Free Standard AU & NZ Shipping For All Book Orders Over $80!
Register      Login
Australian Journal of Chemistry Australian Journal of Chemistry Society
An international journal for chemical science
Shopping Cart: ( empty )
You are here: Home > Journals > CH > CH11023
RESEARCH FRONT
Contents Vol 64(6)

Targeting Nucleic Acids using Dynamic Combinatorial Chemistry

Chandramathi R. Sherman Durai A and Margaret M. Harding A B
+ Author Affiliations
- Author Affiliations

A School of Chemistry, The University of New South Wales, NSW 2052, Australia.

B Corresponding author. Email: harding@unsw.edu.au




Chandramathi R. Sherman Durai graduated with M.Sc. (2002) and M.Phil. (2005) degrees from the Manonmaniam Sundaranar University, Tirunelveli, India. Currently she is pursuing her Ph.D. under the supervision of Professor Margaret M. Harding at the University of New South Wales, Sydney, Australia. Chandramathi’s research is focussed on the design and synthesis of DNA-binding compounds using dynamic combinatorial chemistry.


Margaret M. Harding holds B.Sc. (Honours) (1982), Ph.D. (1987), and D.Sc. (2002) degrees from the University of Sydney and is currently Pro Vice-Chancellor (Research) at the University of New South Wales. She held postdoctoral positions with Professor Jean-Marie Lehn at the Université Louis Pasteur, Strasbourg (1986–1988) and Professor Dudley Williams at the University of Cambridge (1988–1989) followed by an academic appointment at the University of Sydney (1990–2005). In 2005 she was appointed as Professor of Chemistry and the inaugural Dean of Graduate Research at the University of New South Wales. Current research interests are on antifreeze proteins and glycoproteins, DNA recognition, and new synthetic DNA-binding molecules.

Australian Journal of Chemistry 64(6) 671-680 https://doi.org/10.1071/CH11023
Submitted: 14 January 2011  Accepted: 2 March 2011   Published: 27 June 2011

Abstract

Dynamic combinatorial chemistry (DCC) is a powerful method for the identification of novel ligands for the molecular recognition of receptor molecules. The method relies on self-assembly processes to generate libraries of compounds under reversible conditions, allowing a receptor molecule to select the optimal binding ligand from the mixture. However, while DCC is now an established field of chemistry, there are limited examples of the application of DCC to nucleic acids. The requirement to conduct experiments under physiologically relevant conditions, and avoid reaction with, or denaturation of, the target nucleic acid secondary structure, limits the choice of the reversible chemistry, and presents restrictions on the building block design. This review will summarize recent examples of applications of DCC to the recognition of nucleic acids. Studies with duplex DNA, quadruplex DNA, and RNA have utilized mainly thiol disulfide libraries, although applications of imine libraries, in combination with metal coordination, have been reported. The use of thiol disulfide libraries produces lead compounds with limited biostability, and hence design of stable analogues or mimics is required for many applications.


References

[1]  P. L. Privalov, A. I. Dragan, C. Crane-Robinson, K. J. Breslauer, D. P. Remeta, C. A. S. A. Minetti, J. Mol. Biol. 2007, 365, 1.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28Xht1KnsrvM&md5=3b31d9e79851e76ffab07cbff4d5875bCAS | 17055530PubMed |

[2]  D. Jantz, B. T. Amann, G. J. Gatto, J. M. Berg, Chem. Rev. 2004, 104, 789.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3sXps1Smt7k%3D&md5=c732ee66b0d975a75c2e1a1eee5e3be5CAS | 14871141PubMed |

[3]  M. Tateno, K. Yamasaki, N. Amano, J. Kakinuma, H. Koike, M. D. Allen, M. Suzuki, Biopolymers 1997, 44, 335.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1cXms1Gisbg%3D&md5=0e6a0112df51d996bad5439e1db1b4f8CAS | 9782775PubMed |

[4]  G. M. Blackburn, M. J. Gait, Nucleic Acids in Chemistry and Biology 2006 (Royal Society of Chemistry: Cambridge).

[5]  G. Song, J. Ren, Chem. Commun. 2010, 46, 7283.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXht1SntrfK&md5=d16356cffc551fd36b8b7c91f90dafc5CAS |

[6]  S. Fulle, H. Gohlke, J. Mol. Recognit. 2010, 23, 220.
         | 1:CAS:528:DC%2BC3cXitVShsb0%3D&md5=400a9898beab429ccdcecee939206645CAS | 19941322PubMed |

[7]  X.-S. Ye, L.-H. Zhang, Curr. Med. Chem. 2002, 9, 929.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD38XjtlKjtbs%3D&md5=ddc3465659074ce003be00e510a253f3CAS | 11966454PubMed |

[8]  Y. L. Jiang, Z. P. Liu, Mini Rev. Med. Chem. 2010, 10, 726.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXpslSktrs%3D&md5=bb603ac5ab4c020b2d3dd9b6649c214aCAS | 20412042PubMed |

[9]  M. Franceschin, Eur. J. Org. Chem. 2009, 2225.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXmt1agurY%3D&md5=c6111d55f762de5fa2b22997fc182658CAS |

[10]  P. B. Palde, L. O. Ofori, P. C. Gareiss, J. Lerea, B. L. Miller, J. Med. Chem. 2010, 53, 6018.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXps1Whsrg%3D&md5=18270ff0b2b1cbfa16270bd143799a18CAS | 20672840PubMed |

[11]  Y. Wu, R. M. Brosh, FEBS J. 2010, 277, 3470.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXhtFWmsb%2FO&md5=4815db5d3043ec90242be70d78217941CAS | 20670277PubMed |

[12]  R. M. Doss, M. M. Marques, S. Foister, D. M. Chenoweth, P. B. Dervan, J. Am. Chem. Soc. 2006, 128, 9074.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XmtVSisbY%3D&md5=d80c1960ef38dbc6cbdc3b386cdf62d5CAS | 16834381PubMed |

[13]  E. J. Fechter, B. Olenyuk, P. B. Dervan, Angew. Chem. Int. Ed. 2004, 43, 3591.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXlvFKjsb4%3D&md5=07600d8a228d96afcb9d1094285d7b9aCAS |

[14]  I. Haq, J. Ladbury, J. Mol. Recognit. 2000, 13, 188.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3cXlvVGhtro%3D&md5=03d12fb66afa55bfec38138e71425297CAS | 10931556PubMed |

[15]  K. R. Fox, T. Brown, Q. Rev. Biophys. 2005, 38, 311.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XoslSgt70%3D&md5=c94dc055dd1380058c68495ad2da9840CAS | 16737560PubMed |

[16]  T. A. Winters, E. Pastwa, K. Datta, R. D. Neumann, Curr. Genomics 2003, 4, 275.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3sXitFWns7o%3D&md5=49dc448a203a4c5acb0aff83c19fb45dCAS |

[17]  J. M. Lehn, Chemistry 1999, 5, 2455.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1MXmtVKlsbw%3D&md5=92fea3d7f58610efecf8331a9e689c11CAS |

[18]  A. V. Eliseev, J. M. Lehn, Comb. Chem. Biol. 1999, 243, 159.
         | 1:CAS:528:DyaK1MXlslSrsb8%3D&md5=e1dc956a0112ba85c3ddac6896873ed3CAS |

[19]  P. T. Corbett, J. Leclaire, L. Vial, K. R. West, J.-L. Wietor, J. K. M. Sanders, S. Otto, Chem. Rev. 2006, 106, 3652.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XnvVKhsbo%3D&md5=fb7e9fd2403a7adcd1a5422509ae04ebCAS | 16967917PubMed |

[20]  O. Ramström, J.-M. Lehn, Nat. Rev. Drug Discov. 2002, 1, 26.
         | Crossref | GoogleScholarGoogle Scholar | 12119606PubMed |

[21]  S. Otto, K. Severin, Top. Curr. Chem. 2007, 277, 267.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXhtVSrurvJ&md5=5c0bd5e443f51f3770f3525b0d0d6dc2CAS |

[22]  S. Ladame, Org. Biomol. Chem. 2008, 6, 219.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXisVWlsQ%3D%3D&md5=270ab148e93217f9f0adb0dc8443183dCAS | 18174988PubMed |

[23]  J. N. H. Reek, S. Otto (Eds), Dynamic Combinatorial Chemistry: In Drug Discovery, Bioorganic Chemistry, and Materials Science 2010 (Wiley-VCH: Weinheim).

[24]  A. R. Hunt, S. Otto, Chem. Commun. 2011, 47, 847.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXhsF2isrjK&md5=1cfdf819cd12e3e0688efc93e47fcd75CAS |

[25]  S. Ladame, A. M. Whitney, S. Balasubramanian, Angew. Chem. Int. Ed. 2005, 44, 5736.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXhtVejs7bI&md5=61045ebf674bed2c435a14c34916f8a5CAS |

[26]  A. M. Whitney, S. Ladame, S. Balasubramanian, Angew. Chem. Int. Ed. 2004, 43, 1143.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXitV2hsLs%3D&md5=348d1eaf46028ded7505ccb6b8f4508cCAS |

[27]  B. R. McNaughton, B. L. Miller, Org. Lett. 2006, 8, 1803.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XjtFOmt70%3D&md5=0fd0d587f4132f0811ae0f4b38eb196aCAS | 16623555PubMed |

[28]  C. Karan, B. L. Miller, J. Am. Chem. Soc. 2001, 123, 7455.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3MXkvFGisr8%3D&md5=3b54854d60b327b19bd96fbce480f6a5CAS | 11472190PubMed |

[29]  B. Klekota, M. H. Hammond, B. L. Miller, Tetrahedron Lett. 1997, 38, 8639.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK2sXnvFSrtLg%3D&md5=f8459896b24d71c964eead0c152e51daCAS |

[30]  B. Klekota, B. L. Miller, Tetrahedron 1999, 55, 11687.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1MXmt1Gmtr8%3D&md5=ee7458d9583d15fbf39781412218ec9bCAS |

[31]  J. Portugal, M. J. Waring, Eur. J. Biochem. 1987, 167, 281.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaL2sXlsVKqtbc%3D&md5=16504c029c603f32bac16b85ac66166cCAS | 3040405PubMed |

[32]  J. G. Pelton, D. E. Wemmer, Biochemistry 1988, 27, 8088.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaL1cXls1ejsLc%3D&md5=85d4fc2bba3d871595a952fb08d89092CAS | 3233197PubMed |

[33]  S. Tsujita, M. Tanada, T. Kataoka, S. Sasaki, Bioorg. Med. Chem. Lett. 2007, 17, 68.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXislei&md5=d13839cfa5d607887d30b8cc555f2aceCAS | 17046249PubMed |

[34]  S. Dawson, J. P. Malkinson, D. Paumier, M. Searcey, Nat. Prod. Rep. 2007, 24, 109.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXislygtLg%3D&md5=24f3973e001cff3875b342e95828ac87CAS | 17268609PubMed |

[35]  B. R. McNaughton, P. C. Gareiss, B. L. Miller, J. Am. Chem. Soc. 2007, 129, 11306.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXpsFCjtbY%3D&md5=0a977fc9168d3dd5d54e168428830ce7CAS | 17722919PubMed |

[36]  S. C. M. Teixeira, J. H. Thorpe, A. K. Todd, H. R. Powell, A. Adams, L. P. G. Wakelin, W. A. Denny, C. J. Cardin, J. Mol. Biol. 2002, 323, 167.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD38XnslGqsL8%3D&md5=995d1f2c6d8798c92fc8219bce9371a2CAS | 12381312PubMed |

[37]  C. Rajput, R. Rutkaite, L. Swanson, I. Haq, J. A. Thomas, Chemistry 2006, 12, 4611.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XmtVaitb0%3D&md5=9e8c08557e3788c016e281bd955b9543CAS | 16575931PubMed |

[38]  A. Bugaut, K. Jantos, J.-L. Wietor, R. Rodriguez, J. K. M. Sanders, S. Balasubramanian, Angew. Chem. Int. Ed. 2008, 47, 2677.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXkvFejsbg%3D&md5=bbfc76bb978631eb49ed3221e50ac6c5CAS |

[39]  K. Jantos, R. Rodriguez, S. Ladame, S. Shirude Pravin, S. Balasubramanian, J. Am. Chem. Soc. 2006, 128, 13662.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XhtVWkurbF&md5=f19bd6d41622614c788ef88628f00d66CAS | 17044674PubMed |

[40]  M. C. Nielsen, T. Ulven, Chemistry 2008, 14, 9487.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXhsVSntb%2FI&md5=8ef69a3f1af59e604a8a5b348772d639CAS | 18792045PubMed |

[41]  B. Gooch, P. A. Beal, J. Am. Chem. Soc. 2004, 126, 10603.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXmsVWjtbw%3D&md5=72ceca4faf55c3e56082090a6248de26CAS | 15327318PubMed |

[42]  P. C. Gareiss, K. Sobczak, B. R. McNaughton, P. B. Palde, C. A. Thornton, B. L. Miller, J. Am. Chem. Soc. 2008, 130, 16254.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXhtlGns7nO&md5=2f15461a634756a0bb176073a52bfca5CAS | 18998634PubMed |

[43]  A. Bugaut, J.-J. Toulime, B. Rayner, Angew. Chem. Int. Ed. 2004, 43, 3144.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXlt1GntbY%3D&md5=ef5fd884c6d667cf4591dd4bcbf821c4CAS |

[44]  A. Bugaut, K. Bathany, J.-M. Schmitter, B. Rayner, Tetrahedron Lett. 2005, 46, 687.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXhtFGlsrvN&md5=ccfbe002799a827e9b7c23a6e637ef31CAS |

[45]  A. Bugaut, J.-J. Toulmé, B. Rayner, Org. Biomol. Chem. 2006, 4, 4082.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XhtFKitr%2FM&md5=670c581617acef0601dc3961aa91ee46CAS | 17312962PubMed |

[46]  L. Azéma, K. Bathany, B. Rayner, ChemBioChem 2010, 11, 2513.
         | Crossref | GoogleScholarGoogle Scholar | 21104718PubMed |

[47]  F. R. Bowler, J. J. Diaz-Mochon, M. D. Swift, M. Bradley, Angew. Chem. Int. Ed. 2010, 1809.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXivFamsrk%3D&md5=08eec75d3dbf8bc3898896f44ad4b22dCAS |

[48]  D. T. Hickman, N. Sreenivasachary, J.-M. Lehn, Helv. Chim. Acta 2008, 91, 1.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXhvVSluro%3D&md5=e57cb1e56a3fc8aae834acee80889850CAS |

[49]  A. Krezel, W. Bal, Acta Biochim. Pol. 1999, 46, 567.
         | 1:CAS:528:DyaK1MXnsVCrsLo%3D&md5=c1c3539f1a67877dc313cbd27db12d43CAS | 10698265PubMed |

[50]  C. K. Sen, Curr. Top. Cell. Regul. 2001, 36, 1.
         | Crossref | GoogleScholarGoogle Scholar |

[51]  R. F. Ludlow, S. Otto, J. Am. Chem. Soc. 2010, 132, 5984.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXkslKmsLs%3D&md5=e21ef9bd7c76231edc9f1c7ba3fe632bCAS | 20392045PubMed |

[52]  C. C. O’Hare, P. Uthe, H. Mackay, K. Blackmon, J. Jones, T. Brown, B. Nguyen, W. D. Wilson, M. Lee, J. A. Hartley, Biochemistry 2007, 46, 11661.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXhtFSnsL3L&md5=8266d6adbd602efc31883e30d7573060CAS | 17910471PubMed |

[53]  M. Munde, M. Lee, S. Neidle, R. Arafa, D. W. Boykin, Y. Liu, C. Bailly, W. D. Wilson, J. Am. Chem. Soc. 2007, 129, 5688.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXktVyhtb4%3D&md5=a34825ddd856f72ca8574d01fcd8ff60CAS | 17425312PubMed |

[54]  M. Munde, M. A. Ismail, R. Arafa, P. Peixoto, C. J. Collar, Y. Liu, L. Hu, M.-H. David-Cordonnier, A. Lansiaux, C. Bailly, D. W. Boykin, W. D. Wilson, J. Am. Chem. Soc. 2007, 129, 13732.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXhtFKhtbnK&md5=44241235843b948419f392af3c1a4d17CAS | 17935330PubMed |

[55]  J. Lee, V. Guelev, S. Sorey, D. W. Hoffman, B. L. Iverson, J. Am. Chem. Soc. 2004, 126, 14036.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXotlamsLc%3D&md5=73280df26536204784d4c4d181a5f021CAS | 15506767PubMed |

[56]  Y. Chu, S. Sorey, D. W. Hoffman, B. L. Iverson, J. Am. Chem. Soc. 2007, 129, 1304.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXlt1GlsA%3D%3D&md5=bc8d8ee874e8a895a7b13dfdb57037eaCAS | 17263414PubMed |

[57]  J. Portugal, D. J. Cashman, J. O. Trent, N. Ferrer-Miralles, T. Przewloka, I. Fokt, W. Priebe, J. B. Chaires, J. Med. Chem. 2005, 48, 8209.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXht1SrsbrK&md5=ec34ae00804592cffe2e7e350e28a84eCAS | 16366602PubMed |

[58]  L. Hunter, G. R. Condie, M. M. Harding, Tetrahedron Lett. 2010, 51, 5064.
         | Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXhtVGrtbzK&md5=0b861c627ffabf0e69fa45323ab2b73fCAS |