Ioannis Trantakis | Swiss Federal Institute of Technology (ETH) (original) (raw)

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Papers by Ioannis Trantakis

Journal of Agricultural and Food Chemistry, 2012

A method is reported for species quantification by exploiting single-nucleotide polymorphisms (SN... more A method is reported for species quantification by exploiting single-nucleotide polymorphisms (SNPs). These single-base changes in DNA are particularly useful because they enable discrimination of closely related species and/or varieties. As a model, quantitative authentication studies were performed on coffee. These involved the determination of the percentage of Arabica and Robusta species based on a SNP in the chloroplastic trnL(UAA)-trnF(GAA) intraspacer region. Following polymerase chain reaction (PCR), the Robusta-specific and Arabica-specific fragments were subjected to 15 min extension reactions by DNA polymerase using species-specific primers carrying oligo(dA) tags. Biotin was incorporated into the extended strands. The products were captured in streptavidin-coated microtiter wells and quantified by using oligo(dT)-conjugated photoprotein aequorin. Aequorin was measured within 3 s via its characteristic flash-type bioluminescent reaction that was triggered by the addition of Ca 2+ . Because of the close resemblance between the two DNA fragments, during PCR one species serves as an internal standard for the other. The percentage of the total luminescence signal obtained from a certain species was linearly related to the percent content of the sample with respect to this species. The method is accurate and reproducible. The microtiter well-based assay configuration allows high sample throughput and facilitates greatly the automation.

Journal of the American Chemical Society, 2016

Toxicology Letters, 2013

The use of nanotechnology in the food and nutrition industry offers new opportunities to enhance ... more The use of nanotechnology in the food and nutrition industry offers new opportunities to enhance product performance and provide health benefits to consumers. One promising application is food fortification with highly bioavailable nanostructured iron compounds to combat iron deficiency, which is still a major global public health issue. However, the use of engineered nanoparticles (ENP) in foods is raising concerns since the fate and safety of ENP upon ingestion is largely unknown. In the present study, the potential cytotoxicity of amorphous iron phosphate nanoparticles (FePO 4 -NP) produced by flame spray pyrolysis (FSP) to human intestinal epithelial cells was studied in vitro. Cytotoxicity was evaluated with the MTS assay. Food-grade SiO 2 -NP and FSP made SiO 2 /Ag-NP served as negative and positive controls, respectively. The effect of acute NP exposure was studied by incubating cells with different concentrations (0.1-500 g/mL) of FePO 4 -NP, SiO 2 -NP and SiO 2 /Ag-NP for 24 or 48 h. No cytotoxicity was observed, neither after 24 nor 48 h exposure. These results give a first indication that the tested NPs are not directly toxic to the intestinal epithelial cells.

A colorimetric probe for the detection of a mutagenic DNA adduct within a sequence was created. T... more A colorimetric probe for the detection of a mutagenic DNA adduct within a sequence was created. The probe involves incorporation of a synthetic nucleoside that selectively pairs opposite a target DNA adduct into oligonucleotides conjugated to gold nanoparticles (AuNPs).

The programmable assembly of functional nanomaterials has been extensively addressed; however, th... more The programmable assembly of functional nanomaterials has been extensively addressed; however, their selective reversible assembly in response to an external stimulus has been more difficult to realize. The specificity and programmable interactions of DNA have been exploited for the rational self-assembly of DNA-conjugated nanoparticles, and here we demonstrate the sequence-controlled disaggregation of DNA-modified gold nanoparticles simply by employing two complementary oligonucleotides. Target oligonucleotides with perfectly matching sequence enabled dissociation of aggregated nanoparticles, whereas oligonucleotides differing by one nucleotide did not cause disassembly of the aggregated nanoparticles. Physical aspects of this process were characterized by UV−vis absorption, light scattering, and transmission electron microscopy. This strategy for programmed disassembly of gold nanoparticles in response to biological stimuli demonstrates a fundamentally important concept anticipated to be useful for diverse applications involving molecular recognition.

… of Agricultural and …, Jan 1, 2012

A method is reported for species quantification by exploiting single-nucleotide polymorphisms (SN... more A method is reported for species quantification by exploiting single-nucleotide polymorphisms (SNPs). These single-base changes in DNA are particularly useful because they enable discrimination of closely related species and/or varieties. As a model, quantitative authentication studies were performed on coffee. These involved the determination of the percentage of Arabica and Robusta species based on a SNP in the chloroplastic trnL(UAA)-trnF(GAA) intraspacer region. Following polymerase chain reaction (PCR), the Robusta-specific and Arabica-specific fragments were subjected to 15 min extension reactions by DNA polymerase using species-specific primers carrying oligo(dA) tags. Biotin was incorporated into the extended strands. The products were captured in streptavidin-coated microtiter wells and quantified by using oligo(dT)-conjugated photoprotein aequorin. Aequorin was measured within 3 s via its characteristic flash-type bioluminescent reaction that was triggered by the addition of Ca 2+ . Because of the close resemblance between the two DNA fragments, during PCR one species serves as an internal standard for the other. The percentage of the total luminescence signal obtained from a certain species was linearly related to the percent content of the sample with respect to this species. The method is accurate and reproducible. The microtiter well-based assay configuration allows high sample throughput and facilitates greatly the automation.

… of Agricultural and …, Jan 1, 2012

This paper reports DNA-based food authenticity assays, in which species identification is accompl... more This paper reports DNA-based food authenticity assays, in which species identification is accomplished by the naked eye without the need of specialized instruments. Strongly colored nanoparticles (gold nanoparticles) are employed as reporters that enable visual detection. Furthermore, detection is performed in a low-cost, disposable, dipstick-type device that incorporates the required reagents in dry form, thereby avoiding multiple pipetting and incubation steps. Due to its simplicity, the method does not require highly qualified personnel. The procedure comprises the following steps: (i) PCR amplification of the DNA segment that flanks the unique SNP (species marker); (ii) a 15 min extension reaction in which DNA polymerase extends an allele-specific primer only if it is perfectly complementary with the target sequence; (iii) detection of the products of the extension reaction within a few minutes by the naked eye employing the dipstick. No purification is required prior to application of the extension products to the dipstick. The method is general and requires only a unique DNA sequence for species discrimination. The only instrument needed is a conventional thermocycler for PCR, which is common equipment in every DNA laboratory. As a model, the method was applied to the discrimination of Coffea robusta and arabica species in coffee authenticity assessment. As low as 5% of Robusta coffee can be detected in the presence of Arabica coffee.

Journal of the …, Jan 1, 2010

The protein truncation test (PTT) is important in screening for unknown mutations that cause prem... more The protein truncation test (PTT) is important in screening for unknown mutations that cause premature termination of mRNA translation. PTT involves amplification of the interrogated sequence, in vitro transcription/translation, separation of the generated polypeptides, and detection. In this article, we report a bioluminescent protein truncation test, in which the detection of the nascent protein is performed directly in the expression mixture, within seconds, without the need for separation and purification. A DNA fragment encoding apoaequorin is fused, in-frame, downstream of the interrogated sequence. The fusion product is subjected to in vitro, coupled transcription and translation in the presence of coelenterazine. A wild-type DNA template allows translation to continue after the 3′ end of the interrogated sequence, producing a chimeric protein whose C-terminal domain is the photoprotein aequorin. Aequorin is detected, with a high sensitivity, by its characteristic Ca 2+ -triggered, flash-type bioluminescent reaction. Active photoprotein is not produced when a truncating mutation is present in the interrogated sequence. As a model, the method was applied to the detection of truncating mutations in the APC gene (adenomatous polyposis coli).

Chemical Physics …, Jan 1, 2010

The ultrafast dynamics of the DNA fluorescent dye Sybr Green I (SG) has been studied in buffer, s... more The ultrafast dynamics of the DNA fluorescent dye Sybr Green I (SG) has been studied in buffer, singlestranded (ssDNA), double-stranded (dsDNA) and triple-stranded DNA (tsDNA). The fluorescence quantum yield of SG increases dramatically when bound to DNA (including tsDNA). The fluorescence dynamics of the free SG has shown two decay components with 0.15−0.4psand0.15-0.4 ps and 0.15−0.4psand1.3-2.1 ps time constants, depending on the fluorescence wavelength. Upon binding to DNA, the dynamics becomes slower exhibiting four decay components. This is mainly due to the restriction of the internal motions of the dye caused by the relatively rigid environment of the dye complexed with DNA.

Journal of Agricultural and Food Chemistry, 2012

A method is reported for species quantification by exploiting single-nucleotide polymorphisms (SN... more A method is reported for species quantification by exploiting single-nucleotide polymorphisms (SNPs). These single-base changes in DNA are particularly useful because they enable discrimination of closely related species and/or varieties. As a model, quantitative authentication studies were performed on coffee. These involved the determination of the percentage of Arabica and Robusta species based on a SNP in the chloroplastic trnL(UAA)-trnF(GAA) intraspacer region. Following polymerase chain reaction (PCR), the Robusta-specific and Arabica-specific fragments were subjected to 15 min extension reactions by DNA polymerase using species-specific primers carrying oligo(dA) tags. Biotin was incorporated into the extended strands. The products were captured in streptavidin-coated microtiter wells and quantified by using oligo(dT)-conjugated photoprotein aequorin. Aequorin was measured within 3 s via its characteristic flash-type bioluminescent reaction that was triggered by the addition of Ca 2+ . Because of the close resemblance between the two DNA fragments, during PCR one species serves as an internal standard for the other. The percentage of the total luminescence signal obtained from a certain species was linearly related to the percent content of the sample with respect to this species. The method is accurate and reproducible. The microtiter well-based assay configuration allows high sample throughput and facilitates greatly the automation.

Journal of the American Chemical Society, 2016

Toxicology Letters, 2013

The use of nanotechnology in the food and nutrition industry offers new opportunities to enhance ... more The use of nanotechnology in the food and nutrition industry offers new opportunities to enhance product performance and provide health benefits to consumers. One promising application is food fortification with highly bioavailable nanostructured iron compounds to combat iron deficiency, which is still a major global public health issue. However, the use of engineered nanoparticles (ENP) in foods is raising concerns since the fate and safety of ENP upon ingestion is largely unknown. In the present study, the potential cytotoxicity of amorphous iron phosphate nanoparticles (FePO 4 -NP) produced by flame spray pyrolysis (FSP) to human intestinal epithelial cells was studied in vitro. Cytotoxicity was evaluated with the MTS assay. Food-grade SiO 2 -NP and FSP made SiO 2 /Ag-NP served as negative and positive controls, respectively. The effect of acute NP exposure was studied by incubating cells with different concentrations (0.1-500 g/mL) of FePO 4 -NP, SiO 2 -NP and SiO 2 /Ag-NP for 24 or 48 h. No cytotoxicity was observed, neither after 24 nor 48 h exposure. These results give a first indication that the tested NPs are not directly toxic to the intestinal epithelial cells.

A colorimetric probe for the detection of a mutagenic DNA adduct within a sequence was created. T... more A colorimetric probe for the detection of a mutagenic DNA adduct within a sequence was created. The probe involves incorporation of a synthetic nucleoside that selectively pairs opposite a target DNA adduct into oligonucleotides conjugated to gold nanoparticles (AuNPs).

The programmable assembly of functional nanomaterials has been extensively addressed; however, th... more The programmable assembly of functional nanomaterials has been extensively addressed; however, their selective reversible assembly in response to an external stimulus has been more difficult to realize. The specificity and programmable interactions of DNA have been exploited for the rational self-assembly of DNA-conjugated nanoparticles, and here we demonstrate the sequence-controlled disaggregation of DNA-modified gold nanoparticles simply by employing two complementary oligonucleotides. Target oligonucleotides with perfectly matching sequence enabled dissociation of aggregated nanoparticles, whereas oligonucleotides differing by one nucleotide did not cause disassembly of the aggregated nanoparticles. Physical aspects of this process were characterized by UV−vis absorption, light scattering, and transmission electron microscopy. This strategy for programmed disassembly of gold nanoparticles in response to biological stimuli demonstrates a fundamentally important concept anticipated to be useful for diverse applications involving molecular recognition.

… of Agricultural and …, Jan 1, 2012

A method is reported for species quantification by exploiting single-nucleotide polymorphisms (SN... more A method is reported for species quantification by exploiting single-nucleotide polymorphisms (SNPs). These single-base changes in DNA are particularly useful because they enable discrimination of closely related species and/or varieties. As a model, quantitative authentication studies were performed on coffee. These involved the determination of the percentage of Arabica and Robusta species based on a SNP in the chloroplastic trnL(UAA)-trnF(GAA) intraspacer region. Following polymerase chain reaction (PCR), the Robusta-specific and Arabica-specific fragments were subjected to 15 min extension reactions by DNA polymerase using species-specific primers carrying oligo(dA) tags. Biotin was incorporated into the extended strands. The products were captured in streptavidin-coated microtiter wells and quantified by using oligo(dT)-conjugated photoprotein aequorin. Aequorin was measured within 3 s via its characteristic flash-type bioluminescent reaction that was triggered by the addition of Ca 2+ . Because of the close resemblance between the two DNA fragments, during PCR one species serves as an internal standard for the other. The percentage of the total luminescence signal obtained from a certain species was linearly related to the percent content of the sample with respect to this species. The method is accurate and reproducible. The microtiter well-based assay configuration allows high sample throughput and facilitates greatly the automation.

… of Agricultural and …, Jan 1, 2012

This paper reports DNA-based food authenticity assays, in which species identification is accompl... more This paper reports DNA-based food authenticity assays, in which species identification is accomplished by the naked eye without the need of specialized instruments. Strongly colored nanoparticles (gold nanoparticles) are employed as reporters that enable visual detection. Furthermore, detection is performed in a low-cost, disposable, dipstick-type device that incorporates the required reagents in dry form, thereby avoiding multiple pipetting and incubation steps. Due to its simplicity, the method does not require highly qualified personnel. The procedure comprises the following steps: (i) PCR amplification of the DNA segment that flanks the unique SNP (species marker); (ii) a 15 min extension reaction in which DNA polymerase extends an allele-specific primer only if it is perfectly complementary with the target sequence; (iii) detection of the products of the extension reaction within a few minutes by the naked eye employing the dipstick. No purification is required prior to application of the extension products to the dipstick. The method is general and requires only a unique DNA sequence for species discrimination. The only instrument needed is a conventional thermocycler for PCR, which is common equipment in every DNA laboratory. As a model, the method was applied to the discrimination of Coffea robusta and arabica species in coffee authenticity assessment. As low as 5% of Robusta coffee can be detected in the presence of Arabica coffee.

Journal of the …, Jan 1, 2010

The protein truncation test (PTT) is important in screening for unknown mutations that cause prem... more The protein truncation test (PTT) is important in screening for unknown mutations that cause premature termination of mRNA translation. PTT involves amplification of the interrogated sequence, in vitro transcription/translation, separation of the generated polypeptides, and detection. In this article, we report a bioluminescent protein truncation test, in which the detection of the nascent protein is performed directly in the expression mixture, within seconds, without the need for separation and purification. A DNA fragment encoding apoaequorin is fused, in-frame, downstream of the interrogated sequence. The fusion product is subjected to in vitro, coupled transcription and translation in the presence of coelenterazine. A wild-type DNA template allows translation to continue after the 3′ end of the interrogated sequence, producing a chimeric protein whose C-terminal domain is the photoprotein aequorin. Aequorin is detected, with a high sensitivity, by its characteristic Ca 2+ -triggered, flash-type bioluminescent reaction. Active photoprotein is not produced when a truncating mutation is present in the interrogated sequence. As a model, the method was applied to the detection of truncating mutations in the APC gene (adenomatous polyposis coli).

Chemical Physics …, Jan 1, 2010

The ultrafast dynamics of the DNA fluorescent dye Sybr Green I (SG) has been studied in buffer, s... more The ultrafast dynamics of the DNA fluorescent dye Sybr Green I (SG) has been studied in buffer, singlestranded (ssDNA), double-stranded (dsDNA) and triple-stranded DNA (tsDNA). The fluorescence quantum yield of SG increases dramatically when bound to DNA (including tsDNA). The fluorescence dynamics of the free SG has shown two decay components with 0.15−0.4psand0.15-0.4 ps and 0.15−0.4psand1.3-2.1 ps time constants, depending on the fluorescence wavelength. Upon binding to DNA, the dynamics becomes slower exhibiting four decay components. This is mainly due to the restriction of the internal motions of the dye caused by the relatively rigid environment of the dye complexed with DNA.