JBPC  Vol.2 No.2 , May 2011
Analytical consideration of the selectivity of oligonucleotide hybridization
Abstract: Systematic analysis of factors determining efficiency in discrimination of a point substitution (SNP) within specific DNA sequences was carried out in the context of hybridization approach. There are two types of selectivity that are critical for the rational design of highly specific oligonucleotides probes. The first type is the real selectivity of hybridization (fa) that is the ratio of association degrees of targets with an oligonucleotide probe upon the perfect and imperfect complex formation. This type of selectivity reflects the level of discrimination between matched and mismatched signals, which is determined both by experimental conditions and the thermodynamics of oligonucleotide hybridization. The second parameter characterizing the efficiency of SNP discrimination is the limit selectivity of hybridization, which determines the utmost value of fa at a given temperature. This value can be calculated as the ratio of corresponding equilibrium association constants of perfect and imperfect complex formation determined purely by thermodynamics. We have shown that the fa function is the most reliable characteristic describing the hybridization selectivity. For the analytical system designed to reveal any type of perturbation in DNA (e.g. SNP or modification), there is usually a temperature at which fa has its maximum value. The dependency of the fa maximum on different experimental parameters as well as the structural characteristics of a probe are described in details. The results allowed us to postulate points of principle to rationally design the most selective probes on the basis of oli- gonucleotides or their derivatives.
Cite this paper: nullKabilov, M. and Pyshnyi, D. (2011) Analytical consideration of the selectivity of oligonucleotide hybridization. Journal of Biophysical Chemistry, 2, 75-91. doi: 10.4236/jbpc.2011.22011.

[1]   Southern, E.M. (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. Journal of Molecular Biology, 98, 503-517. doi:10.1016/S0022-2836(75)80083-0

[2]   Wetmur, J.G. (1991) DNA probes: Applications of the principles of nucleic acid hybridization. Critical Reviews in Biochemistry and Molecular Biology, 26, 227-259. doi:10.3109/10409239109114069

[3]   Knorre, D.G. and Vlassov, V.V. (1991) Reactive oligonucleotide derivatives as gene-targeted biologically active com- pounds and affinity probes. Genetica, 85, 53-63. doi:10.1007/BF00056106

[4]   Mouritzen, P., Nielsen, A.T., Pfundheller, H.M., Choleva, Y., Kongsbak, L. and Moller, S. (2003) Single nucleotide polymorphism genotyping using locked nucleic acid (LNA). Expert Review of Molecular Diagnostics, 3, 27-38. doi:10.1586/14737159.3.1.27

[5]   Kofiadi, I.A. and Rebrikov, D.V. (2006) Methods for detecting single nucleotide polymorphisms: Allele-specific PCR and hybridization with oligonucleotide probe. Genetika, 42, 22-32.

[6]   Marras, S.A., Tyagi, S. and Kramer, F.R. (2006) Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. Clinical Chimica Acta, 363, 48-60 doi:10.1016/j.cccn.2005.04.037

[7]   Maskos, U. and Southern, E.M. (1992) Parallel analysis of oligodeoxyribonucleotide (oligonucleotide) interactions. I. Analysis of factors influencing oligonucleotide duplex formation. Nucleic Acids Research, 20, 1675-1678. doi:10.1093/nar/20.7.1675

[8]   Relogio, A., Schwager, C., Richter, A., Ansorge, W. and Valcarcel, J. (2002) Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Research, 30, pp. e51. doi:10.1093/nar/30.11.e51

[9]   Sorokin, N.V., Chechetkin, V.R., Livshits, M.A., Pankov, S.V., Donnikov, M.Y., Gryadunov, D.A., Lapa, S.A. and Zasedatelev, A.S. (2005) Discrimination between perfect and mismatched duplexes with oligonucleotide gel microchips: Role of thermodynamic and kinetic effects during hybridization. Journal of Biomolecular Structure and Dynamics, 22, 725-734.

[10]   Roberts, R.W. and Crothers, D.M. (1991) Specificity and stringency in DNA triplex formation. Proceedings of the National Academy of Sciences of the U.S.A., 88, 9397-9401.

[11]   Bonnet, G. Tyagi,, S., Libchaber, A. and Kramer, F.R. (1999) Thermodynamic basis of the enhanced specificity of structured DNA probes. Proceedings of the National Academy of Sciences of the U.S.A., 96, 6171-6176. doi:10.1073/pnas.96.11.6171

[12]   Tsourkas, A., Behlke, M.A., Rose, S.D. and Bao, G. (2003) Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Research, 31, 1319-1330. doi:10.1093/nar/gkg212

[13]   Livshits, M.A., Ivanov, I.B., Mirzabekov, A.D. and Florent’ev, V.L. (1992) DNA sequencing by hybridization with an oligonucleotide matrix (SHOM). The theory of DNA elution after hybridization. Molekuliarnaia Biologiia (Moskva), 26, 1298-1313.

[14]   Dai, H., Meyer, M., Stepaniants, S., Ziman, M. and Stoughton, R. (2002) Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays. Nucleic Acids Research, 30, e86. doi:10.1093/nar/gnf085

[15]   Bishop, J., Blair, S. and Chagovetz, A.M. (2006) A competitive kinetic model of nucleic acid surface hybridization in the presence of point mutants. Biophysical Journal, 90, 831-840. doi:10.1529/biophysj.105.072314

[16]   Bishop, J., Chagovetz, A.M. and Blair, S. (2008) Kinetics of multiplex hybridization: Mechanisms and implications. Biophysical Journal, 94, 1726-1734. doi:10.1529/biophysj.107.121459

[17]   Lucarelli, F., Marrazza, G. and Mascini, M. (2007) Design of an optimal allele-specific oligonucleotide probe for the efficient discrimination of a thermodynamically stable (G x T) mismatch. Analitica Chimica Acta, 603, 82-86. doi:10.1016/j.aca.2007.09.047

[18]   Parinov, S., Barsky, V., Yershov, G., Kirillov, E., Timofeev, E., Belgovskiy, A. and Mirzabekov, A. (1996) DNA sequencing by hybridization to microchip octa and decanucleotides extended by stacked pentanucleotides. Nucleic Acids Research, 24, 2998-3004. doi:10.1093/nar/24.15.2998

[19]   Pyshnyi, D.V., Lokhov, S.G., Podyminogin, M.A., Ivanova, E.M. and Zarytova, V.F. (2000) A new strategy of discrimination of a point mutation by tandem of short oligonucleotides. Nucleosides Nucleotides Nucleic Acids, 19, 1931-1941. doi:10.1080/15257770008045469

[20]   Maldonado-Rodriguez, R. and Beattie, K.L. (2001) Analysis of nucleic acids by tandem hybridization on oligonucleotide microarrays. Methods in Molecular Biology, 170, 157-171.

[21]   Pyshnyi, D.V., Goldberg, E.L. and Ivanova, E.M. (2003) Efficiency of coaxial stacking depends on the DNA duplex structure. Journal of Biomolecular Structure and Dynamics, 21, 459-468.

[22]   Storhoff, J.J., Elghanian, R., Mucic, R.C., Mirkin, C.A. and Letsinger, R.L. (1998) One-pot colorimetric differentiation of polynucleotides with single base imperfections using gold nanoparticle probes. Journal of the American Chemical Society, 120, 1959-1964. doi:10.1021/ja972332i

[23]   Dubertret, B., Calame, M. and Libchaber, A.J. (2001) Single-mismatch detection using gold-quenched fluorescent oligonucleotides. Nature Biotechnology, 19, 365-370. doi:10.1038/86762

[24]   Harris, N.C. and Kiang, C.H. (2006) Defects can increase the melting temperature of DNA-nanoparticle assemblies. The Journal of Physical Chemistry B, 110, 16393-16396. doi:10.1021/jp062287d

[25]   Ratilainen, T., Holmen, A., Tuite, E., Nielsen, P.E. and Norden, B. (2000) Thermodynamics of sequence-specific binding of PNA to DNA. Biochemistry, 39, 7781-7791. doi:10.1021/bi000039g

[26]   Narayan, C.C. and Eric, T.K. (1995) Very High affinity DNA Recognition by bicyclic and cross-linked oligo- nucleotides. Journal of the American Chemical Society, 117, 10434-10442. doi:10.1021/ja00147a004

[27]   Wang, S., Friedman, A.E. and Kool, E.T. (1995) Origins of high sequence selectivity: A stopped-flow kinetics study of DNA/RNA hybridization by duplex- and triplex-forming oligonucleotides. Biochemistry, 34, 9774-9784. doi:10.1021/bi00030a015

[28]   Kutyavin, I.V., Afonina, I.A., Mills, A., Gorn, V.V., Lukhtanov, E.A., Belousov, E.S., Singer, M.J., Walburger, D.K., Lokhov, S.G., Gall, A.A., Dempcy, R., Reed, M.W., Meyer, R.B. and Hedgpeth, J. (2000) 3’-minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Research, 28, 655-661. doi:10.1093/nar/28.2.655

[29]   Abramov, M., Schepers, G., Van Aerschot, A., Van Hummelen, P. and Herdewijn, P. (2008) HNA and ANA high-affinity arrays for detections of DNA and RNA single-base mismatches. Biosensors and Bioelectronics, 23, 1728-1732. doi:10.1016/j.bios.2008.01.033

[30]   Guo, Z., Liu, Q. and Smith, L.M. (1997) Enhanced discri- mination of single nucleotide polymorphisms by artificial mismatch hybridization. Nature Biotechnology, 15, 331-335. doi:10.1038/nbt0497-331

[31]   Burgner, D., D’Amato, M., Kwiatkowski, D.P. and Loakes, D. (2004) Improved allelic differentiation using sequence-specific oligonucleotide hybridization incorporating an additional base-analogue mismatch. Nucleosides Nucleotides Nucleic Acids, 23, 755-765. doi:10.1081/NCN-120039216

[32]   Pyshnaya, I.A., Pyshnyi, D.V., Lomzov, A.A., Zarytova, V.F. and Ivanova, E.M. (2004) The influence of the non-nucleotide insert on the hybridization properties of oligonucleotides. Nucleosides Nucleotides Nucleic Acids, 23, 1065-1071. doi:10.1081/NCN-200026073

[33]   Pyshnyi, D.V., Lomzov, A.A., Pyshnaya, I.A. and Ivanova, E.M. (2006) Hybridization of the bridged oligonucleotides with DNA: Thermodynamic and kinetic studies. Journal of Biomolecular Structure and Dynamics, 23, 567-580.

[34]   Jacobsen, N., Bentzen, J., Meldgaard, M., Jakobsen, M.H., Fenger, M., Kauppinen, S. and Skouv, J. (2002) LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E. Nucleic Acids Research, 30, e100. doi:10.1093/nar/gnf099

[35]   Jacobsen, N., Fenger, M., Bentzen, J., Rasmussen, S.L., Jakobsen, M.H., Fenstholt, J. and Skouv, J. (2002) Genotyping of the apolipoprotein B R3500Q mutation using immobilized locked nucleic acid capture probes. Clinical Chemistry, 48, 657-660.

[36]   Seela, F., Peng, X. and Li, H. (2005) Base-pairing, tautomerism, and mismatch discrimination of 7-halogenated 7-deaza-2’-deoxyisoguanosine: Oligonucleotide duplexes with parallel and antiparallel chain orientation. Journal of the American Chemical Society, 127, 7739-7751. doi:10.1021/ja0425785

[37]   You, Y., Moreira, B.G., Behlke, M.A. and Owczarzy, R. (2006) Design of LNA probes that improve mismatch discrimination. Nucleic Acids Research, 34, e60. doi:10.1093/nar/gkl175

[38]   Lai, J.S. and Kool, E.T. (2004) Selective pairing of poly- fluorinated DNA bases. Journal of the American Chemical Society, 126, 3040-3041. doi:10.1021/ja039571s

[39]   Gao, J., Liu, H. and Kool, E.T. (2004) Expanded-size bases in naturally sized DNA: Evaluation of steric effects in Watson-Crick pairing. Journal of the American Chemical Society, 126, 11826-11831. doi:10.1021/ja048499a

[40]   Liu, H., Gao, J. and Kool, E.T. (2005) Helix-forming properties of size-expanded DNA, an alternative four-base genetic form. Journal of the American Chemical Society, 127, 1396-1402. doi:10.1021/ja046305l

[41]   Gong, J. and Sturla, S.J. (2007) A synthetic nucleoside probe that discerns a DNA adduct from unmodified DNA. Journal of the American Chemical Society, 129, 4882-4883. doi:10.1021/ja070688g

[42]   Monia, B.P., Johnston, J.F., Ecker, D.J., Zounes, M.A., Lima, W.F. and Freier, S.M. (1992) Selective inhibition of mutant Ha-ras mRNA expression by antisense oligonucleotides. The Journal of Biological Chemistry, 267, 19954-19962.

[43]   Hearst, J.E. (1988) A photochemical investigation of the dynamics of oligonucleotide hybridization. Annual Review of Physical Chemistry, 39, 291-315. doi:10.1146/annurev.pc.39.100188.001451

[44]   Shortreed, M.R., Chang, S.B., Hong, D.,. Phillips, M, Campion, B., Tulpan, D.C., Andronescu, M., Condon, A., Hoos, H.H. and Smith, L.M. (2005) A thermodynamic approach to designing structure-free combinatorial DNA word sets. Nucleic Acids Research, 33, 4965-4977. doi:10.10Xar/gki812

[45]   SantaLucia Jr., J. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proceedings of the National Academy of Sciences of the U.S.A., 95, 1460-1465. doi:10.1073/pnas.95.4.1460

[46]   Allawi, H.T. and SantaLucia Jr., J. (1997) Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry, 36, 10581-10594. doi:10.1021/bi962590c

[47]   Allawi, H.T. and SantaLucia Jr., J. (1998) Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: Sequence dependence and pH effects. Biochemistry, 37, 9435-9444. doi:10.1021/bi9803729

[48]   Allawi, H.T. and SantaLucia Jr., J. (1998) Thermodynamics of internal C.T mismatches in DNA. Nucleic Acids Reseach, 26, 2694-2701. doi:10.1093/nar/26.11.2694

[49]   Allawi, H.T. and SantaLucia Jr., J. (1998) Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA. Biochemistry, 37, 2170-2179. doi:10.1021/bi9724873

[50]   Peyret, N., Seneviratne, P.A., Allawi, H.T. and SantaLucia Jr., J. (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. Biochemistry, 38, 3468-3477. doi:10.1021/bi9825091

[51]   Vessman, J., Stefan, R.I., Van Staden, J.F., Danzer, K., Lindner, W., Burns, D.T., Fajgelj, A. and Muller, H. (2001) Selectivity in analytical chemistry. Pure and Applied Chemistry, 73, 1381-1386. doi:10.1351/pac200173081381

[52]   Von Hippel, P.H. and Berg, O.G. (1986) On the specificity of DNA-protein interactions. Proceedings of the National Academy of Sciences of the U.S.A., 83, 1608-1612. doi:10.1073/pnas.83.6.1608

[53]   SantaLucia Jr., J. and Hicks, D. (2004) The thermodynamics of DNA structural motifs. Annual Review of Biophysics and Biomolecular Structure, 33, 415-440. doi:10.1146/annurev.biophys.32.110601.141800

[54]   Urakawa, H., El, F.S., Smidt, H., Smoot, J.C., Tribou, E.H., Kelly, J.J., Noble, P.A. and Stahl, D.A. (2003) Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Applied and Environmental Microbiology, 69, 2848-2856. doi:10.1128/AEM.69.5.2848-2856.2003

[55]   Demidov, V.V. and Frank-Kamenetskii, M.D. (2004) Two sides of the coin: affinity and specificity of nucleic acid interactions. Trends in Biochemical Sciences, 29, 62-71. doi:10.1016/j.tibs.2003.12.007

[56]   Barnes III, T.W. and Turner, D.H. (2001) C5-(1-propynyl)-2’-deoxy-pyrimidines enhance mismatch penalties of DNA:RNA duplex formation. Biochemistry, 40, 12738-12745. doi:10.1021/bi011033+

[57]   Peng, X., Li, H. and Seela, F. (2006) pH-Dependent mismatch discrimination of oligonucleotide duplexes containing 2’-deoxytubercidin and 2- or 7-substituted derivatives: Protonated base pairs formed between 7-deazapurines and cytosine. Nucleic Acids Research, 34, 5987-6000.