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Effect of Aptamer Binding on the Electron-Transfer Properties of Redox Cofactors


In vitro selection or SELEX has allowed for the identification of functional nucleic acids (FNAs) that can potentially mimic and replace protein enzymes. These FNAs likely interact with cofactors, just like enzymes bind cofactors in their active sites. Investigating how FNA binding affects cofactor properties is important for understanding how an active site is formed and for developing useful enzyme mimics. Oxidoreductase enzymes contain cofactors in their active sites that allow the enzymes to do redox chemistry. In certain applications, these redox cofactors act as electron-transfer shuttles that transport electrons between the enzymes’ active sites and electrode surfaces. Three redox cofactors commonly found in oxidoreductases are flavin adenine dinucleotide, nicotinamide adenine dinucleotide (NAD+), and pyrroloquinoline quinone (PQQ). We are interested in investigating how DNA aptamers that bind these cofactors influence the cofactors’ redox abilities and if these aptamer-cofactor complexes could serve as redox catalysts. We employed cyclic voltammetry and amperometry to study the electrochemical properties of NAD+ and PQQ when bound to DNA aptamers. Our results suggest that the aptamers provide a stable environment for the cofactor to participate in redox reactions, although enhanced redox activity was not observed. This work provides a foundation for the development of new FNAs capable of redox activity.

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  • Arechederra MN, Addo PK, Minteer SD (2011) Poly(neutral red) as a NAD+ reduction catalyst and a NADH oxidation catalyst: towards the development of a rechargeable biobattery. Electrochim Acta 56:1585

    Article  CAS  Google Scholar 

  • Banks CE, Crossley A, Salter C, Wilkins SJ, Compton RG (2006) Carbon nanotubes contain metal impurities which are responsible for the “electrocatalysis” seen at some nanotube-modified electrodes. Angew Chem Int Ed 45:2533

    Article  CAS  Google Scholar 

  • Baum DA, Silverman SK (2008) Deoxyribozymes: useful DNA catalysts in vitro and in vivo. Cell Mol Life Sci 65:2156

    Article  CAS  PubMed  Google Scholar 

  • Burgstaller P, Famulok M (1994) Isolation of RNA aptamers for biological cofactors by in vitro selection. Angew Chem Int Ed 33:1084

    Article  Google Scholar 

  • Duine JA (2001) Cofactor diversity in biological oxidations: implications and applications. Chem Rec 1:74

    Article  CAS  PubMed  Google Scholar 

  • Durand F, Stines-Chaumeil C, Flexer V, Andre I, Mano N (2010) Designing a highly active soluble PQQ-glucose dehydrogenase for efficient glucose biosensors and biofuel cells. Biochem Biophys Res Commun 402:750

    Article  CAS  PubMed  Google Scholar 

  • Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818

    Article  CAS  PubMed  Google Scholar 

  • Ellington AD, Szostak JW (1992) Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures. Nature 355:850

    Article  CAS  PubMed  Google Scholar 

  • Emahi I, Mulvihill IM, Baum DA (2015) Pyrroloquinoline quinone maintains redox activity when bound to a DNA aptamer. RSC Adv 5:7450

    Article  CAS  Google Scholar 

  • Goran J, Favela C, Rust I, Stevenson K (2014) Enhanced electrochemical oxidation of NADH at carbon nanotube electrodes using methylene green: is polymerization necessary? J Electrochem Soc 161:H3042

    Article  Google Scholar 

  • Han H, Tachikawa H (2005) Electrochemical determination of thiols at single-wall carbon nanotubes and PQQ modified electrodes. Front Biosci 10:931

    Article  CAS  PubMed  Google Scholar 

  • Hao YuE, Scott K (2010) Enzymatic biofuel cells—fabrication of enzyme electrodes. Energies 3:23

    Article  Google Scholar 

  • Heyduk T, Lee JC (1990) Application of fluorescence energy transfer and polarization to monitor Escherichia coli cAMP receptor protein and lac promoter interaction. Proc Natl Acad Sci USA 87:1744

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Huizenga DE, Szostak JW (1995) A DNA aptamer that binds adenosine and ATP. Biochemistry 34:656

    Article  CAS  PubMed  Google Scholar 

  • Itoh S, Kato N, Mure M, Ohshiro Y (1987) Kinetic studies on the oxidation of thiols by coenzyme PQQ. Bull Chem Soc Jpn 60:420

    Article  Google Scholar 

  • Itoh S, Kinugawa M, Mita N, Ohshiro Y (1989) Efficient NAD+-regeneration system with heteroaromatic o-quinones and molecular oxygen. J Chem Soc Chem Commun (11):694

  • Kanninen P, Ruiz V, Kallio T, Anoshkin IV, Kauppinen EI, Kontturi K (2010) Simple immobilization of pyrroloquinoline quinone on few-walled carbon nanotubes. Electrochem Commun 12:1257

    Article  CAS  Google Scholar 

  • Karyakin AA, Ivanova YN, Karyakina EE (2003) Equilibrium (NAD+/NADH) potential on poly(neutral red) modified electrode. Electrochem Commun 5:677

    Article  CAS  Google Scholar 

  • Katz E, Schlereth DD, Schmidt H-L (1994) Electrochemical study of pyrroloquinoline quinone covalently immobilized as a monolayer onto a cystamine-modified gold electrode. J Electroanal Chem 367:59

    Article  CAS  Google Scholar 

  • Kim J, Jia H, Wang P (2006) Challenges in biocatalysis for enzyme-based biofuel cells. Biotechnol Adv 24:296

    Article  CAS  PubMed  Google Scholar 

  • Korang J, Emahi I, Grither WR, Baumann SM, Baum DA, McCulla RD (2013) Photoinduced DNA cleavage by atomic oxygen precursors in aqueous solutions. RSC Adv 3:12390

    Article  CAS  Google Scholar 

  • Ksenzhek OS, Petrova SA (1983) Electrochemical properties of flavins in aqueous solutions. Bioelectrochem Bioener 11:105

    Article  CAS  Google Scholar 

  • Lauhon CT, Szostak JW (1995) RNA aptamers that bind flavin and nicotinamide redox cofactors. J Am Chem Soc 117:1246

    Article  CAS  PubMed  Google Scholar 

  • Ohshiro Y, Itoh S (1989) The chemistry and biomimetics of PQQ. In: Jongejan JA, Duine JA (eds) PQQ and quinoproteins. Springer, Dordrecht, pp 195–204

    Chapter  Google Scholar 

  • Rasmussen M, Abdellaoui S, Minteer SD (2015) Enzymatic biofuel cells: 30 years of critical advancements. Biosens Bioelectron. doi:10.1016/j.bios.2015.06.029

    PubMed  Google Scholar 

  • Rojas AM, Gonzalez PA, Antipov E, Klibanov AM (2007) Specificity of a DNA-based (DNAzyme) peroxidative biocatalyst. Biotechnol Lett 29:227

    Article  CAS  PubMed  Google Scholar 

  • Sun G, Zhou J, Yu F, Zhang Y, Pang J, Zheng L (2012) Electrochemical capacitive properties of CNT fibers spun from vertically aligned CNT arrays. J Solid State Electrochem 16:1775

    Article  CAS  Google Scholar 

  • Travascio P, Li Y, Sen D (1998) DNA-enhanced peroxidase activity of a DNA-aptamer-hemin complex. Chem Biol 5:505

    Article  CAS  PubMed  Google Scholar 

  • Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505

    Article  CAS  PubMed  Google Scholar 

  • van Kleef MG, Jongejan J, Duine J (1989) Factors relevant in the reaction of PQQ with amino acids. In: Jongejan JA, Duine JA (eds) PQQ and quinoproteins. Springer, Dordrecht, pp 217–226

    Chapter  Google Scholar 

  • Willner I, Arad G, Katz E (1998) A biofuel cell based on pyrroloquinoline quinone and microperoxidase-1 monolayer-functionalized electrodes. Bioelectroch Bioener 44:209

    Article  CAS  Google Scholar 

  • Wilson C, Szostak JW (1998) Isolation of a fluorophore-specific DNA aptamer with weak redox activity. Chem Biol 5:609

    Article  CAS  PubMed  Google Scholar 

  • Zhao T (2009) Micro fuel cells: principles and applications. Academic Press, San Diego

    Google Scholar 

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The authors thank Dr. Tomasz Heyduk for assistance with the fluorescence anisotropy studies. The authors also thank members of the Baum Lab for technical assistance, especially Praveen Bagavandoss and Lucy Freitag who worked in the lab as part of the Students and Teachers as Research Scientists (STARS) program administered by the University of Missouri – St. Louis.

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Correspondence to Dana A. Baum.

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Emahi, I., Gruenke, P.R. & Baum, D.A. Effect of Aptamer Binding on the Electron-Transfer Properties of Redox Cofactors. J Mol Evol 81, 186–193 (2015).

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