51
|
Hövelmann F, Bethge L, Seitz O. Single labeled DNA FIT probes for avoiding false-positive signaling in the detection of DNA/RNA in qPCR or cell media. Chembiochem 2012; 13:2072-81. [PMID: 22936610 DOI: 10.1002/cbic.201200397] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Indexed: 12/13/2022]
Abstract
Oligonucleotide hybridization probes that fluoresce upon binding to complementary nucleic acid targets allow the real-time detection of DNA or RNA in homogeneous solution. The most commonly used probes rely on the distance-dependent interaction between a fluorophore and another label. Such dual-labeled oligonucleotides signal the change of the global conformation that accompanies duplex formation. However, undesired nonspecific binding events and/or probe degradation also lead to changes in the label-label distance and, thus, to ambiguities in fluorescence signaling. Herein, we introduce singly labeled DNA probes, "DNA FIT probes", that are designed to avoid false-positive signals. A thiazole orange (TO) intercalator dye serves as an artificial base in the DNA probe. The probes show little background because the attachment mode hinders 1) interactions of the "TO base" in cis with the disordered nucleobases of the single strand, and 2) intercalation of the "TO nucleotide" with double strands in trans. However, formation of the probe-target duplex enforces stacking and increases the fluorescence of the TO base. We explored open-chain and carbocyclic nucleotides. We show that the incorporation of the TO nucleotides has no effect on the thermal stability of the probe-target complexes. DNA and RNA targets provided up to 12-fold enhancements of the TO emission upon hybridization of DNA FIT probes. Experiments in cell media demonstrated that false-positive signaling was prevented when DNA FIT probes were used. Of note, DNA FIT probes tolerate a wide range of hybridization temperature; this enabled their application in quantitative polymerase chain reactions.
Collapse
Affiliation(s)
- Felix Hövelmann
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany
| | | | | |
Collapse
|
52
|
Matsumura T, Niwa T, Nakada M. Pd-catalyzed reductive cleavage of alkyl aryl sulfides with triethylsilane that is accelerated by trialkylsilyl chloride. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.06.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
53
|
Kam Y, Rubinstein A, Nissan A, Halle D, Yavin E. Detection of endogenous K-ras mRNA in living cells at a single base resolution by a PNA molecular beacon. Mol Pharm 2012; 9:685-93. [PMID: 22289057 DOI: 10.1021/mp200505k] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Detection of mRNA alterations is a promising approach for identifying biomarkers as means of differentiating benign from malignant lesions. By choosing the KRAS oncogene as a target gene, two types of molecular beacons (MBs) based on either phosphothioated DNA (PS-DNA-MB) or peptide nucleic acid (TO-PNA-MB, where TO = thiazole orange) were synthesized and compared in vitro and in vivo. Their specificity was examined in wild-type KRAS (HT29) or codon 12 point mutation (Panc-1, SW480) cells. Incubation of both beacons with total RNA extracted from the Panc-1 cell line (fully complementary sequence) showed a fluorescent signal for both beacons. Major differences were observed, however, for single mismatch mRNA transcripts in cell lines HT29 and SW480. PS-DNA-MB weakly discriminated such single mismatches in comparison to TO-PNA-MB, which was profoundly more sensitive. Cell transfection of TO-PNA-MB with the aid of PEI resulted in fluorescence in cells expressing the fully complementary RNA transcript (Panc-1) but undetectable fluorescence in cells expressing the K-ras mRNA that has a single mismatch to the designed TO-PNA-MB (HT29). A weaker fluorescent signal was also detected in SW480 cells; however, these cells express approximately one-fifth of the target mRNA of the designed TO-PNA-MB. In contrast, PS-DNA-MB showed no fluorescence in all cell lines tested post PEI transfection. Based on the fast hybridization kinetics and on the single mismatch discrimination found for TO-PNA-MB we believe that such molecular beacons are promising for in vivo real-time imaging of endogenous mRNA with single nucleotide polymorphism (SNP) resolution.
Collapse
Affiliation(s)
- Yossi Kam
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, PO Box 12065, Jerusalem 91120, Israel
| | | | | | | | | |
Collapse
|
54
|
Furukawa K, Hattori M, Ohki T, Kitamura Y, Kitade Y, Ueno Y. Nucleic acid probe containing fluorescent tricyclic base-linked acyclonucleoside for detection of single nucleotide polymorphisms. Bioorg Med Chem 2011; 20:16-24. [PMID: 22177406 DOI: 10.1016/j.bmc.2011.11.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Revised: 11/19/2011] [Accepted: 11/21/2011] [Indexed: 11/16/2022]
Abstract
The development of a reliable and simple method for detecting single nucleotide polymorphisms (SNPs), common genetic variations in the human genome, is currently an important research area because SNPs are important for identifying disease-causing genes and for pharmacogenetic studies. Here, we developed a novel method for SNP detection. We designed and synthesized DNA probes containing a fluorescent tricyclic base-linked acyclonucleoside P. The type of nucleobases involved in the SNP sites in the DNA and RNA targets could be determined using four DNA probes containing P. Thus, this system would provide a novel and simple method for detecting SNPs in DNA and RNA targets.
Collapse
Affiliation(s)
- Kinji Furukawa
- Department of Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | | | | | | | | | | |
Collapse
|
55
|
Berndt F, Sajadi M, Ernsting NP, Mahrwald R. Covalent linkage of N-methyl-6-oxyquinolinium betaine to trehalose. Carbohydr Res 2011; 346:2960-4. [DOI: 10.1016/j.carres.2011.10.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 10/07/2011] [Accepted: 10/12/2011] [Indexed: 10/16/2022]
|
56
|
Arisawa M, Toriyama F, Yamaguchi M. Rhodium-catalyzed phenylthiolation reaction of heteroaromatic compounds using α-(phenylthio)isobutyrophenone. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.02.077] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
57
|
Tonelli A, Tedeschi T, Germini A, Sforza S, Corradini R, Medici MC, Chezzi C, Marchelli R. Real time RNA transcription monitoring by Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes: norovirus detection. MOLECULAR BIOSYSTEMS 2011; 7:1684-92. [PMID: 21399831 DOI: 10.1039/c0mb00353k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes have been reported as a valuable strategy for DNA analysis; however, no investigations targeting RNA molecules and no comparisons between different derivatization approaches have been reported so far. In this work, two TO-conjugated PNAs for genogroup II noroviruses (NoV GII) detection were designed and synthesized. Both the probes target the most conserved stretch of nucleotides identified in the open reading frame 1-2 (ORF1-ORF2) junction region and differ for the dye conjugation strategy: one PNA is end-labelled with the TO molecule tethered by a linker; the other probe bears the TO molecule directly linked to the PNA backbone, replacing a conventional nucleobase. The spectroscopic properties of the two PNA probes were studied and their applicability to NoVs detection, using an isothermal assay, was investigated. Both probes showed good specificity and high fluorescence enhancement upon hybridization, especially targeting RNA molecules. Moreover, the two probes were successfully employed for NoVs detection from stool specimens in an isothermal-based amplification assay targeting RNA 'amplicons'. The probes showed to be specific even in the presence of high concentrations of non-target RNA.
Collapse
Affiliation(s)
- Alessandro Tonelli
- Department of Organic and Industrial Chemistry, University of Parma, Vle GP Usberti 17/A, 43124 Parma, Italy
| | | | | | | | | | | | | | | |
Collapse
|
58
|
Melzig L, Metzger A, Knochel P. Pd- and Ni-Catalyzed Cross-Coupling Reactions of Functionalized Organozinc Reagents with Unsaturated Thioethers. Chemistry 2011; 17:2948-56. [DOI: 10.1002/chem.201002850] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Indexed: 11/10/2022]
|
59
|
Kummer S, Knoll A, Socher E, Bethge L, Herrmann A, Seitz O. Fluoreszenzbildgebung der mRNA von Influenza-H1N1 in lebenden infizierten Zellen durch FIT-PNA mit einem einzigen Chromophor. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005902] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
60
|
Kummer S, Knoll A, Socher E, Bethge L, Herrmann A, Seitz O. Fluorescence imaging of influenza H1N1 mRNA in living infected cells using single-chromophore FIT-PNA. Angew Chem Int Ed Engl 2011; 50:1931-4. [PMID: 21328673 DOI: 10.1002/anie.201005902] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 10/22/2010] [Indexed: 01/13/2023]
Affiliation(s)
- Susann Kummer
- Department of Biology, Humboldt University Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
| | | | | | | | | | | |
Collapse
|
61
|
Rioz-Martínez A, de Gonzalo G, Pazmiño DET, Fraaije MW, Gotor V. Enzymatic Synthesis of Novel Chiral Sulfoxides Employing Baeyer-Villiger Monooxygenases. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000890] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
62
|
Jiang D, Seela F. Oligonucleotide duplexes and multistrand assemblies with 8-aza-2'-deoxyisoguanosine: a fluorescent isoG(d) shape mimic expanding the genetic alphabet and forming ionophores. J Am Chem Soc 2010; 132:4016-24. [PMID: 20192268 DOI: 10.1021/ja910020n] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
8-Aza-2'-deoxyisoguanosine (4) is the first fluorescent shape mimic of 2'-deoxyisoguanosine (1a); its fluorescence is stronger in alkaline medium than under neutral conditions. Nucleoside 4, which was synthesized from 8-aza-2'-deoxyguanosine via a 4,6-diamino intermediate after selective deamination, was incorporated in oligodeoxyribonucleotides using phosphoramidite 11. Duplexes with 4 x m(5)iC(d) (5-methyl-2'-deoxyisocytidine) base pairs are more stable than those incorporating dG-dC pairs, thereby expanding the genetic alphabet by a fluorescent orthogonal base pair. As demonstrated by T(m) measurements, the base pair stability decreases in the order m(5)iC(d) x 4 >> dG x 4 > dT x 4 > or = dC x 4 >> dA x 4. A better base pairing selectivity of 4 against the canonical nucleosides dT, dC, dA, and dG is observed than for the degenerated base pairing of 1a. The base pair stability changes can be monitored by nucleobase anion fluorescence sensing. The fluorescence change correlates to the DNA base pair stability. Oligonucleotide 5'-d(T(4)4(4)T(4)) (22), containing short runs of nucleoside 4, forms stable multistranded assemblies (ionophores) with K(+) in the central cavity. They are quite stable at elevated temperature but are destroyed at high pH value.
Collapse
Affiliation(s)
- Dawei Jiang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | | |
Collapse
|
63
|
Deligeorgiev T, Kaloyanova S, Lesev N, Vaquero JJ. An easy and fast ultrasonic selective S-alkylation of hetaryl thiols at room temperature. ULTRASONICS SONOCHEMISTRY 2010; 17:783-788. [PMID: 20362486 DOI: 10.1016/j.ultsonch.2010.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 02/15/2010] [Accepted: 03/04/2010] [Indexed: 05/29/2023]
Abstract
A series of 2-alkylthio derivatives of hetaryl thiols were synthesized by selective S-alkylation with alkyl halides (bromides and iodides) with ultrasonic irradiation at room temperature. The reaction was found to be generally applicable to hetaryl thiol derivatives with different substituents in the aromatic nucleus and various alkyl halides. The reaction gives high to excellent yields of products with high purity.
Collapse
|
64
|
Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 658] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| |
Collapse
|
65
|
Bethge L, Singh I, Seitz O. Designed thiazole orange nucleotides for the synthesis of single labelled oligonucleotides that fluoresce upon matched hybridization. Org Biomol Chem 2010; 8:2439-48. [PMID: 20448904 DOI: 10.1039/c000697a] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Probe molecules that enable the detection of specific DNA sequences are used in diagnostic and basic research. Most methods rely on the specificity of hybridization reactions, which complicates the detection of single base mutations at low temperature. Significant efforts have been devoted to the development of oligonucleotides that allow discrimination of single base mutations at temperatures where both the match and the mismatch probe-target complexes coexist. Oligonucleotides that contain environmentally sensitive fluorescence dyes such as thiazole orange (TO) provide single nucleotide specific fluorescence. However, most previously reported dye-DNA conjugates showed only little if any difference between the fluorescence of the single and the double stranded state. Here, we introduce a TO-containing acyclic nucleotide, which is coupled during automated oligonucleotide synthesis and provides for the desired fluorescence-up properties. The study reveals the conjugation mode as the most important issue. We show a design that leads to low fluorescence of the unbound probe (background) yet permits TO to adopt fluorescent binding modes after the probe-target complex has formed. In these probes, TO replaces a canonical nucleobase. Of note, the fluorescence of the "TO-base" remains low when a base mismatch is positioned in immediate vicinity.
Collapse
Affiliation(s)
- Lucas Bethge
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, Berlin, D-12489, Germany
| | | | | |
Collapse
|
66
|
Hainke S, Seitz O. Binaphthyl-DNA: stacking and fluorescence of a nonplanar aromatic base surrogate in DNA. Angew Chem Int Ed Engl 2010; 48:8250-3. [PMID: 19790219 DOI: 10.1002/anie.200903194] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sven Hainke
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | | |
Collapse
|
67
|
Murru S, Mondal P, Yella R, Patel BK. Copper(I)-Catalyzed Cascade Synthesis of 2-Substituted 1,3-Benzothiazoles: Direct Access to Benzothiazolones. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900711] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
68
|
Takei F, Igarashi M, Hagihara M, Oka Y, Soya Y, Nakatani K. Secondary-Structure-Inducible Ligand Fluorescence Coupled with PCR. Angew Chem Int Ed Engl 2009; 48:7822-4. [DOI: 10.1002/anie.200902449] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
69
|
Takei F, Igarashi M, Hagihara M, Oka Y, Soya Y, Nakatani K. Secondary-Structure-Inducible Ligand Fluorescence Coupled with PCR. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902449] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
70
|
Ueno Y, Komatsuzaki S, Takasu K, Kawai S, Kitamura Y, Kitade Y. Synthesis and Properties of Oligonucleotides Containing Novel Fluorescent Biaryl Units. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900567] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
71
|
Hainke S, Seitz O. Binaphthyl-DNA: Stapelung und Fluoreszenz eines nichtplanaren aromatischen Basensurrogates in DNA. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903194] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
72
|
Zhu JQ, Fang HC, Chen BY, Feng MS, Li JN. Tris(2-hydroxy-ethyl)ammonium 1,3-benzo-thia-zole-2-thiol-ate. Acta Crystallogr Sect E Struct Rep Online 2009; 65:o1640. [PMID: 21582904 PMCID: PMC2969305 DOI: 10.1107/s160053680902248x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 06/12/2009] [Indexed: 11/14/2022]
Abstract
In the title compound, C(6)H(16)NO(3) (+)·C(7)H(4)NS(2) (-), the cations and anions are connected by O-H⋯N and O-H⋯S hydrogen bonding. Weak C-H⋯O hydrogen bonding between adjacent cations helps to stabilize the crystal structure.
Collapse
Affiliation(s)
- Ji-Qin Zhu
- School of Chemistry and the Environment, South China Normal University, Guangzhou 510631, People’s Republic of China
| | - Hua-Cai Fang
- School of Chemistry and the Environment, South China Normal University, Guangzhou 510631, People’s Republic of China
| | - Bi-Yun Chen
- School of Chemistry and the Environment, South China Normal University, Guangzhou 510631, People’s Republic of China
| | - Mao-Song Feng
- School of Chemistry and the Environment, South China Normal University, Guangzhou 510631, People’s Republic of China
| | - Jing-Ning Li
- School of Chemistry and the Environment, South China Normal University, Guangzhou 510631, People’s Republic of China
| |
Collapse
|
73
|
Piepenbrock MOM, Anderson KM, Sansam BCR, Clarke N, Steed JW. Structural similarity of hydrogen-bonded and metal-coordinated abiotic base pairs allows oligonucleotide-like mutual stacking,. CrystEngComm 2009. [DOI: 10.1039/b815252g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
74
|
Seela F, Jiang D, Xu K. 8-Aza-2′-deoxyguanosine: Base pairing, mismatch discrimination and nucleobase anion fluorescence sensing in single-stranded and duplex DNA. Org Biomol Chem 2009; 7:3463-73. [DOI: 10.1039/b908017a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
75
|
Socher E, Bethge L, Knoll A, Jungnick N, Herrmann A, Seitz O. Low-noise stemless PNA beacons for sensitive DNA and RNA detection. Angew Chem Int Ed Engl 2008; 47:9555-9. [PMID: 18949813 DOI: 10.1002/anie.200803549] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Elke Socher
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | | | | | | | | | | |
Collapse
|
76
|
Socher E, Bethge L, Knoll A, Jungnick N, Herrmann A, Seitz O. Stammlose PNA-Beacons für die empfindliche DNA- und RNA-Detektion mit geringem Hintergrundrauschen. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200803549] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
77
|
Socher E, Jarikote DV, Knoll A, Röglin L, Burmeister J, Seitz O. FIT probes: peptide nucleic acid probes with a fluorescent base surrogate enable real-time DNA quantification and single nucleotide polymorphism discovery. Anal Biochem 2008; 375:318-30. [PMID: 18249184 DOI: 10.1016/j.ab.2008.01.009] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 01/08/2008] [Accepted: 01/08/2008] [Indexed: 11/19/2022]
Abstract
The ability to accurately quantify specific nucleic acid molecules in complex biomolecule solutions in real time is important in diagnostic and basic research. Here we describe a DNA-PNA (peptide nucleic acid) hybridization assay that allows sensitive quantification of specific nucleic acids in solution and concomitant detection of select single base mutations in resulting DNA-PNA duplexes. The technique employs so-called FIT (forced intercalation) probes in which one base is replaced by a thiazole orange (TO) dye molecule. If a DNA molecule that is complementary to the FIT-PNA molecule (except at the site of the dye) hybridizes to the probe, the TO dye exhibits intense fluorescence because stacking in the duplexes enforces a coplanar arrangement even in the excited state. However, a base mismatch at either position immediately adjacent to the TO dye dramatically decreases fluorescence, presumably because the TO dye has room to undergo torsional motions that lead to rapid depletion of the excited state. Of note, we found that the use of d-ornithine rather than aminoethylglycine as the PNA backbone increases the intensity of fluorescence emitted by matched probe-target duplexes while specificity of fluorescence signaling under nonstringent conditions is also increased. The usefulness of the ornithine-containing FIT probes was demonstrated in the real-time PCR analysis providing a linear measurement range over at least seven orders of magnitude. The analysis of two important single nucleotide polymorphisms (SNPs) in the CFTR gene confirmed the ability of FIT probes to facilitate unambiguous SNP calls for genomic DNA by quantitative PCR.
Collapse
Affiliation(s)
- Elke Socher
- Institut für Chemie, Humboldt-Universität zu Berlin, D-12489 Berlin, Germany
| | | | | | | | | | | |
Collapse
|