Technological applications arising from the interactions of DNA bases with metal ions

Current Opinion in Biotechnology

Volumn 28, Issue , 2014, Pages 17-24

  Park, Ki Soo ^a   Park, Hyun Gyu ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BASIS; ENZYMATIC REACTION; FLUORESCENCE PROPERTIES; INORGANIC NANOMATERIALS; METAL-BASE PAIRS; NATURALLY OCCURRING; SILVER NANOCLUSTERS; TECHNOLOGICAL APPLICATIONS;

FLUORESCENCE; NANOSTRUCTURED MATERIALS; NUCLEIC ACIDS;

METAL IONS;

COPPER ION; DNA; DOUBLE STRANDED DNA; GRAPHENE OXIDE; METAL ION; PROTON; SILVER NANOPARTICLE;

BASE PAIRING; DNA BINDING; DNA SEQUENCE; ELECTRIC CONDUCTIVITY; ENZYME MECHANISM; FLUORESCENCE ANALYSIS; HYDROGEL; MOLECULAR INTERACTION; NANOANALYSIS; NANOBIOTECHNOLOGY; NANOFABRICATION; NANOSENSOR; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; REVIEW; THERMOSTABILITY;

BASE PAIRING; DNA; FLUORESCENCE; IONS; METAL NANOPARTICLES; METALS; NANOSTRUCTURES; NUCLEOSIDES; SILVER;

EID: 84888081719     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2013.10.013     Document Type: Review

References (48)

1. Berti L., Burley G.A. Nucleic acid and nucleotide-mediated synthesis of inorganic nanoparticles. Nat Nanotechnol 2008, 3:81-87.
2. Takezawa Y., Shionoya M. Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs. Acc Chem Res 2012, 45:2066-2076.
3. Latorre A., Somoza A. DNA-mediated silver nanoclusters: synthesis, properties and applications. Chembiochem 2012, 13:951-958.
4. 2+ and other divalent metal-ions. Biochem Cell Biol 1993, 71:162-168.
5. II-thymine base pairs in DNA duplexes. J Am Chem Soc 2006, 128:2172-2173.
6. Ono A., Cao S., Togashi H., Tashiro M., Fujimoto T., Machinami T., Oda S., Miyake Y., Okamoto I., Tanaka Y. Specific interactions between silver(I) ions and cytosine-cytosine pairs in DNA duplexes. Chem Commun 2008, 4825-4827.
7. Urata H., Yamaguchi E., Nakamura Y., Wada S. Pyrimidine-pyrimidine base pairs stabilized by silver(I) ions. Chem Commun 2011, 47:941-943.
8. Ono A., Torigoe H., Tanaka Y., Okamoto I. Binding of metal ions by pyrimidine base pairs in DNA duplexes. Chem Soc Rev 2011, 40:5855-5866.
9. Ihara T., Ishii T., Araki N., Wilson A.W., Jyo A. Silver ion unusually stabilizes the structure of a parallel-motif DNA triplex. J Am Chem Soc 2009, 131:3826-3827.
10. +-mediated DNA base pairing: extraordinarily stable pyrrolo-dC-pyrrolo-dC pairs binding two silver ions. J Org Chem 2013, 78:9457-9463.
11. Park K.S., Lee J.Y., Park H.G. Mismatched pyrrolo-dC-modified duplex DNA as a novel probe for sensitive detection of silver ions. Chem Commun 2012, 48:4549-4551.
12. Tao Y., Lin Y., Ren J., Qu X.G. Self-assembled, functionalized graphene and DNA as a universal platform for colorimetric assays. Biomaterials 2013, 34:4810-4817.
13. Liu F., Ha H.D., Han D.J., Seo T.S. Photoluminescent graphene oxide microarray for multiplex heavy metal ion analysis. Small 2013, 10.1002/smll.201300499.
14. Yang R., Jin J., Long L., Wang Y., Wang H., Tan W. Reversible molecular switching of molecular beacon: controlling DNA hybridization kinetics and thermodynamics using mercury(II) ions. Chem Commun 2009, 322-324.
15. Wang Y., Li J., Wang H., Jin J., Liu J., Wang K., Tan W., Yang R. Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes. Anal Chem 2010, 82:6607-6612.
16. Ding J., Qin W., Zhang Y., Wang X. Potentiometric aptasensing based on target-induced conformational switch of a DNA probe using a polymeric membrane silver ion-selective electrode. Biosens Bioelectron 2013, 45:148-151.
17. Liu J.M., Yan X.P. Competitive aptamer bioassay for selective detection of adenosine triphosphate based on metal-paired molecular conformational switch and fluorescent gold nanoclusters. Biosens Bioelectron 2012, 36:135-141.
18. Wang Y., Li J., Jin J., Wang H., Tang H., Yang R., Wang K. Strategy for molecular beacon binding readout: separating molecular recognition element and signal reporter. Anal Chem 2009, 81:9703-9709.
19. Thomas J.M., Yu H.Z., Sen D. A mechano-electronic DNA switch. J Am Chem Soc 2012, 134:13738-13748.
20. II-T base pairing. Angew Chem Int Ed 2010, 49:6516-6519.
21. Park K.S., Jung C., Park H.G. "Illusionary" polymerase activity triggered by metal ions: use for molecular logic-gate operations. Angew Chem Int Ed 2010, 49:9757-9760.
22. I ion mediated formation of a C-A mispair by DNA polymerases. Angew Chem Int Ed 2012, 51:6464-6466.
23. Li F., Feng Y., Liu S., Tang B. Triggered activity of a nicking endonuclease for mercuric(II) ion-mediated duplex-like DNA cleavage. Chem Commun 2011, 47:6347-6349.
24. Bi S., Ji B., Zhang Z., Zhu J.J. Metal ions triggered ligase activity for rolling circle amplification and its application in molecular logic gate operations. Chem Sci 2013, 4:1858-1863.
25. 2+ detection. Anal Chem 2013, 85:4586-4593.
26. + and cysteine. Chem Eur J 2009, 15:3347-3350.
27. 2+) using target-induced DNAzyme cascade with catalytic and molecular beacons. Analyst 2012, 137:2799-2805.
28. 2+ controlled streptavidin-binding aptamer. Chem Commun 2013, 49:164-166.
29. Richards C.I., Choi S., Hsiang J.C., Antoku Y., Vosch T., Bongiorno A., Tzeng Y.L., Dickson R.M. Oligonucleotide-stabilized Ag nanocluster fluorophores. J Am Chem Soc 2008, 130:5038-5039.
30. Gwinn E.G., O'Neill P., Guerrero A.J., Bouwmeester D., Fygenson D.K. Sequence-dependent fluorescence of DNA-hosted silver nanoclusters. Adv Mater 2008, 20:279-283.
31. Ai J., Guo W., Li B., Li T., Li D., Wang E. DNA G-quadruplex-templated formation of the fluorescent silver nanocluster and its application to bioimaging. Talanta 2012, 88:450-455.
32. Feng L., Huang Z., Ren J., Qu X. Toward site-specific, homogeneous and highly stable fluorescent silver nanoclusters fabrication on triplex DNA scaffolds. Nucleic Acids Res 2012, 40:e122.
33. Sengupta B., Springer K., Buckman J.G., Story S.P., Abe O.H., Hasan Z.W., Prudowsky Z.D., Rudisill S.E., Degtyareva N.N., Petty J.T. DNA templates for fluorescent silver clusters and i-motif folding. J Phys Chem C 2009, 113:19518-19524.
34. Guo W., Yuan J., Dong Q., Wang E. Highly sequence-dependent formation of fluorescent silver nanoclusters in hybridized DNA duplexes for single nucleotide mutation identification. J Am Chem Soc 2010, 132:932-934.
35. Huang Z., Pu F., Hu D., Wang C., Ren J., Qu X. Site-specific DNA-programmed growth of fluorescent and functional silver nanoclusters. Chem Eur J 2011, 17:3774-3780.
36. Ma K., Cui Q., Liu G., Wu F., Xu S., Shao Y. DNA abasic site-directed formation of fluorescent silver nanoclusters for selective nucleobase recognition. Nanotechnology 2011, 22:305502.
37. Cui Q., Ma K., Shao Y., Xu S., Wu F., Liu G., Teramae N., Bao H. Gap site-specific rapid formation of fluorescent silver nanoclusters for label-free DNA nucleobase recognition. Anal Chim Acta 2012, 724:86-91.
38. Yeh H.C., Sharma J., Han J.J., Martinez J.S., Werner J.H. A DNA-silver nanocluster probe that fluoresces upon hybridization. Nano Lett 2010, 10:3106-3110.
39. Yeh H.C., Sharma J., Shih I.M., Vu D.M., Martinez J.S., Werner J.H. A fluorescence light-up Ag nanocluster probe that discriminates single-nucleotide variants by emission color. J Am Chem Soc 2012, 134:11550-11558.
40. Zhang M., Guo S.M., Li Y.R., Zuo P., Ye B.C. A label-free fluorescent molecular beacon based on DNA-templated silver nanoclusters for detection of adenosine and adenosine deaminase. Chem Commun 2012, 48:5488-5490.
41. Huang Z., Pu F., Lin Y., Ren J., Qu X. Modulating DNA-templated silver nanoclusters for fluorescence turn-on detection of thiol compounds. Chem Commun 2011, 47:3487-3489.
42. Lan G.Y., Huang C.C., Chang H.T. Silver nanoclusters as fluorescent probes for selective and sensitive detection of copper ions. Chem Commun 2010, 46:1257-1259.
43. 2+ ion. Chem Commun 2009, 3395-3397.
44. Yu J., Choi S., Richards C.I., Antoku Y., Dickson R.M. Live cell surface labeling with fluorescent Ag nanocluster conjugates. Photochem Photobiol 2008, 84:1435-1439.
45. Sun Z., Wang Y., Wei Y., Liu R., Zhu H., Cui Y., Zhao Y., Gao X. Ag cluster-aptamer hybrid: specifically marking the nucleus of live cells. Chem Commun 2011, 47:11960-11962.
46. Li T., Zhang L., Ai J., Dong S., Wang E. Ion-tuned DNA/Ag fluorescent nanoclusters as versatile logic device. ACS Nano 2011, 5:6334-6338.
47. Guo W., Yuan J., Wang E. Strand exchange reaction modulated fluorescence "off-on" switching of hybridized DNA duplex stabilized silver nanoclusters. Chem Commun 2011, 47:10930-10932.
48. Guo W., Orbach R., Mironi-Harpaz I., Seliktar D., Willner I. Fluorescent DNA hydrogels composed of nucleic acid-stabilized silver nanoclusters. Small 2013, 10.1002/smll.201300055.