Skip to main content
SpringerLink
Log in

Quantum chemical investigations of AlN-doped C60 for use as a nano-biosensor in detection of mispairing between DNA bases

  • Published:
Journal of Biosciences Aims and scope Submit manuscript

Abstract

Quantum chemical calculations were carried out to study the electronic structure and stability of adenine–thymine and the rare tautomer of adenine–thymine base pairs along with their Cu2+ complexes and their interactions with AlN-modified fullerene (C58AlN) using Density Functional Theory (B3LYP method). Since, these two forms of base pairs and their Cu2+ complexes have almost similar electronic structures, their chemical differentiation is an extremely difficult task. In this investigation, we have observed that AlN-doped C60 could be used as a potentially viable nanoscale sensor to detect these two base pairs as well as their Cu2+ complexes.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5

Similar content being viewed by others

References

  • Ali-Torres J, Rodriguez-Santiago L and Sodupe M 2011 Computational calculations of pKa values of imidazole in Cu(II) complexes of biological relevance. Phys. Chem. Chem. Phys. 13 7852–7861

    Article  CAS  PubMed  Google Scholar 

  • Becke AD 1993 Density‐functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98 5648–5652

    Article  CAS  Google Scholar 

  • Bertran J, Rodrıguez-Santiago L and Sodupe M 1999 The Different Nature of Bonding in Cu+-Glycine and Cu2+-Glycine. J. Phys. Chem. B 103 2310–2317

    Article  CAS  Google Scholar 

  • Brothers EN, Izmaylov AF, Normand JO, Barone V and Scuseria GE 2008 Accurate solid-state band gaps via screened hybrid electronic structure calculations. J. Chem. Phys. 129 11102–11106

    Article  Google Scholar 

  • Burda JV, Sponer J and Hobza P 1996 Ab initio study of the interaction of guanine and adenine with various mono- and bivalent metal cations (Li+, Na+, K+, Rb+, Cs+; Cu+, Ag+, Au+; Mg2+, Ca2+, Sr2+, Ba2+; Zn2+, Cd2+, and Hg2+). J. Phys. Chem. 100 7250–7255

    Article  CAS  Google Scholar 

  • Burda JV, Sponer J, Leszczynski J and Hobza P 1997 Interaction of DNA base pairs with various metal cations (Mg2+, Ca2+, Sr2+, Ba2+, Cu+, Ag+, Au+, Zn2+, Cd2+, and Hg2+): Nonempirical ab initio calculations on structures, energies, and nonadditivity of the interaction. J. Phys. Chem. B 101 9670–9677

    Article  CAS  Google Scholar 

  • Cardullo F, Diederich F, Echegoyen L, Habicher T, Jayaraman N, Leblanc RM, Stoddart JF and Wang SP 1998 Stable Langmuir and Langmuir−Blodgett films of fullerene−glycodendron. Conjugates Langmuir 14 1955–1959

    Article  CAS  Google Scholar 

  • Chenon MT, Pugmire RJ, Grant DM, Panzica RP and Townsend LB 1975 Carbon-13 magnetic resonance. XXVI. Quantitative determination of the tautomeric populations of certain purines. J. Am. Chem. Soc. 97 4636–4642

    Article  CAS  PubMed  Google Scholar 

  • Cysewski P, Jeziorek D and Olinski R 1998 Structure and tautomeric properties of thymine derivatives generated by hydroxyl radical in aerobic conditions. J. Chem. Soc. Faraday Trans. 94 1813–1821

    Article  CAS  Google Scholar 

  • Diederich F and Thilgen C 1996 Covalent fullerene chemistry. Science 271 317–324

    Article  CAS  Google Scholar 

  • Dreyfus M, Dodin G, Bensaude O and Dubois JE 1975 Tautomerism of purines. I. N(7)H.dha. N(9)H equilibrium in adenine. J. Am. Chem. Soc. 97 2369–2376

    Article  CAS  PubMed  Google Scholar 

  • Fan JC, Shang ZC, Liang J, Liu XH and Jin H 2010 Systematic theoretical investigations on the tautomers of thymine in gas phase and solution. J. Mol. Struct. T. 939 106–111

    Article  CAS  Google Scholar 

  • Felder D, Carreon MD, Gallani JL, Guillon D, Nierengarten JF, Thierry C and Deschenaux R 2001 Amphiphilic fullerene-cholesterol derivatives: Synthesis and preparation of Langmuir and Langmuir-Blodgett Films. Helv. Chim. Acta 84 1119–1132

    Article  CAS  Google Scholar 

  • Florian J, Hrouda V and Hobza P 1994 Proton Transfer in the Adenine–thymine Base Pair. J. Am. Chem. Soc. 116 1457–1460

    Article  CAS  Google Scholar 

  • Florian J and Leszczynski J 1996 Spontaneous DNA mutations induced by proton transfer in the guanine-cytosine base pairs: an energetic perspective. J. Am. Chem. Soc. 118 3010–3017

    Article  CAS  Google Scholar 

  • Freixas F, Matito E, Poater J and Sola M 2008 On the performance of some aromaticity indices: A critical assessment using a test set. J. Comput. Chem. 29 1543–1554

    Article  Google Scholar 

  • Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, et al. 2004 Gaussian 03, Revision C.02 (Wallingford CT: Gaussian, Inc)

    Google Scholar 

  • Goyal RN, Chatterjee S, Rana ARS and Chasta H 2011 Application of modified pyrolytic graphite electrode as a sensor in the simultaneous assay of adenine and adenosine monophosphate. Sens. Actuators B 156 198–203

    Article  CAS  Google Scholar 

  • Guerra CF, Bickelhaupt FM, Saha S and Wang F 2006 Adenine tautomers: relative stabilities, ionization energies, and mismatch with cytosine. J. Phys. Chem. A 110 4012–4020

    Article  CAS  Google Scholar 

  • Izmaylov AF and Scuseria GE 2008 Why are time-dependent density functional theory excitations in solids equal to band structure energy gaps for semilocal functionals, and how does nonlocal Hartree–Fock-type exchange introduce excitonic effects? J. Chem. Phys. 129 034101–034111

    Article  PubMed  Google Scholar 

  • Janthon P, Vines F, Kozlov SM, Limtrakul J and Illas F 2013 Theoretical assessment of grapheme-metal contacts. J. Chem. Phys. 138 244701–244708

    Article  PubMed  Google Scholar 

  • Jiao D, Wang H, Zhang Y and Tang Y 2009 A DFT study of thymine and its tautomers. Canadian J. Chem. 87 406–415

    Article  CAS  Google Scholar 

  • Karlin KD and Tyeklar Z 1993 Bioinorganic Chemistry of Copper (New York: Chapman & Hall)

    Book  Google Scholar 

  • Krainara N, Nokbin S, Luksirikul P, Sirijaraensre J, Meemanvit R, Khongpracha P, Pantu P and Limtrakul J 2007 Paper presented at the 2007 NSTI Nanotechnology Conference and Trade Show, NSTI Nanotech 2007, Technical Proceedings, Santa Clara, CA

  • Krainara N, Illas F and Limtrakul J 2012 Interaction of adenine Cu (II) complexes with BN-doped fullerene differentiates electronically equivalent tautomers. Chem. Phys. Lett. 537 88–93

    Article  CAS  Google Scholar 

  • Lamsabhi AM, Alcami M, Mo O, Yañez M and Tortajada J 2004 Association of Cu2+ with uracil and its thio derivatives: a theoretical study. Chem. Phys. Chem. 5 1871–1878

    CAS  PubMed  Google Scholar 

  • Lamsabhi AM, Alcami M, Mo O, Yañez M and Tortajada J 2006 Gas-phase deprotonation of uracil−Cu2+ and thiouracil−Cu2+ complexes. J. Phys. Chem. A 110 1943–1950

    Article  CAS  PubMed  Google Scholar 

  • Lamsabhi AM, Alcami M, Mo O, Yañez M, Tortajada J and Salpin JY 2007 Unimolecular reactivity of uracil–Cu2+ complexes in the gas phase. Chem. Phys. Chem. 8 181–187

    CAS  PubMed  Google Scholar 

  • Lee C, Yang W and Parr RG 1988 Development of the colle-salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37 785–789

    Article  CAS  Google Scholar 

  • Luna A, Alcami M, Mo O and Yañez M 2000 Cu+ binding energies. Dramatic failure of the G2 method vs. good performance of the B3LYP approach. Chem. Phys. Lett. 320 129–138

    Article  CAS  Google Scholar 

  • Mirkin A and Caldwell WB 1996 Thin film, fullerene-based materials. Tetrahedron 52 5113–5130

    Article  CAS  Google Scholar 

  • Nierengarten JF 2000 Fullerodendrimers: a new class of compounds for supramolecular chemistry and materials science applications. Chem. Eur. J. 6 3667–3670

    Article  CAS  PubMed  Google Scholar 

  • Noguera M, Bertran J and Sodupe M 2004 A Quantum chemical study of Cu2+ interacting with guanine−cytosine base pair. Electrostatic and oxidative effects on intermolecular proton- transfer processes. J. Phys. Chem. A 108 333–341

    Article  CAS  Google Scholar 

  • Noguera M, Bertran J and Sodupe M 2008 Cu2+/+ cation coordination to adenine−thymine base pair. Effects on intermolecular proton-transfer processes. J. Phys. Chem. B 112 4817–4825

    Article  CAS  PubMed  Google Scholar 

  • Nowak MJ, Lapinski L, Kwiatkowski JS and Leszczynski J 1996 Molecular structure and infrared spectra of adenine. Experimental matrix isolation and density functional theory study of adenine 15N isotopomers. J. Phys. Chem. 100 3527–3534

    Article  CAS  Google Scholar 

  • Pray L 2008 DNA replication and causes of mutation, Nature Education 1(1)

  • Reed AE, Weinstock RB and Weinhold F 1985 Natural population analysis. J. Chem. Phys. 83 735–746

    Article  CAS  Google Scholar 

  • Sheng R, Ni F and Cotton TM 1991 Determination of purine bases by reversed phase high performance liquid chromatography using real time surface enhanced Raman spectroscopy. Anal. Chem. 63 437–442

    Article  CAS  Google Scholar 

  • Sponer J, Burda JV, Sabat M, Leszczynki J and Hobza P 1998a Interaction between the guanine−cytosine watson−crick DNA base pair and hydrated Group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and Group IIb (Zn2+, Cd2+, Hg2+) metal cations. J. Phys. Chem. A 102 5951–5957

    Article  CAS  Google Scholar 

  • Sponer J, Sabat M, Burda JV, Doody AM, Leszczynki J and Hobza P 1998b Stabilization of the purine. Purine. Pyrimidine DNA base triplets by divalent metal cations. J. Biomol. Struct. Dyn. 16 139–143

    Article  CAS  PubMed  Google Scholar 

  • Sponer J, Sponer JE, Gorb L, Leszczynski J and Lippert B 1999 Metal-stabilized rare tautomers and mispairs of DNA bases: N6-metalated adenine and N4-metalated cytosine, theoretical and experimental views. J. Phys. Chem. A 103 11406–11413

    Article  CAS  Google Scholar 

  • Tehrani ZA, Fattahi A and Pourjavadi A 2009 Interaction of Mg2+, Ca2+, Zn2+ and Cu+ with cytosine nucleosides: Influence of metal on sugar puckering and stability of N-glycosidic bond, a DFT study. J. Mol. Struct. THEOCHEM 913 117–125

    Article  CAS  Google Scholar 

  • Tkeshelashvili LK, McBride T, Spence K and Loeb LA 1991 Mutation spectrum of copper induced DNA damage. J. Biol. Chem. 266 6401–6406

    CAS  PubMed  Google Scholar 

  • Trujillo C, Lamsabhi AM, Mo O and Yañez M 2008 The importance of the oxidative character of doubly charged metal cations in binding neutral bases. [Urea-M]2+ and [thiourea-M]2+ (M =Mg, Ca, Cu) complexes. Phys. Chem. Chem. Phys. 10 3229–3235

    Article  CAS  PubMed  Google Scholar 

  • Wang HS, Ju HX and Chen HY 2002 Simultaneous determination of guanine and adenine in DNA using an electrochemically pretreated glassy carbon electrode. Anal. Chim. Acta 461 243–250

    Article  CAS  Google Scholar 

  • Wiberg KB 1968 Application of the pople-santry-segal CNDO method to the cyclopropylcarbinyl and cyclobutyl cation and to bicyclobutane. Tetrahedron 24 1083–1096

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors (SAS, NB and AA) would like to acknowledge the support of the Ministry of Higher Education, Kingdom of Saudi Arabia, for supporting this research through a grant (PCSED-012-12) under the Promising Centre for Sensors and Electronic Devices at Najran University, Saudi Arabia.

Author information

Authors and Affiliations

  1. Promising Centre for Sensors and Electronic Devices, Najran University, Najran, KSA

    Shamoon Ahmad Siddiqui, Nadir Bouarissa & A Al-Hajry

  2. Department of Physics, College of Arts and Science, Najran University, Najran, KSA

    Shamoon Ahmad Siddiqui, Nadir Bouarissa & A Al-Hajry

  3. Department of Applied Sciences, School of Engineering and Technology, Sharda University, Greater Noida, 201 306, India

    Tabish Rasheed

Authors
  1. Shamoon Ahmad Siddiqui
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nadir Bouarissa
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tabish Rasheed
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. A Al-Hajry
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shamoon Ahmad Siddiqui.

Additional information

Corresponding editor: B JAGADEESHWAR RAO

MS received 06 November 2013; accepted 12 August 2014

Corresponding editor:B Jagadeeshwar Rao

[Siddiqui SA, Bouarissa N, Rasheed T and Al-Hajry A 2014 Quantum chemical investigations of AlN-doped C60 for use as a nano-biosensor in detection of mispairing between DNA bases. J. Biosci. 39 1–9] DOI 10.1007/s12038-014-9475-3

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Siddiqui, S.A., Bouarissa, N., Rasheed, T. et al. Quantum chemical investigations of AlN-doped C60 for use as a nano-biosensor in detection of mispairing between DNA bases. J Biosci 39, 761–769 (2014). https://doi.org/10.1007/s12038-014-9475-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12038-014-9475-3

Keywords

Search

Navigation