Single nucleotide polymorphism genotyping by two colour melting curve analysis using the MGB Eclipse™ Probe System in challenging sequence environment
© Henry Stewart Publications 2004
Received: 9 January 2004
Accepted: 9 January 2004
Published: 1 March 2004
Probe and primer design for single nucleotide polymorphism (SNP) detection can be very challenging for A-T DNA-rich targets, requiring long sequences with lower specificity and stability, while G-C-rich DNA targets present limited design options to lower GC-content sequences only. We have developed the MGB Eclipsee™ Probe System, which is composed of the following elements: MGB Eclipse probes and primers, specially developed software for the design of probes and primers, a unique set of modified bases and a Microsoft Excel macro for automated genotyping, which ably solves, in large part, this challenge. Fluorogenic MGB Eclipse probes are modified oligo-nucleotides containing covalently attached duplex-stabilising dihydrocyclopyrroloindole tripeptide (DPI3), the MGB ligand (MGB™ is a trademark of Epoch Biosciences, Bothell, WA), which has the combined properties of allowing the use of short sequences and providing great mismatch discrimination. The MGB moiety prevents probe degradation during polymerase chain reaction (PCR), allowing the researcher to use real time data; alternatively, hybridisation can be accurately measured by a post-PCR two-colour melt curve analysis. Using MGB Eclipse probes and primers containing modified bases further enhances the analysis of difficult SNP targets. G- or C-rich sequences can be refractory to analysis due to Hoogsteen base pairing. Substitution of normal G with Epoch's modified G prevents Hoogsteen base pairing, allowing both superior PCR and probe-based analysis of GC-rich targets. The use of modified A and T bases allows better stabilisation by significantly increasing the Tm of the oligonucleotides. Modified A creates A-T base pairs that have a stability slightly lower than a G-C base pair, and modified T creates T-A base pairs that have a stability about 30 per cent higher than the unmodified base pair. Together, the modified bases permit the use of short probes, providing good mismatch discrimination and primers that allow PCR of refractory targets. The combination of MGB Eclipse probes and primers enriched with the MGB ligand and modified bases has allowed the analysis of refractory SNPs, where other methods have failed.
The MGB moiety at the 5' end of MGB Eclipse probes effectively blocks the exonuclease activity of Taq, preserving the intact probe (Figures 1b and 1c). This allows amplified DNA targets to be accurately genotyped by analysis of the real-time data or by our preferred method, a fluorogenic melt curve analysis. After the completion of PCR, both MGB probes (each with a different fluorescent reporter dye) are annealed to the amplified SNP-containing sequence. The DNA duplexes are denatured over a time course and the decrease in the fluorescent signal of each probe is measured. Comparison of the two-colour melting curves allows differentiation of sequence variants of the target. This melt analysis, following the real-time data analysis, provides further conformation of the genotype call. In concert, the real-time data, the combination of two-colour melt curve analysis, the modified bases and the MGB moiety provide a rich system to specifically detect challenging SNPs. A comparison of real time and melting curve formats is described, and examples of genotyping are discussed.
Materials and methods
Synthesis of fluorogenic MGB probes and PCR primers
Fluorogenic MGB Eclipse probes were synthesised on an MGB-quencher solid support using commercially available reversed 5'-DNA phosphoramidites, as described elsewhere . This approach was taken due to the insolubility of the MGB-quencher and the lack of a corresponding phosphoramidite derivative. Fluorescent reporter groups (fluorescein and 5'-tetrachlorofluorescein) were introduced using the corresponding phosphoramidites. A conventional glycol linker was introduced between the DNA sequence and the fluorescent dye to increase the distance between the fluorescent dye and quencher. MGB Eclipse probes and primers containing modified G (Super G™, Epoch Biosciences, Bothell, WA) were prepared as described elsewhere, using a dimethylformmide (DMF) protecting group. MGB Eclipse probes and primers containing modified A and T (Figure 1d and 1e; Super A™, Super T™, Epoch Biosciences, Bothell, WA) were prepared using conventional DNA synthesis protocols, the probes were synthesised using reversed phosphoramidites and the primers synthesised using forward phosphoramidites (synthesised by methods described in WO 0164958). MGB Eclipse probes were purified by reverse phase HPLC, dried and re-dissolved in 1 × TE buffer. Concentrations were determined by measuring the 340 nm absorbance of the DPI3 chromophore in the MGB Eclipse probe  and were formulated as a 20 × solution (4 μM of each probe). Primers were formulated as a 20 × mixture composed of an excess primer (40 μM) and a limiting primer (2 μM) to ensure the excess synthesis of the target strand for the complementary MGB Eclipse probe.
Probe and primer design
MGB Eclipse probes and primers were designed to SNP-containing target sequences (150 bp up and downstream of the SNP of interest) using the MGB Eclipse™ Design Software 3.0 (http://www.epochbio.com/products/MGBEclipse_Software.htm). This program utilises thermodynamic parameters and nearest neighbour parameters that were determined for the MGB moiety, the Eclipse Dark Quencher and all the modified bases. The software was run in the Express Mode, and in each case the best choice was used for further study.
One hundred and two unrelated Centre d'Etude du Polymorphisme Humain (CEPH) DNA samples were obtained from the Coriell Institute of Medical Research (http://locus.umdnj.edu/) after specifying that the DNA samples were to be used for research purposes only. A list of the templates used is available at http://snp500cancer.nci.nih.gov.
Real time PCR using MGB Eclipse probes
Real time PCR was conducted on either an ABI Prism® 7900 Sequence Detection System (SDS) (Applied Biosystems, Foster City, CA), or on a MJ Research PTC-200 Peltier Thermal Cycler (Waltham, MA) . On both instruments, 50 cycles of a three-step PCR (95°C for five seconds, 58°C for 20 seconds and 76°C for 30 seconds) profile were run after an initial 2 minutes at 95°C. If necessary, fluorescent data were collected at 58°C with an ABI 7900 SDS. Commercially available 2 × Jump Start™ Taq Ready Mix™ for Quantitative PCR with 2 mM final Mg++ concentration (Sigma Catalog #D 74403) supplemented with JumpStart Taq Polymerase (Sigma Catalog #90 4184) to a final amount of 0.37 U/μl was used. The final concentration of both probes was 0.2 μM; the concentration of limiting primer was 0.1 μM and excess primer was 2 μM. Each 5 μl reaction solution contained 10 ng of genomic DNA lyophilised in 96- or 384-well plates with a SPD 1010 SpeedVac® (ThermoSavant, NY) prior to reaction set-up. Routinely, 102 CEPH DNA samples were tested in triplicates using a 384-well plate. A Biomek® 2000 Laboratory Automation Station (Beckman Coulter, USA) was used to set up PCR reactions.
Genotyping analysis using fluorogenic melt curves and MGB Eclipse probes
After completion of PCR, the plate was transferred to the ABI PRISM 7900 SDS (if PCR was performed in an MJ Research Cycler), and the instrument was set for dissociation curve analysis using fluorescein and tetrachlorofluorescein detection. The thermal profile was set using an initial denaturing temp of 95°C for 30 seconds, an annealing temp of 30°C and a final temperature of 80°C. The ramp rate was set to 10 per cent, which is ~1 degree per ten seconds. After reaching the final temperature, the collected data were saved for analysis. Melt curve data can be graphically visualised as the first derivative of the melt curve over temperature. For automated genotyping, the data are exported to Microsoft® Excel (Microsoft Corporation, Redmond, WA) and analysed using the MGB Eclipse Melt Macro available from Epoch Biosciences (http://www.epochbio.com).
Results and discussion
Design of MGB Eclipse probes and primers
SNP detection using fluorogenic probes and PCR requires robust amplification and exquisite ability to distinguish between alleles. Unfortunately, many interesting and important SNPs can be buried in folded or aggregated regions of DNA, making analysis problematic . G-C-rich regions of DNA are especially difficult to amplify and probe, as G bases are prone to forming secondary structures such as G-tetrads (Hoogsteen base pairing) and parallel stranded duplexes [12–15]. Hybridisation assays can be carried out at higher temperatures to melt out complex secondary structures, but this requires probes that bind to the desired DNA strands at these elevated temperatures and often results in mismatches not being detected such as the T-G mismatch (the hardest mismatch to detect). Long probes (20-30 nt) can be used for A-T-rich sequences, but these frequently require very stringent hybridisation conditions to allow the detection of SNPs in DNA duplexes with very small melting temperature differences [9, 16]. We have previously shown that standard probes lacking the MGB moiety don't discriminate well, if at all, if the SNP is located in regions with high AT content .
The use of fluorogenic MGB probes has helped solve the problem of genotyping A-T-rich sequences and this technology has been adopted for use in both TaqMan MGB and MGB Eclipse Systems. For MGB Eclipse, a probe Tm of 59-63°C (with 2.0 mM Mg++ PCR buffer and probe concentrations of 0.2 μM) is used as a default setting in the MGB Eclipse Design Software. This Tm is desirable, since it ensures efficient hybridisation-triggered fluorescence at the middle of the dissociation temperature range (40-80°C), but does not block PCR at the primer extension temperature of 76°C. As described below, actual Tm--as measured by fluorogenic melting curve analysis--is usually lower than calculated, since the concentration of the single strand DNA (ssDNA) target is variable.
Comparison of real time and melting curve SNP assays
The power of a melt curve is in the examination of the signal reported at a range of temperatures for each probe. This allows easy discrimination of the signal for each probe. Any probe bound to a mismatch will necessarily be less thermodynamically stable (usually with Tm about 5-10°C lower) than the same probe bound to a perfect match. By melt curve analysis, a high level of discrimination over a range of temperatures can be utilised to make genotype calls. Genotype calling is highly accurate, since unique melting curve patterns are observed for wild-type, mutant and heterozygous alleles, using two differently labelled MGB Eclipse probes specific for wild-type and mutants, respectively.
The advantage of melting curve analysis over endpoint fluorescence read is that sample-to-sample variations in PCR yield and/or template DNA amount and quality do not affect the Tm of the samples with the same genotype and consequently do not affect genotyping calls. By contrast, endpoint detection makes calls based on final fluorescence intensity after PCR, which strongly depends on the quality of the samples and PCR yield. In some cases, these differences in fluorescence can lead to the wrong genotype call .
MGB Eclipse probes with modified A and T bases for genotyping A-T-rich targets
MGB Eclipse probes with modified G bases for genotyping G-C rich targets
As described earlier, G-C-rich regions of DNA are especially difficult to amplify and probe, since G bases are prone to forming secondary structures such as G-tetrads and parallel stranded duplexes [12–15]. We have reported that formerly inaccessible G-rich probes can be easily prepared using modified G, an analogue of the naturally occurring dG base. Modified G (Super G, also called pyrazolopyrimidine G, PPG, or 8-aza-7deaza-guanine) hybridises with a similar affinity to natural dG, but shows little propensity to form unwanted secondary structures or aggregates . Many of these 'non-ideal' complexes can arise from hydrogen bonding (Hoogsteen bonds) to the N-7 position of guanine. Modified G removes these complexes by exchanging the nitrogen at the 7-position with the carbon at the 8-position of guanine.
Automated genotyping by melting curve analysis on the ABI PRISM 7900
A sample with a value of 1 only in the fluorescein channel is typed as a homozygous allele Fa, while a value of 1 in only the tetrachlorofluorescein channel represents a homozygous allele Fb. Values of 1 in both channels represent a heterozygous sample (Figure 7c). A zero value in both channels may be a no template control (NTC), as is the case in Figure 7 (well A7) or indicates that the sample needs manual attention, as PCR may have failed. The macro normally sets probe Tm and signal threshold parameters automatically.
This project has been funded in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. NO1-CO-12400 and the National Institute of Allergy and Infectious Diseases, Grant Number 1R43-A1052905-01A1. The content of this manuscript does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products or organisations imply endorsement by the US Government. The publisher or recipient acknowledges the right of the US Government to retain a non-exclusive, royalty-free licence in and to any copyright covering the article. Michael W. Reed is acknowledged for his assistance in the preparation of the manuscript. We also thank Vladimir Gorn, Irina Shishkina and Zinaida Sergueeva for the synthesis and purification of the probes and primers.
- Didenko VV: 'DNA probes using fluorescence resonance energy transfer (FRET): Designs and applications'. Biotechniques. 2001, 31: 1106-1121.PubMed CentralPubMedGoogle Scholar
- Shi MM: 'Technologies for individual genotyping: Detection of genetic polymorphisms in drug targets and disease genes'. Am J Pharmacogenomics. 2002, 2: 197-205.View ArticlePubMedGoogle Scholar
- Watt JR, Davis PW: 'Kinetics of G-quartet-mediated tetramer formation'. Biochemistry. 1996, 15: 8002-8008.View ArticleGoogle Scholar
- Peyret N, Seneviratne PA, Allawi HT, SantaLucia J: 'Nearest-neighbor, thermodynamics and NMR of DNA sequences with internal A·A, C·C, G·G and T·T mismatches'. Biochemistry. 1999, 38: 3468-3477. 10.1021/bi9825091.View ArticlePubMedGoogle Scholar
- Mohanty D, Bansal M: 'Conformational polymorphism in telomeric structures: Loop orientation and interloop pairing in d(G4TnG4)'. Biopolymers. 1994, 34: 1187-1211. 10.1002/bip.360340908.View ArticlePubMedGoogle Scholar
- Afonina IA, Reed MW, Lusby E, et al: '5' Minor groove binder-conjugated DNA probes for quantitative DNA detection by hybridization-triggered fluorescence'. BioTechniques. 2002, 32: 940-949.PubMedGoogle Scholar
- de Kok JB, Wiegerinck ET, Giesendorf BA, Swinkels DW: 'Rapid genotyping of single nucleotide polymorphisms using novel minor groove binding DNA oligonucleotides (MGB probes)'. Hum Mutat. 2002, 19: 554-559. 10.1002/humu.10076.View ArticlePubMedGoogle Scholar
- McGuigan FAA, Ralston SH: 'Single nucleotide polymorphism detection: Allelic discrimination using Taqman'. Psychiatr Genet. 2002, 12: 133-136. 10.1097/00041444-200209000-00003.View ArticlePubMedGoogle Scholar
- Kutyavin IV, Afonina IA, Mills A, et al: '3'-Minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures'. Nucleic Acids Res. 2000, 28: 655-661. 10.1093/nar/28.2.655.PubMed CentralView ArticlePubMedGoogle Scholar
- Afonina I, Belousov Y, Metcalf M, et al: 'Single nucleotide polymorphism detection with MGB Eclipse™ assays'. J Clin Ligand Assay. 2003, 25 (3): 268-275.Google Scholar
- Southern EM, Case-Green SC, Elder JK, et al: 'Arrays of complementary oligonucleotides for analyzing the hybridization behavior of nucleic acids'. Nucleic Acids Res. 1994, 22: 1368-1373. 10.1093/nar/22.8.1368.PubMed CentralView ArticlePubMedGoogle Scholar
- Henderson E, Hardin CC, Walk SK, et al: 'Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs'. Cell. 1987, 51: 899-908. 10.1016/0092-8674(87)90577-0.View ArticlePubMedGoogle Scholar
- Marsh TC, Vesenka J, Henderson E: 'A new DNA nanostructure, the G-wire, imaged by scanning probe microscopy'. Nucleic Acids Res. 1995, 23: 696-700. 10.1093/nar/23.4.696.PubMed CentralView ArticlePubMedGoogle Scholar
- Lu M, Guo Q, Kallenbach NR: 'Thermodynamics of G-tetraplex formation by telomeric DNAs'. Biochemistry. 1993, 32: 598-601. 10.1021/bi00053a027.View ArticlePubMedGoogle Scholar
- Hardin CC, Watson T, Corregan M, Bailey C: 'Cation-dependent transition between the quadruplex and Watson-Crick hairpin forms of d(CGCG3GCG)'. Biochemistry. 1992, 31: 833-841. 10.1021/bi00118a028.View ArticlePubMedGoogle Scholar
- Kutyavin IV, Lukhtanov EA, Gamper HB, Meyer RB: 'Oligonucleotides with conjugated dihydropyrroloindole tripeptides: Base composition and backbone effects on hybridization'. Nucleic Acids Res. 1997, 25: 3718-3723. 10.1093/nar/25.18.3718.PubMed CentralView ArticlePubMedGoogle Scholar
- Applied Biosystems: ABI PRISM® 7900HT Sequence Detection User Guide. 2002, Foster City, CA, USA: Applied Biosystems.Google Scholar
- Parkhurst KM, Parkhurst LJ: 'Detection of point mutation in DNA by fluorescence energy transfer'. J Biomed Optics. 1996, 1: 435-441. 10.1117/12.250674.View ArticleGoogle Scholar
- Kutyavin IA, Lokhov SG, Afonina IA, et al: 'Reduced aggregation and improved specificity of G-rich oligodeoxyribonucleotides containing pyrazolo[3,4-d]pyrimidine guanine bases'. Nucleic Acids Res. 2002, 30: 4952-4959. 10.1093/nar/gkf631.PubMed CentralView ArticlePubMedGoogle Scholar