Skip to main content

DNA in Metal Catalysis

  • Chapter
  • First Online:
Topics in Organometallic Chemistry

Abstract

The DNA molecule, which contains the blueprint of life, has played a pivotal role in the biological revolution. In recent years, many non-biological applications of this remarkable molecule have been explored. In this chapter we will review the use of DNA in metal catalysis. Three general approaches will be discussed: metal-dependent DNAzymes, DNA-templated catalysis, and the recently introduced concept of DNA-based asymmetric catalysis

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

Abbreviations

A:

Adenosine

bpy:

2,2′-Bipyridine

C:

Cytidine

D–A:

Diels–Alder

dA:

Deoxyadenosine

dC:

Deoxycytidine

DCM:

Dichloromethane

dG:

Deoxyguanosine

ds-DNA:

Double-stranded DNA

dT:

Deoxythymidine

DTT:

Dithiothreitol

G:

Guanosine

HRP:

Horseradish peroxidase

MMPP:

Magnesium bis(monoperoxyphthalate)

MPIX:

Mesoporphyrin IX

NMM:

N-Methylmesoporphyrin

Nu:

Nucleophile

PNA:

Peptide nucleic acid

ss-DNA:

Single-stranded DNA

st-DNA:

Salmon testes DNA

tpy:

2,2′:6′,2′′-Terpyridine

TSA:

Transition state analog

U:

Uridine

References

  1. Lewin B (2007) Genes IX. Jones & Bartlett, Sudbury

    Google Scholar 

  2. Feldkamp U, Niemeyer CM (2006) Angew Chem Int Ed 45:1856

    Article  CAS  Google Scholar 

  3. Clever GH, Kaul C, Carell T (2007) Angew Chem Int Ed 46:6226

    Article  CAS  Google Scholar 

  4. Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S (1983) Cell 35: 849

    Google Scholar 

  5. Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR (1982) Cell 31:147

    Article  PubMed  CAS  Google Scholar 

  6. Joyce GF (2004) Annu Rev Biochem 73:791

    Article  PubMed  CAS  Google Scholar 

  7. Nissen P, Hansen J, Ban N, Moore PB, Steitz TA (2000) Science 289:920

    Article  PubMed  ADS  CAS  Google Scholar 

  8. Breaker RR (1997a) Chem Rev 97:371

    Article  CAS  Google Scholar 

  9. Bartel DP, Unrau PJ (1999) Trends Biochem Sci 24:M9

    Article  CAS  Google Scholar 

  10. Fiammengo R, Jäschke A (2005) Curr Opin Biotechnol 16:614

    PubMed  CAS  Google Scholar 

  11. Sen D, Geyer CR (1998) Curr Opin Chem Biol 2:680

    Article  PubMed  CAS  Google Scholar 

  12. Ma Z, Taylor J-S (2000) Proc Natl Acad Sci USA 97:11159

    Article  PubMed  ADS  CAS  Google Scholar 

  13. Sigel RKO, Pyle AM (2007) Chem Rev 107:97

    Article  PubMed  CAS  Google Scholar 

  14. Kim H-K, Liu J, Li J, Nagraj N, Li M, Pavot CM-B, Lu Y (2007a) J Am Chem Soc 129:6896

    Article  CAS  Google Scholar 

  15. Bonaccio M, Credali A, Peracchi A (2004) Nucleic Acids Res 32:916

    Article  PubMed  CAS  Google Scholar 

  16. He Q-C, Zhou J-M, Zhou D-M, Nakamatsu Y, Baba T, Taira K (2002) Biomacromolecules 3:69

    Article  PubMed  CAS  Google Scholar 

  17. Ota N, Warashina M, Hirano K, Hatanaka K, Taira K (1998) Nucleic Acids Res 26:3385

    Article  PubMed  CAS  Google Scholar 

  18. Santoro SW, Joyce GF (1998) Biochemistry 37:13330

    Article  PubMed  CAS  Google Scholar 

  19. Sugimoto N, Okumoto Y, Ohmichi T (1999) J Chem Soc, Perkin Trans 2 1999:1381

    Article  Google Scholar 

  20. Wang Y, Silverman SK (2005a) Angew Chem Int Ed 44:5863

    Article  CAS  Google Scholar 

  21. Geyer CR, Sen D (1997) Chem Biol 4:579

    Article  PubMed  CAS  Google Scholar 

  22. Perrin DM, Garestier T, Hélène C (2001) J Am Chem Soc 123:1556

    Article  PubMed  CAS  Google Scholar 

  23. Ting R, Thomas JM, Lermer L, Perrin DM (2004a) Nucleic Acids Res 32:6660

    Article  CAS  Google Scholar 

  24. Bittker JA, Phillips KJ, Liu DR (2002) Curr Opin Chem Biol 6:367

    Article  PubMed  CAS  Google Scholar 

  25. Breaker RR (2004) Nature 432:838

    Article  PubMed  ADS  CAS  Google Scholar 

  26. Höbartner C, Silverman SK (2007) Biopolymers 87:279

    Article  PubMed  CAS  Google Scholar 

  27. Li Y, Breaker RR (1999a) Curr Opin Struct Biol 9:315

    Article  CAS  Google Scholar 

  28. Lu Y (2002) Chem Eur J 8:4588

    Article  CAS  Google Scholar 

  29. Peracchi A (2005) ChemBioChem 6:1316

    Article  PubMed  CAS  Google Scholar 

  30. Breaker RR (1997b) Nat Biotechnol 15:427

    Article  CAS  Google Scholar 

  31. Breaker RR, Joyce GF (1994) Chem Biol 1:223

    Article  PubMed  CAS  Google Scholar 

  32. Breaker RR, Joyce GF (1995) Chem Biol 2:655

    Article  PubMed  CAS  Google Scholar 

  33. Santoro SW, Joyce GF (1997) Proc Natl Acad Sci USA 94:4262

    Article  PubMed  ADS  CAS  Google Scholar 

  34. delCardayré SB, Raines RT (1994) Biochemistry 33:6031

    Article  PubMed  Google Scholar 

  35. Cruz RPG, Withers JB, Li Y (2004) Chem Biol 11:57

    Article  PubMed  CAS  Google Scholar 

  36. Nowakowski J, Shim PJ, Prasad GS, Stout CD, Joyce GF (1999) Nat Struct Biol 6:151

    Article  PubMed  CAS  Google Scholar 

  37. Zaborowska Ż, Fürste JP, Erdmann VA, Kurreck J (2002) J Biol Chem 277:40617

    Article  PubMed  CAS  Google Scholar 

  38. Zaborowska Å», Schubert S, Kurreck J, Erdmann VA (2005) FEBS Lett 579:554

    Article  PubMed  CAS  Google Scholar 

  39. Nawrot B, Widera K, Wojcik M, Rebowska B, Nowak G, Stec WJ (2007) FEBS J 274:1062

    Article  PubMed  CAS  Google Scholar 

  40. Peracchi A (2000) J Biol Chem 275:11693

    Article  PubMed  CAS  Google Scholar 

  41. Peracchi A, Bonaccio M, Clerici M (2005) J Mol Biol 352:783

    Article  PubMed  CAS  Google Scholar 

  42. Liu J, Lu Y (2002) J Am Chem Soc 124:15208

    Article  PubMed  CAS  Google Scholar 

  43. Kim H-K, Rasnik I, Liu J, Ha T, Lu Y (2007b) Nat Chem Biol 3:763

    Article  CAS  Google Scholar 

  44. Kurreck J, Bieber B, Jahnel R, Erdmann VA (2002) J Biol Chem 277:7099

    Article  PubMed  CAS  Google Scholar 

  45. Lusic H, Young DD, Lively MO, Deiters A (2007) Org Lett 9:1903

    Article  PubMed  CAS  Google Scholar 

  46. Ting R, Lermer L, Perrin DM (2004b) J Am Chem Soc 126:12720

    Article  CAS  Google Scholar 

  47. Keiper S, Vyle JS (2006) Angew Chem Int Ed 45:3306

    Article  CAS  Google Scholar 

  48. Liu Y, Sen D (2004) J Mol Biol 341:887

    Article  PubMed  CAS  Google Scholar 

  49. Levy M, Ellington AD (2002) Chem Biol 9:417

    Article  PubMed  CAS  Google Scholar 

  50. Mei SHJ, Liu Z, Brennan JD, Li Y (2003) J Am Chem Soc 125:412

    Article  PubMed  CAS  Google Scholar 

  51. Nutiu R, Mei S, Liu Z, Li Y (2004) Pure Appl Chem 76:1547

    Article  CAS  Google Scholar 

  52. Achenbach JC, Nutiu R, Li Y (2005a) Anal Chim Acta 534:41

    Article  CAS  Google Scholar 

  53. Stojanovic MN, de Prada P, Landry DW (2001) ChemBioChem 2:411

    Article  PubMed  CAS  Google Scholar 

  54. Wang DY, Sen D (2001) J Mol Biol 310:723

    Article  PubMed  CAS  Google Scholar 

  55. Wang DY, Lai BHY, Feldman AR, Sen D (2002a) Nucleic Acids Res 30:1735

    Article  CAS  Google Scholar 

  56. Silverman SK (2005) Nucleic Acids Res 33:6151

    Article  PubMed  CAS  Google Scholar 

  57. Achenbach JC, Chiuman W, Cruz RPG, Li Y (2004) Curr Pharm Biotech 5:321

    Article  CAS  Google Scholar 

  58. Isaka Y (2007) Curr Opin Mol Ther 9:132

    PubMed  CAS  Google Scholar 

  59. Li J, Zheng W, Kwon AH, Lu Y (2000) Nucleic Acids Res 28:481

    Article  PubMed  CAS  Google Scholar 

  60. Li J, Lu Y (2000) J Am Chem Soc 122:10466

    Article  CAS  Google Scholar 

  61. Liu J, Lu Y (2007) J Am Chem Soc 129:9838

    Article  PubMed  CAS  Google Scholar 

  62. Liu J, Lu Y (2003) J Am Chem Soc 125:6642

    Article  PubMed  CAS  Google Scholar 

  63. Liu J, Lu Y (2004b) Chem Mater 16:3231

    Article  CAS  Google Scholar 

  64. Liu J, Lu Y (2004d) Anal Chem 76:1627

    Article  CAS  Google Scholar 

  65. Liu J, Lu Y (2004a) J Fluoresc 14:343

    Article  CAS  Google Scholar 

  66. Liu J, Lu Y (2004c) J Am Chem Soc 126:12298

    Article  CAS  Google Scholar 

  67. Liu J, Lu Y(2006) Org Biomol Chem 4:3435

    Article  PubMed  CAS  Google Scholar 

  68. Lederman H, Macdonald J, Stefanovic D, Stojanovic MN (2006) Biochemistry 45:1194

    Article  PubMed  CAS  Google Scholar 

  69. Stojanovic MN, Stefanovic D (2003) J Am Chem Soc 125:6673

    Article  PubMed  CAS  Google Scholar 

  70. Stojanovic MN, Mitchell TE, Stefanovic D (2002) J Am Chem Soc 124:3555

    Article  PubMed  CAS  Google Scholar 

  71. Chen Y, Wang M, Mao C (2004) Angew Chem Int Ed 43:3554

    Article  CAS  Google Scholar 

  72. Tian Y, He Y, Chen Y, Yin P, Mao C (2005) Angew Chem Int Ed 44:4355

    Article  CAS  Google Scholar 

  73. Carmi N, Shultz LA, Breaker RR (1996) Chem Biol 3:1039

    Article  PubMed  CAS  Google Scholar 

  74. Carmi N, Breaker RR (2001) Bioorg Med Chem 9:2589

    Article  PubMed  CAS  Google Scholar 

  75. Carmi N, Balkhi SR, Breaker RR (1998) Proc Natl Acad Sci USA 95:2233

    Article  PubMed  ADS  CAS  Google Scholar 

  76. Cuenoud B, Szostak JW (1995) Nature 375:611

    Article  PubMed  ADS  CAS  Google Scholar 

  77. Silverman AP, Kool ET (2006) Chem Rev 106:3775

    Article  PubMed  CAS  Google Scholar 

  78. Levy M, Ellington AD (2001) Bioorg Med Chem 9:2581

    Article  PubMed  CAS  Google Scholar 

  79. Li Y, Breaker RR (2001) Methods 23:179

    Article  PubMed  CAS  Google Scholar 

  80. Sreedhara A, Li Y, Breaker RR (2004) J Am Chem Soc 126:3454

    Article  PubMed  CAS  Google Scholar 

  81. Silverman SK (2004) Org Biomol Chem 2:2701

    Article  PubMed  CAS  Google Scholar 

  82. Flynn-Charlebois A, Wang Y, Prior TK, Rashid I, Hoadley KA, Coppins RL, Wolf AC, Silverman SK (2003a) J Am Chem Soc 125:2444

    Article  CAS  Google Scholar 

  83. Flynn-Charlebois A, Prior TK, Hoadley KA, Silverman SK (2003b) J Am Chem Soc 125:5346

    Article  CAS  Google Scholar 

  84. Ricca BL, Wolf AC, Silverman SK (2003) J Mol Biol 330:1015

    Article  PubMed  CAS  Google Scholar 

  85. Wang Y, Silverman SK (2003) J Am Chem Soc 125:6880

    Article  PubMed  CAS  Google Scholar 

  86. Purtha WE, Coppins RL, Smalley MK, Silverman SK (2005) J Am Chem Soc 127:13124

    Article  PubMed  CAS  Google Scholar 

  87. Wang Y, Silverman SK (2005b) Biochemistry 44:3017

    Article  CAS  Google Scholar 

  88. Coppins RL, Silverman SK (2004) J Am Chem Soc 126:16426

    Article  PubMed  CAS  Google Scholar 

  89. Achenbach JC, Jeffries GA, McManus SA, Billen LP, Li Y (2005b) Biochemistry 44:3765

    Article  CAS  Google Scholar 

  90. Li Y, Breaker RR (1999b) Proc Natl Acad Sci USA 96:2746

    Article  ADS  CAS  Google Scholar 

  91. McManus SA, Li Y(2007) Biochemistry 46:2198

    Article  PubMed  CAS  Google Scholar 

  92. Wang W, Billen LP, Li Y (2002b) Chem Biol 9:507

    Article  CAS  Google Scholar 

  93. Li Y, Liu Y, Breaker RR (2000) Biochemistry 39:3106

    Article  PubMed  CAS  Google Scholar 

  94. Sheppard TL, Ordoukhanian P, Joyce GF (2000) Proc Natl Acad Sci USA 97:7802

    Article  PubMed  ADS  CAS  Google Scholar 

  95. Baum DA, Silverman SK (2007) Angew Chem Int Ed 46:3502

    Article  CAS  Google Scholar 

  96. Li Y, Sen D (1996) Nat Struct Biol 3:743

    Article  PubMed  CAS  Google Scholar 

  97. Travascio P, Li Y, Sen D (1998) Chem Biol 5:505

    Article  PubMed  CAS  Google Scholar 

  98. Cochran AG, Schultz PG (1990) Science 249:781

    Article  PubMed  ADS  CAS  Google Scholar 

  99. Li Y, Sen D (1997) Biochemistry 36:5589

    Article  PubMed  CAS  Google Scholar 

  100. Li Y, Sen D (1998) Chem Biol 5:1

    Article  PubMed  Google Scholar 

  101. Sugimoto N, Toda T, Ohmichi T (1998) Chem Commun 1998:1533

    Article  Google Scholar 

  102. Rojas AM, Gonzalez PA, Antipov E, Klibanov AM (2007) Biotechnol Lett 29:227

    Article  PubMed  CAS  Google Scholar 

  103. Boutorin AS, Vlassov VV, Kazakov SA, Kutiavin IV, Podyminogin MA (1984) FEBS Lett 172:43

    Article  Google Scholar 

  104. Chu BCF, Orgel LE (1985) Proc Natl Acad Sci USA 82:963

    Article  PubMed  ADS  CAS  Google Scholar 

  105. Dreyer GB, Dervan PB (1985) Proc Natl Acad Sci USA 82:968

    Article  PubMed  ADS  CAS  Google Scholar 

  106. Moser HE, Dervan PB (1987) Science 238:645

    Article  PubMed  ADS  CAS  Google Scholar 

  107. Le Doan T, Perrouault L, Hélène C, Chassignol M, Thuong NT (1986) Biochemistry 25:6736

    Article  PubMed  CAS  Google Scholar 

  108. Le Doan T, Perrouault L, Chassignol M, Thuong NT, Hélène C (1987) Nucleic Acids Res 15:8643

    Article  Google Scholar 

  109. Dubey I, Pratviel G, Meunier B (2000) J Chem Soc, Perk Trans 1 2000:3088

    Article  Google Scholar 

  110. Pitié M, Casas C, Lacey CJ, Pratviel G, Bernadou J, Meunier B (1993) Angew Chem Int Ed Engl 32:557

    Article  Google Scholar 

  111. Magda D, Miller RA, Sessler JL, Iverson BL (1994) J Am Chem Soc 116:7439

    Article  CAS  Google Scholar 

  112. Magda D, Crofts S, Lin A, Miles D, Wright M, Sessler JL (1997) J Am Chem Soc 119:2293

    Article  CAS  Google Scholar 

  113. Bergstrom DE, Gerry NP (1994) J Am Chem Soc 116:12067

    Article  CAS  Google Scholar 

  114. Chen C-HB, Sigman D (1986) Proc Natl Acad Sci USA 83:7147

    Article  PubMed  ADS  CAS  Google Scholar 

  115. Chen C-HB, Sigman D (1988) J Am Chem Soc 110:6570

    Article  CAS  Google Scholar 

  116. François J-C, Saison-Behmoaras T, Chassignol M, Thuong NT, Sun J-S, Hélène C (1988) Biochemistry 27:2272

    Article  PubMed  Google Scholar 

  117. François J-C, Saison-Behmoaras T, Chassignol M, Thuong NT, Hélène C (1989a) J Biol Chem 264:5891

    Google Scholar 

  118. François J-C, Saison-Behmoaras T, Barbier C, Chassignol M, Thuong NT, Hélène C (1989b) Proc Natl Acad Sci USA 86:9702

    Article  ADS  Google Scholar 

  119. Sergeyev DS, Godovikova TS, Zarytova VF (1991) FEBS Lett 280:271

    Article  PubMed  CAS  Google Scholar 

  120. Sergeyev DS, Godovikova TS, Zarytova VF (1995) Nucleic Acids Res 23:4400

    Article  PubMed  CAS  Google Scholar 

  121. Czlapinski JL, Sheppard TL (2004) Chem Commun 2004:2468

    Article  CAS  Google Scholar 

  122. Bashkin JK, Xie J, Daniher AT, Sampath U, Kao JL-F (1996) J Org Chem 61:2314

    Article  CAS  Google Scholar 

  123. Bergstrom DE, Chen J (1996) Bioorg Med Chem Lett 6:2211

    Article  CAS  Google Scholar 

  124. Putnam WC, Daniher AT, Trawick BN, Bashkin JK (2001) Nucleic Acids Res 29:2199

    Article  PubMed  CAS  Google Scholar 

  125. Bashkin JK, Frolova EI, Sampath U (1994) J Am Chem Soc 116:5981

    Article  CAS  Google Scholar 

  126. Daniher AT, Bashkin JK (1998) Chem Commun 1998:1077

    Article  Google Scholar 

  127. Sakamoto S, Tamura T, Furukawa T, Komatsu Y, Ohtsuka E, Kitamura M, Inoue H (2003) Nucleic Acids Res 31:1416

    Article  PubMed  CAS  Google Scholar 

  128. Groves JT, Kady IO (1993) Inorg Chem 32:3868

    Article  CAS  Google Scholar 

  129. Kady IO, Groves JT (1993) Bioorg Med Chem Lett 3:1367

    Article  CAS  Google Scholar 

  130. Kuzuya A, Mizoguchi R, Komiyama M (2001) Chem Lett 30:584

    Article  Google Scholar 

  131. Komiyama M, Kuzuya A, Mizoguchi R (2002) Bull Chem Soc Jpn 75:2547

    Article  CAS  Google Scholar 

  132. Kuzuya A, Mizoguchi R, Morisawa F, Machida K, Komiyama M (2002a) J Am Chem Soc 124:6887

    Article  CAS  Google Scholar 

  133. Kuzuya A, Machida K, Mizoguchi R, Komiyama M (2002b) Bioconjugate Chem 13:365

    Article  CAS  Google Scholar 

  134. Kuzuya A, Mizoguchi R, Sasayama T, Zhou J-M, Komiyama M (2004) J Am Chem Soc 126:1430

    Article  PubMed  CAS  Google Scholar 

  135. Kuzuya A, Shi Y, Sasayama T, Komiyama M (2005) J Biol Inorg Chem 10:270

    Article  PubMed  CAS  Google Scholar 

  136. Brunner J, Mokhir A, Krämer R (2003) J Am Chem Soc 125:12410

    Article  PubMed  CAS  Google Scholar 

  137. Boll I, Krämer R, Brunner J, Mokhir A (2005) J Am Chem Soc 127:7849

    Article  PubMed  CAS  Google Scholar 

  138. Zelder FH, Brunner J, Krämer R (2004) Chem Commun 2004:902

    Article  CAS  Google Scholar 

  139. Boll I, Jentzsch E, Krämer R, Mokhir A (2006) Chem Commun 2006:3447

    Article  CAS  Google Scholar 

  140. Gartner ZJ, Liu DR (2001) J Am Chem Soc 123:6961

    Article  PubMed  CAS  Google Scholar 

  141. Gartner ZJ, Tse BN, Grubina R, Doyon JB, Snyder TM, Liu DR (2004) Science 305:1601

    Article  PubMed  ADS  CAS  Google Scholar 

  142. Li X, Liu DR (2004) Angew Chem Int Ed 43:4848

    Article  CAS  Google Scholar 

  143. Graf N, Göritz M, Krämer R (2006) Angew Chem Int Ed 45:4013

    Article  CAS  Google Scholar 

  144. Graf N, Krämer R (2006) Chem Commun 2006:4375

    Article  CAS  Google Scholar 

  145. Ward TR (2005) Chem Eur J 11:3798

    Article  CAS  Google Scholar 

  146. Erkkila KE, Odom DT, Barton JK (1999) Chem Rev 99:2777

    Article  PubMed  CAS  Google Scholar 

  147. Roelfes G, Feringa BL (2005) Angew Chem Int Ed 44:3230

    Article  CAS  Google Scholar 

  148. Roelfes G, Boersma AJ, Feringa BL (2006) Chem Commun 2006:635

    Article  CAS  Google Scholar 

  149. Grieco PA(ed) 1998 Organic synthesis in water, 1st edn. Blackie, London

    Google Scholar 

  150. Lindström UM (ed) 2007 Organic reactions in water: principles, strategies and applications, 1st edn. Blackwell, Oxford

    Google Scholar 

  151. Evans DA, Fandrick KR, Song H-J (2005) J Am Chem Soc 127:8942

    Article  PubMed  CAS  Google Scholar 

  152. Boersma AJ, Feringa BL, Roelfes G (2007) Org Lett 9:3647

    Article  PubMed  CAS  Google Scholar 

  153. Coquière D, Feringa BL, Roelfes G (2007) Angew Chem Int Ed 46:9308

    Article  CAS  Google Scholar 

  154. Shibata N, Yasui H, Nakamura S, Toru T (2007) Synlett 2007:1153

    Article  CAS  Google Scholar 

  155. Roelfes G (2007) Mol Biosyst 3:126

    Article  PubMed  CAS  Google Scholar 

  156. Caprioara M, Fiammengo R, Engeser M, Jäschke A (2007) Chem Eur J 13:2089

    Article  CAS  Google Scholar 

  157. Ropartz L, Meeuwenoord NJ, van der Marel GA, van Leeuwen PWNM, Slawin AMZ, Kamer PCJ (2007) Chem Commun 2007:1556

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag London

About this chapter

Cite this chapter

Dijk, E., Feringa, B., Roelfes, G. (2008). DNA in Metal Catalysis. In: Topics in Organometallic Chemistry. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3418_2008_2

Download citation

  • DOI: https://doi.org/10.1007/3418_2008_2

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

Publish with us

Policies and ethics