PL EN


Preferences help
enabled [disable] Abstract
Number of results
2008 | 55 | 4 | 713-720
Article title

Effects of mismatches and insertions on discrimination accuracy of nucleic acid probes

Content
Title variants
Languages of publication
EN
Abstracts
EN
Effective discrimination of non-complementary nucleotides is an important factor to ensure the accuracy of hybridization-based nucleic acid analyses. The current study investigates the effects of the chemical nature, the positions, the numbers, and the cooperative behavior of mismatches as well as insertions on 20-mer and 30-mer duplexes. We observed the hybridization stability trend affected by mismatches: G:T ≈ G:G > G:A > A:A ≈ T:T > A:C ≈ T:C > C:C. The experimental data show that mismatches at the center of the oligonucleotide probes have a more profound destabilizing effect on the hybridization stability than those at either ends. Insertions also demonstrate a similar destabilizing effect as mismatches. These results provide useful information for designing DNA microarray nucleotide probes and for improving the discrimination accuracy of hybridization-based detections.
Publisher

Year
Volume
55
Issue
4
Pages
713-720
Physical description
Dates
published
2008
received
2008-06-06
revised
2008-10-20
accepted
2008-11-19
(unknown)
2008-11-28
Contributors
author
  • Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, China
author
  • Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, China
  • Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, China
author
  • Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, China
author
  • Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, China
References
  • Allawi HT, SantaLucia J Jr (1998) Nearest neighbor thermodynamic parameters for internal G·A mismatches in DNA. Biochemistry 37: 2170-2179
  • Berns A (2000) Cancer - gene expression in diagnosis. Nature 403: 491-492.
  • Blohm DH, Guiseppi-Elie A (2001) New developments in microarray technology. Curr Opin Biotech 12: 41-47.
  • Boulard Y, Cognet JA, Fazakerley GV (1997) Solution structure as a function of pH of two central mismatches, C·T and C·C, in the 29 to 39 K-ras gene sequence, by nuclear magnetic resonance and molecular dynamics. J Mol Biol 268: 331-347.
  • Brookes AJ (1999) The essence of SNPs. Gene 234: 177-186.
  • Brown T, Hunter WN, Kneale G, Kennard O (1986) Molecular structure of the G·A base pair in DNA and its implications for the mechanism of transversion mutations. Proc Natl Acad Sci USA 83: 2402-2406
  • Cheng L, Wing HW (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98: 31-36.
  • Cognet JA, Arpa JG, Le Bret M, Marel GA, Boom JH, Fazakerley GV (1991) Solution conformation of an oligonucleotide containing a G·G mismatch determined by nuclear magnetic resonance and molecular mechanics. Nucleic Acids Res 19: 6771-6779.
  • Debouck C, Goodfellow PN (1999) DNA microarrays in drug discovery and development. Nat Genet 21: 48-50.
  • Fersht AR, Knill-Jones JW, Tsui WC (1982) Kinetic basis of spontaneous mutation misinsertion frequencies, proofreading specificities and cost of proofreading by DNA polymerases of Escherichia coli. J Mol Biol 156: 37-51.
  • Gao Xl, Patel DJ (1987) NMR Studies of A·C mismatches in DNA dodecanucleotides at acidic pH. J Biol Chem 262: 16973-16984.
  • Huertas D, Bellsolell L, Casasnovas JM, Coll M, Azorín F (1993) Alternating d(GA)n DNA sequences form antiparallel stranded homoduplexes stabilized by the formation of G·A base pairs. EMBO J 12: 4029-4038.
  • Hunter WN, Brown T, Kennard O (1987a) Structural features and hydration of a dodecamer duplex containing two C·A mispairs. Nucleic Acids Res 15: 6589-6605.
  • Hunter WN, Brown T, Kneale G, Anand NN, Rabinovich D, Kennard O (1987b) The structure of guanosine-thymidine mismatches in B-DNA at 2.5-Å resolution. J Biol Chem 262: 9962-9970.
  • Ikuta S, Takagi K, Wallace RB, Itakura K (1987) Dissociation kinetics of 19 base paired oligonucleotide-DNA duplexes containing different single mismatched base pairs. Nucleic Acids Res 15: 797-811.
  • Jaishree TN, Wang AH (1993) NMR studies of pH-dependent conformational polymorphism of alternating (C-T)n sequences. Nucleic Acids Res 21: 3839-3844.
  • Kennerson ML, Warburton T, Nelis E, Brewer M, Polly P, De Jonghe P, Timmerman V, Nicholson GA (2007) Mutation scanning the GJB1 gene with high-resolution melting analysis: implications for mutation scanning of genes for Charcot-Marie-Tooth disease. Clin Chem 53: 349-352.
  • Ke SH, Wartell RM (1993) Influence of nearest neighbor sequence on the stability of base pair mismatches in long DNA: determination by temperature-gradient gel electrophoresis. Nucleic Acids Res 21: 5137-5143.
  • Kramer B, Kramer W, Fritz HJ (1984) Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of E. coli. Cell 38: 879-887.
  • Lane AN, Jenkins TC, Brown DJS, Brown T (1991) N.m.r. determination of the solution conformation and dynamics of the A·G mismatch in the d(CGCAAATTGGCG)2 dodecamer. Biochem J 279: 269-281.
  • Laurie AD, Smith MP, George PM (2007) Detection of factor viii gene mutations by high-resolution melting analysis. Clin Chem 53: 2211-2214.
  • Leonard GA, Thomson J, Watson WP, Brown T (1990) High-resolution structure of a mutagenic lesion in DNA. Proc Natl Acad Sci USA 87: 9573-9576.
  • Liew M, Seipp M, Durtschi J, Margraf RL, Dames S, Erali M, Voelkerding K, Wittwer C (2007) Closed-Tube SNP genotyping without labeled probes: a comparison between unlabeled probe and amplicon melting. Am J Clin Pathol 127: 341-348.
  • Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14: 1675-1680.
  • Lu AL, Welsh K, Clark S, Su SS, Modrich P (1984) Repair of DNA base-pair mismatches in extracts of Escherichia colii. Cold Spring Harbor Symp. Quant. Biol 49: 589-596
  • Marx J (2000) DNA arrays reveal cancer in its many forms. Science 289: 1670-1672.
  • Skelly JV, Edwards KJ, Jenkins TC, Neidle S (1993) Crystal structure of an oligonucleotide duplex containing G·G base pairs: influence of mispairing on DNA backbone conformation. Proc Natl Acad Sci USA 90: 804-808.
  • Tikhomirova A, Beletskaya IV, Chalikian TV (2006) Stability of DNA duplexes containing GG, CC, AA, and TT mismatches. Biochemistry 45: 10563-10571.
  • Trotta E, Paci M (1998) Solution structure of DAP1 selectively bound in the minor groove of a DNA T·T mismatch-containing site: NMR and molecular dynamics studys. Nucleic Acids Res 26: 4706-4713.
  • Zhen G, Liu QH, Smith LM (1997) Enhanced discrimination of single nucleotide polymorphisms by artificial mismatch hybridization. Nat Biotechnol 15: 331-335.
Document Type
Publication order reference
Identifiers
YADDA identifier
bwmeta1.element.bwnjournal-article-abpv55p713kz
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.