Publications

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Journal Article
Use of cyclodextrins as scavengers of inhibitory photo-products in light controlled in vitro synthesis of RNA, {Vidal Pinheiro}, André, Conde João, Parola {António Jorge}, Lima {João Carlos}, and Baptista {Pedro Viana} , Journal of Photochemistry and Photobiology A: Chemistry, jun, Volume 213, Number 2-3, p.147–151, (2010) Abstract

We recently reported on the use of caged nucleotides to attain full control of enzymatic polymerization of RNA solely by light. In the absence of light no RNA formation was possible due to the efficient caging by the coumarin moiety; after irradiation, caged ATP was released with quantitative precision and RNA polymerization was resumed. As photolabile protecting group [7-(diethylamino) coumarin-4-yl]methyl] (DEACM) was used due to its high absorbance in the visible region of the spectrum, fast deprotection kinetics and absence of radical intermediates. However, the 7-diethylamino-4-hydroxymethylcoumarin photo-product (DEACM-OH) was shown to inhibit the transcription reaction for concentrations higher than 30 μM [5]. This inhibition has been associated with poor water solubility, which is commonly dealt with via cumbersome chemical modifications of the protecting moiety. To overcome inhibition, we evaluated the use of molecular scavengers to sequester DEACM-OH formed after irradiation. Determination of association constants of coumarin with β-cyclodextrins allowed the assessment of its capability to remove free coumarin molecules from solution. The influence of β-cyclodextrin in transcription reaction was also assessed. Results show that β-cyclodextrin can be successfully used as scavenger as it increases the DEACM-OH threshold concentration for inhibition, amplifying the efficiency of light controlled in vitro transcription.

Using Au-nanoprobes por point-of-need diagnostics of TB., Baptista, Pedro, Veigas {Bruno Miguel Ribeiro}, Portugal Isabel, Couto I., and Viveiros M. , Magazine da Sociedade Portuguesa de Microbiologia, jan, Volume 2012, Number 1, (2012) Abstract

Tuberculosis remains one of the most serious infectious diseases worldwide requiring new tools to circumvent current molecular diagnostics limitations. Nanodiagnostics, i.e. nanotechnology based diagnostics, may do just that by decreasing the time needed for the molecular characterisation of the infecting agent, and allowing for miniaturisation and portability for point-of-need adapted to remote regions without suitable lab equipment.

Vanadium(IV) complexes with methyl-substituted 8-hydroxyquinolines: Catalytic potential in the oxidation of hydrocarbons and alcohols with peroxides and biological activity, Palion-Gazda, Joanna, Luz André, Raposo {Luis R. }, Choroba Katarzyna, Nycz {Jacek E. }, Bieńko Alina, Lewińska Agnieszka, Erfurt Karol, Baptista {Pedro V. }, Machura Barbara, Fernandes {Alexandra R. }, Shul’pina {Lidia S. }, Ikonnikov {Nikolay S. }, and Shul’pin {Georgiy B. } , Molecules, oct, Volume 26, Number 21, (2021) Abstract

Methyl-substituted 8-hydroxyquinolines (Hquin) were successfully used to synthetize five-coordinated oxovanadium(IV) complexes: [VO(2,6-(Me)2-quin)2 ] (1), [VO(2,5-(Me)2-quin)2 ] (2) and [VO(2-Me-quin)2 ] (3). Complexes 1–3 demonstrated high catalytic activity in the oxidation of hydrocarbons with H2 O2 in acetonitrile at 50◦ C, in the presence of 2-pyrazinecarboxylic acid (PCA) as a cocatalyst. The maximum yield of cyclohexane oxidation products attained was 48%, which is high in the case of the oxidation of saturated hydrocarbons. The reaction leads to the formation of a mixture of cyclohexyl hydroperoxide, cyclohexanol and cyclohexanone. When triphenylphosphine is added, cyclohexyl hydroperoxide is completely converted to cyclohexanol. Consideration of the regioand bond-selectivity in the oxidation of n-heptane and methylcyclohexane, respectively, indicates that the oxidation proceeds with the participation of free hydroxyl radicals. The complexes show moderate activity in the oxidation of alcohols. Complexes 1 and 2 reduce the viability of colorectal (HCT116) and ovarian (A2780) carcinoma cell lines and of normal dermal fibroblasts without showing a specific selectivity for cancer cell lines. Complex 3 on the other hand, shows a higher cytotoxicity in a colorectal carcinoma cell line (HCT116), a lower cytotoxicity towards normal dermal fibroblasts and no effect in an ovarian carcinoma cell line (order of magnitude HCT116 > fibroblasts > A2780).

Water safety screening via multiplex LAMP-Au-nanoprobe integrated approach, Oliveira, {Beatriz B. }, Veigas Bruno, Carlos {Fábio Ferreira}, Sánchez-Melsió Alexandre, Balcázar {José Luís}, Borrego {Carles M. }, and Baptista {Pedro Viana} , Science of the Total Environment, nov, Volume 741, (2020) Abstract

Contaminated water resources remain a major global concern regarding public health. The majority of water safety protocols include indicators of microbial contamination to evaluate the potential risk to public health and are key elements of quality guidelines. Among these, markers for total coliforms and fecal coliforms are strong indicators of co-contamination with other pathogens. Traditional methods, recurring to slow and cumbersome culture-based approaches, have been gradually replaced by molecular methods, capable of faster and more specific screening. These are usually PCR-based methods that may allow for multiple pathogen detection but require dedicated laboratory equipment, hindering the rapid on-site assessment. Here, we used a multiplex Loop-Mediated Isothermal Amplification (mLAMP) strategy for the amplification of two markers associated with the contamination by total and fecal coliforms (e.g. Escherichia coli) — lacZ and uidA genes, respectively — thus allowing for single tube multiplex detection. The mLAMP products were then subject to an Au-nanoprobe colorimetric detection assay for precise discrimination of targets. This approach was validated in 22 water samples that were also screened for the presence of lacZ and uidA using standard and quantitative PCR, with the capability for discriminating the contamination level, e.g. a semi-quantitative evaluation of water quality.

Miscellaneous
Colorimetric method and kit for the detection of specific nucleic acid sequences using metal nanoparticles functionalized with modified oligonucleotides, Tavares, {Jose Ricardo Ramos Franco}, Baptista {Pedro Miguel Ribeiro Viana}, Doria {Goncalo Maria Reimão Pinto De Franca}, and de Flores {Alcino Orfeu Leão} , mar, (2010) Abstract

The present invention relates to a colorimetric method for the detection of specific nucleic acids sequences, including mutations or single nucleotide polymorphisms within nucleic acid sequences, through the aggregation of nanoparticles functionalized with modified oligonucleotides, induced by an increase of the medium's ionic strength. Another aspect of the present invention relates with the development of a kit based on the method of the present invention, allowing for a quick and easy detection of specific nucleic acids sequences, including mutations or single nucleotide polymorphisms within nucleic acid sequences.

Colorimetric method and kit for the detection of specific nucleic acid sequences using metal nanoparticles functionalized with modified oligonucleotides, Tavares, {Jose Ricardo Ramos Franco}, Baptista {Pedro Miguel Ribeiro Viana}, Doria {Goncalo Maria Reimao Pinto De Franca}, and Flores {Alcino Orfeu De Leao} , jan, (2010) Abstract

The present invention relates to a colorimetric method for the detection of specific nucleic acids sequences, including mutations or single nucleotide polymorphisms within nucleic acid sequences, through the aggregation of nanoparticles functionalized with modified oligonucleotides, induced by an increase of the medium's ionic strength. Another aspect of the present invention relates with the development of a kit based on the method of the present invention, allowing for a quick and easy detection of specific nucleic acids sequences, including mutations or single nucleotide polymorphisms within nucleic acid sequences.

Colorimetric method and kit for the detection of specific nucleic acid sequences using metal nanoparticles functionalized with modified oligonucleotides, Tavares, {Jose Ricardo Ramos Franco}, Baptista {Pedro Miguel Ribeiro Viana}, Doria {Goncalo Maria Reimao Pinto De Franca}, and Flores {Alcino Orfeu De Leao} , nov, (2008) Abstract

The present invention relates to a colorimetric method for the detection of specific nucleic acids sequences, including mutations or single nucleotide polymorphisms within nucleic acid sequences, through the aggregation of nanoparticles functionalized with modified oligonucleotides, induced by an increase of the medium's ionic strength. Another aspect of the present invention relates with the development of a kit based on the method of the present invention, allowing for a quick and easy detection of specific nucleic acids sequences, including mutations or single nucleotide polymorphisms within nucleic acid sequences.

Detection and quantification system of biological matter constituted by one or more optical sensors and one or more light sources, associated process and related applications, Martins, {Rodrigo Ferrao De Paiva}, Baptista {Pedro Miguel Ribeiro Viana}, and Fortunato {Elvira Maria Correia} , dec, (2009) Abstract
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Detection and quantification system of biological matter constituted by one or more optical sensors and one or more light sources, associated process and related applications, Martins, {Rodrigo Ferrao De Paiva}, Baptista {Pedro Miguel Ribeiro Viana}, and Fortunato {Elvira Maria Correia} , may, (2009) Abstract

The present invention relates to a system and process for detection and/or qualitative and quantitative identification of the biological material, such as specific sequences of nucleic acids or proteins as antibodies, present in biological samples. The system is composed by one or more light sources (1) combined with one or more integrated optical photo sensors, or not, and various electronic components (4), necessary for obtaining/ processing of the signal emitted by the metal nanoprobes functionalized with a solution of biological composite, as well as also a micro-controller and a microprocessor, fixed or portable. This photosensor structure is able to detect and to quantify the colour variations produced by metal nanoprobes, being this preferentially gold, functionalized by oligonucleotides complementary to specific DNA/RNA sequences, proteins, as for instance antibodies and/or antigens related with certain disease, or other sample or solution of biological composite, that are to be investigated. The detection and quantification process is based on the response of a photosensor, singular or integrated, based on thin film technology of amorphous, nanocrystalline or microcrystalline silicon and their alloys, as well as the new active ceramic semiconductors, amorphous and not amorphous.

Detection and quantification system of biological matter constituted by one or more optical sensors and one or more light sources, associated process and related applications, Martins, {Rodrigo Ferrao De Paiva}, Baptista {Pedro Miguel Ribeiro Viana}, and Fortunato {Elvira Maria Correia} , mar, (2008) Abstract

The present invention relates to a system and process for detection and/or qualitative and quantitative identification of the biological material, such as specific sequences of nucleic acids or proteins as antibodies, present in biological samples. The system is composed by one or more light sources (1) combined with one or more integrated optical photo sensors, or not, and various electronic components (4), necessary for obtaining/ processing of the signal emitted by the metal nanoprobes functionalized with a solution of biological composite, as well as also a micro-controller and a microprocessor, fixed or portable. This photosensor structure is able to detect and to quantify the colour variations produced by metal nanoprobes, being this preferentially gold, functionalized by oligonucleotides complementary to specific DNA/RNA sequences, proteins, as for instance antibodies and/or antigens related with certain disease, or other sample or solution of biological composite, that are to be investigated. The detection and quantification process is based on the response of a photosensor, singular or integrated, based on thin film technology of amorphous, nanocrystalline or microcrystalline silicon and their alloys, as well as the new active ceramic semiconductors, amorphous and not amorphous.

Detection and quantification system of biological, matter constituted by one or more optical sensors and one or more light sources, associated process and related applications, Martins, {Rodrigo Ferrão De Paiva}, Baptista {Pedro Miguel Ribeiro Viana}, and Fortunato {Elvira Maria Correia} , feb, (2010) Abstract

The present invention relates to a system and process for detection and/or qualitative and quantitative identification of the biological material, such as specific sequences of nucleic acids or proteins as antibodies, present in biological samples. The system is composed by one or more light sources (1) combined with one or more integrated optical photo sensors, or not, and various electronic components (4), necessary for obtaining/processing of the signal emitted by the metal nanoprobes functionalized with a solution of biological composite, as well as also a micro-controller and a microprocessor, fixed or portable. This photosensor structure is able to detect and to quantify the colour variations produced by metal nanoprobes, being this preferentially gold, functionalized by oligonucleotides complementary to specific DNA/RNA sequences, proteins, as for instance antibodies and/or antigens related with certain disease, or other sample or solution of biological composite, that are to be investigated. The detection and quantification process is based on the response of a photosensor, singular or integrated, based on thin film technology of amorphous, nanocrystalline or microcrystalline silicon and their alloys, as well as the new active ceramic semiconductors, amorphous and not amorphous.

Método colorimétrico e estojo de detec{\c c}ão de sequências específicas de ácidos nucleicos através de nanopartículas metálicas funcionalizadas com oligonucleótidos modificados, Tavares, {José Ricardo Ramos Franco}, Baptista {Pedro Miguel Ribeiro Viana}, Dória {Goncalo Maria Reimao Pinto De Franca}, and de Flores {Alcino Orfeu Leão} , nov, (2008) Abstract

O presente invento relaciona-se com um método colorimétrico de detec{\c c}ão de sequências específicas de ácidos nucleicos, incluindo muta{\c c}ões ou polimorfismos de nucleótido único em sequências de ácidos nucleicos, através da agrega{\c c}ão de nanopartículas funcionalizadas com oligonucleótidos modificados induzida por um aumento da for{\c c}a iónica do meio. Outro aspecto do presente invento relaciona-se com o desenvolvimento de um estojo que ao aplicar a metodologia objecto da presente inven{\c c}ão, permite a rápida e fácil detec{\c c}ão de sequências específicas de ácidos nucleicos, incluindo muta{\c c}ões ou polimorfismos de nucleótido único em sequências de ácidos nucleicos.

Método colorimétrico e estojo de detec{\c c}ão de sequências específicas de ácidos nucléicos através de nanopartículas metálicas funcionalizadas com oligonucleotídos modificados., Tavares, {Jose Ricardo Ramos Franco}, Baptista {Pedro Miguel Ribeiro Viana}, Dória {Goncalo Maria Reimao Pinto De Franca}, and Flores {Alcino Orfeu De Leao} , nov, (2014) Abstract
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Método para controlo de reac{\c c}ões enzimáticas de síntese de ácidos nucleicos através de nucleótidos funcionalizados com derivados de cumarina fotolábeis, Pinheiro, {André Alexandre Cotta Guerra Vidal}, {De Lima} {João Carlos Dos Santos Silva Pereira} E., and Baptista {Pedro Miguel Ribeiro Viana} , mar, (2009) Abstract

O presente invento relaciona-se com um método para controlo de reac{\c c}ões enzimáticas de síntese de ácidos nucleicos, recorrendo a nucleótidos funcionalizados com derivados de 4-metilcumarinas (1) protectores e fotolábeis. Quando ligado aos nucleótidos (2), o grupo cumarinico (3) impede que estes sejam utilizados como substrato por parte das enzimas, impossibilitando a ocorrência de reac{\c c}ão. Através de irradia{\c c}ão com radia{\c c}ão electromagnética, o grupo cumarinico é libertado, ficando o nucleótido disponível para a reac{\c c}ão. Desta forma, as reac{\c c}ões enzimáticas de síntese de ácidos nucleicos podem ser controladas através da luz.

Porphyrin Pigments in Polychaeta: Explorations on the Evolution of Haem Metabolism in Marine Eumetazoans, Martins, C., Rodrigo {A. P. }, Madeira C., D'Ambrosio M., Goncalves C., Parola {A. J. }, Grosso {A. R. }, Baptista {P. V. }, Fernandes {A. R. }, and Costa {P. M. } , jan, Volume 18, (2020) Abstract
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Sistema de deteccion y cuantificacion de material biologico constituido por uno o mas sensores opticos y una o mas fuentes de luz, proceso asociado y aplicaciones relacionadas., Martins, {Rodrigo Ferrao De Paiva}, Baptista {Pedro Miguel Ribeiro Viana}, and Fortunato {Elvira Maria Correia} , sep, (2011) Abstract

Sistema para detección, identificación y cuantificación en material biológico, compuesto por una o más fuentes de luz (1) combinado con uno o más fotosensores ópticos (6 y 7) y diversos componentes electrónicos (4), necesarios para obtener/procesar la señal emitida caracterizado por: a) La fuente de luz (1), pulsada (2) o no, compuesta de láseres de estado sólido de baja energía o diodos emisores de luz, cuyo rango de longitud de onda está localizado entre 400 y 800 nm con una intensidad de luminosidad controlable que varía entre los valores de 0.01 mW/cm 2 y 100 mW/cm 2 ; b) El fotosensor, sencillo (6 y 7a) y (6 y 7b) o integrado (6, 4 y 7) compuesto de películas delgadas de silicio amorfo o nanocristalino o microcristalino y/o por semiconductores de cerámica tales como IGZO, IAgZO, SnZIO, GZIO, CuOIZ, GITO, entre otros, y basado en estructuras tipo pi'ii'n o MIS, que funciona en un rango de longitudes de onda desde el infrarrojo hasta el ultravioleta, y prové una información cualitativa y cuantitativa basada en la hibridización especifica y selectiva de sondas funcionalizadas con nanopartículas de metal; c) Siendo provista la eliminación del sistema a través de una fuente de energía convencional o a través de baterías fotovoltaicas, que dan portabilidad al sistema, siendo focalizada la luz emitida sobre la muestra, preferiblemente utilizando microlentes, siendo la muestra o muestras no fijadas físicamente al sensor o sensores, colocando la muestra biológica referida (5) sobre el lado opuesto (6) del sustrato donde se deposita el fotosensor (6 y 7).

Sistema de detec{\c c}ão e quantifica{\c c}ão de matéria biológica constituído por um ou mais sensores ópticos e uma ou mais fontes luminosas, processo associado e respectivas utiliza{\c c}ões, Martins, {Rodrigo Ferrao De Paiva}, Pedro {Miguel Ribeiro Viana Baptista}, and Fortunato {Elvira Maria Correia} , mar, (2008) Abstract

O presente invento relaciona-se com um novo sistema e processo para detec{\c c}ão e/ou identifica{\c c}ão qualitativa e quantitativa de matéria biológica, tais como sequências específicas de ácidos nucleicos ou proteínas, como anticorpos, presentes em amostras biológicas. O sistema é constituído por uma ou mais fontes luminosas combinadas, com um ou mais fotossensores ópticos integrados, ou não, e componentes electrónicos vários, necessários para obten{\c c}ão/condicionamento do sinal emitido por nanossondas de metal funcionalizadas com a solu{\c c}ão de composto biológico, bem como ainda um micro-controlador e um microprocessador, portável ou fixo. Este fotossensor é capaz de detectar e quantificar as diferen{\c c}as colorimétricas produzidas por nanossondas de metal, sendo este preferencialmente o ouro, funcionalizadas por oligonucleotídeos complementares às sequências específicas de ADN/ARN, proteínas, como por exemplo anticorpos e/ou antigénios relacionados com determinada doen{\c c}a, ou outra amostra ou solu{\c c}ão de composto biológico, que se pretende pesquisar. O processo de detec{\c c}ão e quantifica{\c c}ão baseia-se na resposta de um fotossensor, singular ou integrado, baseado na tecnologia de filmes finos de sílicio amorfo, nanocristalino ou mícrocristalino, e suas ligas, e também nos novos cerâmicos semicondutores activos, amorfos e não morfos. O referido sistema e processo de detec{\c c}ão e/ou identifica{\c c}ão de matéria biológica tem aplica{\c c}ão na biotecnologia, incluindo a biomedicina.

Sistema de dete{\c c}ão e quantifica{\c c}ão de matéria biológica constituído por um ou mais sensores óticos e uma ou mais fontes luminosas, processo associado e respectivas utiliza{\c c}ões, Martins, {Rodrigo Ferrao De Paiva}, Baptista {Pedro Miguel Ribeiro Viana}, and Fortunato {Elvira Maria Correia} , oct, (2013) Abstract

sistema de dete{\c c}ão e quantifica{\c c}ão de matéria biológica constituído por um ou mais sensores óticos e uma ou mais fontes luminosas, processo associado e aplica{\c c}ões relacionadas a inven{\c c}ão atual relaciona- se a um sistema e a um processo para a dete{\c c}ão e/ou a identifica{\c c}ão qualitativa e quantitativa do material biológico, tal como seqüências específicas de ácidos nucleicos ou de proteínas como anticorpos, presente em amostras biológicas. o sistema é composto por uma ou mais fontes luminosas ( 1) combinadas com um ou mais fotosensores óticos integrados, ou não, e vários componentes eletrônicos ( 4) , necessários para obter/processar o sinal emitido pelas nanosondas de metal funcionalizadas com uma solu{\c c}ão de compósi to biológico, assim como igualmente um microcontrolador e um microprocessador, reparados ou portátil. esta estrutura do fotosensor pode detectar e determinar as varia{\c c}ões da cor produzidas por nanosondas do metal, sendo este preferencialmente ouro, funcionalizado pelos oligonucleotídeos complementares às seqüências específicas, as proteínas de dna/rna, como por exemplo os anticorpos e/ou os antígenos relativos a determinada doen{\c c}a, ou a outra amostra ou solu{\c c}ão de composto biológico, que devem ser investigada. a dete{\c c}ão e o processo da quantifica{\c c}ão são baseados na resposta de um fotosensor, singular ou integrados, baseado na tecnologia da película fina de silicones amorfos, nanocristalinos ou microcristalino e suas ligas, assim como os semicondutores cerâmicos ativos novos, amorfos e não amorfos.