Influence of Magnetic Microparticles Isolation on Adenine Homonucleotides Structure

. 2014 Feb 25 ; 7 (3) : 1455-1472. [epub] 20140225

Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid28788525

The electroactivity of purine and pyrimidine bases is the most important property of nucleic acids that is very useful for determining oligonucleotides using square wave voltammetry. This study was focused on the electrochemical behavior of adenine-containing oligonucleotides before and after their isolation using paramagnetic particles. Two peaks were detected-peak A related to the reduction of adenine base and another peak B involved in the interactions between individual adenine strands and contributes to the formation of various spatial structures. The influence of the number of adenine bases in the strand in the isolation process using paramagnetic particles was investigated too.

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Watson J.D., Crick F.H. Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature. 1953;171:737–738. PubMed

Cortesi R., Campioni M., Ravani L., Drechsler M., Pinotti M., Esposito E. Cationic lipid nanosystems as carriers for nucleic acids. New Biotech. 2014;31:44–54. PubMed

Goncharova I. Ag(I)-mediated homo and hetero pairs of guanosine and cytidine: Monitoring by circular dichroism spectroscopy. Spectrochim. Acta A Mol. Biomol. Spectrosc. 2014;118:221–227. PubMed

Choi J.K., Reed A., Balaz M. Chiroptical properties, binding affinity, and photostability of a conjugated zinc porphyrin dimer complexed with left-handed Z-DNA and right-handed B-DNA. Dalton Trans. 2014;43:563–567. PubMed

Thomas J.M., Yu H.-Z., Sen D. DNA electronic switches based on analyte-responsive aptamers. Methods Mol. Biol. 2014;1103:267–276. PubMed

Von Hippel P.H., Johnson N.P., Marcus A.H. Fifty years of DNA “breathing”: Reflections on old and new approaches. Biopolymers. 2013;99:923–954. PubMed PMC

Palecek E., Bartosik M. Electrochemistry of Nucleic Acids. Chem. Rev. 2012;112:3427–3481. PubMed

Palecek E. Oszillographische polarographie der nucleinsauren und ihrer bestandteile. Naturwissenschaften. 1958;45:186–187. (in German)

Palecek E. Oscillographic polarography of highly polymerized deoxyribonucleic acid. Nature. 1960;188:656–657. PubMed

Palecek E. Oszillographische polarographie der ucleinsaurekomponenten. Collect. Czech Chem. Commun. 1960;25:2283–2289. (in German)

Palecek E. Oscillographic polarography of deoxyribonucleic and apurinic acids. Biochem. Mosc. 1960;25:619–624.

Palecek E. Past, present and future of nucleic acids electrochemistry. Talanta. 2002;56:809–819. PubMed

Palecek E. Fifty Years of Nucleic Acid Electrochemistry. Electroanalysis. 2009;21:239–251.

Hynek D., Prasek J., Koudelka P., Chomoucka J., Trnkova L., Adam V., Hubalek J., Kizek R. Advantages and progress in the analysis of DNA by using mercury and amalgam electrodes—Review. Curr. Phys. Chem. 2011;1:299–324.

Odea J.J., Osteryoung J.G. Characterization of quasi-reversible surface processes by square-wave voltammetry. Anal. Chem. 1993;65:3090–3097.

Osteryoung J., Odea J.J. Square-wave voltammetry. Electroanal. Chem. 1986;14:209–308.

Osteryoung J.G., Osteryoung R.A. Square-wave voltammetry. Anal. Chem. 1985;57:A101–A110.

Bard A.J., Faulkner L.R. Electrochemical Methods—Fundamentals and Applications. Wiley-VCH; New York, NY, USA: 2001.

Huska D., Adam V., Hubalek J., Trnkova L., Eckschlager T., Stiborova M., Provaznik I., Kizek R. Off-line coupling of automated pipetting system with square wave voltammetry as a tool for study of drug-DNA interaction. Chim. Oggi Chem. Today. 2010;28:18–20.

Huska D., Adam V., Krizkova S., Hrabeta J., Eckschlager T., Stiborova M., Kizek R. An electrochemical study of interaction of an anticancer alkaloid ellipticine with DNA. Chim. Oggi Chem. Today. 2010;28:15–17.

Huska D., Hubalek J., Adam V., Kizek R. Miniaturized electrochemical detector as a tool for detection of DNA amplified by PCR. Electrophoresis. 2008;29:4964–4971. PubMed

Huska D., Adam V., Babula P., Hrabeta J., Stiborova M., Eckschlager T., Trnkova L., Kizek R. Square-wave voltammetry as a tool for investigation of doxorubicin interactions with DNA isolated from neuroblastoma cells. Electroanalysis. 2009;21:487–494.

Palecek E., Billova S., Havran L., Kizek R., Miculkova A., Jelen F. DNA hybridization at microbeads with cathodic stripping voltammetric detection. Talanta. 2002;56:919–930. PubMed

Jelen F., Tomschik M., Palecek E. Adsorptive stripping square-wave voltammetry of DNA. J. Electroanal. Chem. 1997;423:141–148.

Mairal T., Ozalp V.C., Sanchez P.L., Mir M., Katakis I., O’Sullivan C.K. Aptamers: Molecular tools for analytical applications. Anal. Bioanal. Chem. 2008;390:989–1007. PubMed

Song K.M., Lee S., Ban C. Aptamers and their biological applications. Sensors. 2012;12:612–631. PubMed PMC

Ni X., Castanares M., Mukherjee A., Lupold S.E. Nucleic acid aptamers: Clinical applications and promising new horizons. Curr. Med. Chem. 2011;18:4206–4214. PubMed PMC

Tombelli S., Minunni A., Mascini A. Analytical applications of aptamers. Biosens. Bioelectron. 2005;20:2424–2434. PubMed

Archer M.J., Lin B.C., Wang Z., Stenger D.A. Magnetic bead-based solid phase for selective extraction of genomic DNA. Anal. Biochem. 2006;355:285–297. PubMed

Cler L., Bu D.W., Lewis C., Euhus D. A comparison of five methods for extracting DNA from paucicellular clinical samples. Mol. Cell. Probes. 2006;20:191–196. PubMed

Ki J.S., Chang K.B., Roh H.J., Lee B.Y., Yoon J.Y., Jang G.Y. Direct DNA isolation from solid biological sources without pretreatments with proteinase-K and/or homogenization through automated DNA extraction. J. Biosci. Bioeng. 2007;103:242–246. PubMed

Becker C., Hodenius M., Blendinger G., Sechi A., Hieronymus T., Muller-Schulte D., Schmitz-Rode T., Zenke M. Uptake of magnetic nanoparticles into cells for cell tracking. J. Magn. Magn. Mater. 2007;311:234–237.

Cao Z.J., Li Z.X., Zhao Y.J., Song Y.M., Lu J.Z. Magnetic bead-based chemiluminescence detection of sequence-specific DNA by using catalytic nucleic acid labels. Anal. Chim. Acta. 2006;557:152–158.

Kim D.K., Zhang Y., Voit W., Rao K.V., Muhammed M. Synthesis and characterization of surfactant-coated superparamagnetic monodispersed iron oxide nanoparticles. J. Magn. Magn. Mater. 2001;225:30–36.

Kinoshita T., Seino S., Mizukoshi Y., Nakagawa T., Yamamoto T.A. Functionalization of magnetic gold/iron-oxide composite nanoparticles with oligonucleotides and magnetic separation of specific target. J. Magn. Magn. Mater. 2007;311:255–258.

Palecek E., Fojta M. Magnetic beads as versatile tools for electrochemical DNA and protein biosensing. Talanta. 2007;74:276–290. PubMed

Ngomsik A.F., Bee A., Draye M., Cote G., Cabuil V. Magnetic nano- and microparticles for metal removal and environmental applications: A review. Comptes Rendus Chim. 2005;8:963–970.

Matsunaga T., Kawasaki M., Yu X., Tsujimura N., Nakamura N. Chemiluminescence enzyme immunoassay using bacterial magnetic particles. Anal. Chem. 1996;68:3551–3554. PubMed

Palecek E., Kizek R., Havran L., Billova S., Fojta M. Electrochemical enzyme-linked immunoassay in a DNA hybridization sensor. Anal. Chim. Acta. 2002;469:73–83.

Masarik M., Huska D., Adam V., Hubalek J., Provaznik I., Trnkova L., Eckschlager T., Stiborova M., Kizek R. Square wave voltammetry as a tool for study of ellipticine-DNA interaction. Int. J. Mol. Med. 2010;26:S46–S46.

Trnkova L., Kizek R., Vacek J. Square wave and elimination voltammetric analysis of azidothymidine in the presence of oligonucleotides and chromosomal DNA. Bioelectrochemistry. 2004;63:31–36. PubMed

Studnickova M., Trnkova L., Zetek J., Glatz Z. Reduction of guanosine at a mercury-electrode. Bioelectrochem. Bioenerg. 1989;21:83–86.

Bartosik M., Palecek E. Square wave stripping voltammetry of unlabeled single- and double-stranded DNAs. Electroanalysis. 2011;23:1311–1319.

Kool E.T. Preorganization of DNA: Design principles for improving nucleic acid recognition by synthetic oligonucleotides. Chem. Rev. 1997;97:1473–1487. PubMed PMC

Morgado C.A., Jurecka P., Svozil D., Hobza P., Sponer J. Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions. Phys. Chem. Chem. Phys. 2010;12:3522–3534. PubMed

Sponer J., Riley K.E., Hobza P. Nature and magnitude of aromatic stacking of nucleic acid bases. Phys. Chem. Chem. Phys. 2008;10:2595–2610. PubMed

Sponer J., Leszczynski J., Hobza P. Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with inclusion of electron correlation. J. Phys. Chem. 1996;100:1965–1974.

Sponer J., Leszczynski J., Hobza P. Hydrogen bonding and stacking of DNA bases: A review of quantum-chemical ab initio studies. J. Biomol. Struct. Dyn. 1996;14:117–135. PubMed

Kurita N., Danilov V.I., Anisimov V.M. The structure of Watson-Crick DNA base pairs obtained by MP2 optimization. Chem. Phys. Lett. 2005;404:164–170.

Asami H., Yagi K., Ohba M., Urashima S., Saigusa H. Stacked base-pair structures of adenine nucleosides stabilized by the formation of hydrogen-bonding network involving the two sugar groups. Chem. Phys. 2013;419:84–89.

Bravaya K.B., Kostko O., Ahmed M., Krylov A.I. The effect of pi-stacking, H-bonding, and electrostatic interactions on the ionization energies of nucleic acid bases: adenine-adenine, thymine-thymine and adenine-thymine dimers. Phys. Chem. Chem. Phys. 2010;12:2292–2307. PubMed

Kabelac M., Hobza P. At nonzero temperatures, stacked structures of methylated nucleic acid base pairs and microhydrated nonmethylated nucleic acid base pairs are favored over planar hydrogen-bonded structures: A molecular dynamics simulations study. Chem. Eur. J. 2001;7:2067–2074. PubMed

Plutzer C., Hunig I., Kleinermanns K. Pairing of the nucleobase adenine studied by IR-UV double-resonance spectroscopy and ab initio calculations. Phys. Chem. Chem. Phys. 2003;5:1158–1163.

Kabelac M., Hobza P. Potential energy and free energy surfaces of all ten canonical and methylated nucleic acid base pairs: Molecular dynamics and quantum chemical ab initio studies. J. Phys. Chem. B. 2001;105:5804–5817.

Huska D., Adam V., Trnkova L., Kizek R. Dependence of adenine isolation efficiency on the chain length evidenced using paramagnetic particles and voltammetry measurements. J. Magn. Magn. Mater. 2009;321:1474–1477.

Hynek D., Krejcova L., Zitka O., Adam V., Trnkova L., Sochor J., Stiborova M., Eckschlager T., Hubalek J., Kizek R. Electrochemical study of doxorubicin interaction with different sequences of single stranded oligonucleotides, Part I. Int. J. Electrochem. Sci. 2012;7:13–33.

Prasek J., Huska D., Jasek O., Zajickova L., Trnkova L., Adam V., Kizek R., Hubalek J. Carbon composite micro- and nano-tubes-based electrodes for detection of nucleic acids. Nanoscale Res. Lett. 2011;6:385–390. PubMed PMC

Huska D., Hubalek J., Adam V., Vajtr D., Horna A., Trnkova L., Havel L., Kizek R. Automated nucleic acids isolation using paramagnetic microparticles coupled with electrochemical detection. Talanta. 2009;79:402–411. PubMed

Long G.L., Winefordner J.D. Limit of detection. Anal. Chem. 1983;55:A712–A724.

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