem.5b00231.

References

Soukup G, Breaker R . Allosteric nucleic acid catalysts. Curr Opin Struct Biol. 2000; 10(3):318-25. DOI: 10.1016/s0959-440x(00)00090-7. View

Rosenzweig B, Ross N, Tagore D, Jayawickramarajah J, Saraogi I, Hamilton A . Multivalent protein binding and precipitation by self-assembling molecules on a DNA pentaplex scaffold. J Am Chem Soc. 2009; 131(14):5020-1. DOI: 10.1021/ja809219p. View

Portela C, Albericio F, Eritja R, Castedo L, Mascarenas J . ds-Oligonucleotide-peptide conjugates featuring peptides from the leucine-zipper region of Fos as switchable receptors for the oncoprotein Jun. Chembiochem. 2007; 8(10):1110-4. DOI: 10.1002/cbic.200700115. View

Gorska K, Manicardi A, Barluenga S, Winssinger N . DNA-templated release of functional molecules with an azide-reduction-triggered immolative linker. Chem Commun (Camb). 2011; 47(15):4364-6. DOI: 10.1039/c1cc10222b. View

Roglin L, Ahmadian M, Seitz O . DNA-controlled reversible switching of peptide conformation and bioactivity. Angew Chem Int Ed Engl. 2007; 46(15):2704-7. DOI: 10.1002/anie.200603889. View

Ma Z, Taylor J . Nucleic acid-triggered catalytic drug release. Proc Natl Acad Sci U S A. 2000; 97(21):11159-63. PMC: 17170. DOI: 10.1073/pnas.97.21.11159. View

Oshovsky G, Reinhoudt D, Verboom W . Supramolecular chemistry in water. Angew Chem Int Ed Engl. 2007; 46(14):2366-93. DOI: 10.1002/anie.200602815. View

Dittmer W, Reuter A, Simmel F . A DNA-based machine that can cyclically bind and release thrombin. Angew Chem Int Ed Engl. 2004; 43(27):3550-3. DOI: 10.1002/anie.200353537. View

Fasting C, Schalley C, Weber M, Seitz O, Hecht S, Koksch B . Multivalency as a chemical organization and action principle. Angew Chem Int Ed Engl. 2012; 51(42):10472-98. DOI: 10.1002/anie.201201114. View

10.

Zhou C, Yang Z, Liu D . Reversible regulation of protein binding affinity by a DNA machine. J Am Chem Soc. 2012; 134(3):1416-8. DOI: 10.1021/ja209590u. View

11.

Hahn M, Muir T . Manipulating proteins with chemistry: a cross-section of chemical biology. Trends Biochem Sci. 2005; 30(1):26-34. DOI: 10.1016/j.tibs.2004.10.010. View

12.

Tan W, Wang K, Drake T . Molecular beacons. Curr Opin Chem Biol. 2004; 8(5):547-53. DOI: 10.1016/j.cbpa.2004.08.010. View

13.

Kleiner R, Dumelin C, Liu D . Small-molecule discovery from DNA-encoded chemical libraries. Chem Soc Rev. 2011; 40(12):5707-17. PMC: 4435721. DOI: 10.1039/c1cs15076f. View

14.

Marras S, Kramer F, Tyagi S . Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res. 2002; 30(21):e122. PMC: 135848. DOI: 10.1093/nar/gnf121. View

15.

Seeman N . At the crossroads of chemistry, biology, and materials: structural DNA nanotechnology. Chem Biol. 2004; 10(12):1151-9. DOI: 10.1016/j.chembiol.2003.12.002. View

16.

Shin D, Sinkeldam R, Tor Y . Emissive RNA alphabet. J Am Chem Soc. 2011; 133(38):14912-5. PMC: 3179766. DOI: 10.1021/ja206095a. View

17.

Teller C, Willner I . Functional nucleic acid nanostructures and DNA machines. Curr Opin Biotechnol. 2010; 21(4):376-91. DOI: 10.1016/j.copbio.2010.06.001. View

18.

Cai J, Rosenzweig B, Hamilton A . Inhibition of chymotrypsin by a self-assembled DNA quadruplex functionalized with cyclic peptide binding fragments. Chemistry. 2008; 15(2):328-32. DOI: 10.1002/chem.200801637. View

19.

Negin S, Smith B, Unger A, Leevy W, Gokel G . Hydraphiles: a rigorously studied class of synthetic channel compounds with in vivo activity. Int J Biomed Imaging. 2013; 2013:803579. PMC: 3562588. DOI: 10.1155/2013/803579. View

20.

Williams B, Diehnelt C, Belcher P, Greving M, Woodbury N, Johnston S . Creating protein affinity reagents by combining peptide ligands on synthetic DNA scaffolds. J Am Chem Soc. 2009; 131(47):17233-41. PMC: 2796340. DOI: 10.1021/ja9051735. View