Publications in the Year: 2008

Journal Article

Baptista, P, Pereira E, Eaton P, c}alo Doria G{\c, Miranda A, Gomes I, Quaresma P, Franco R. 2008. Gold nanoparticles for the development of clinical diagnosis methods, jun. Analytical and Bioanalytical Chemistry. 391:943–950., Number 3: Springer Abstract

The impact of advances in nanotechnology is particularly relevant in biodiagnostics, where nanoparticle-based assays have been developed for specific detection of bioanalytes of clinical interest. Gold nanoparticles show easily tuned physical properties, including unique optical properties, robustness, and high surface areas, making them ideal candidates for developing biomarker platforms. Modulation of these physicochemical properties can be easily achieved by adequate synthetic strategies and give gold nanoparticles advantages over conventional detection methods currently used in clinical diagnostics. The surface of gold nanoparticles can be tailored by ligand functionalization to selectively bind biomarkers. Thiol-linking of DNA and chemical functionalization of gold nanoparticles for specific protein/antibody binding are the most common approaches. Simple and inexpensive methods based on these bio-nanoprobes were initially applied for detection of specific DNA sequences and are presently being expanded to clinical diagnosis.

Silva, {LB }, Baptista P, Raniero L, c}alo Doria G{\c, de Martins {RFP}, Fortunato {EMC}. 2008. Characterization of optoelectronic platform using an amorphous/nanocrystalline silicon biosensor for the specific identification of nucleic acid sequences based on gold nanoparticle probes, jun. Sensors and Actuators B: Chemical. 132:508–511., Number 2: Elsevier Abstract

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Pinheiro, {AV}, Baptistap P, Lima {JC}. 2008. Light activation of transcription: photocaging of nucleotides for control over RNA polymerization, aug. Nucleic Acids Research. 36, Number 14: Oxford University Press Abstract

We describe the use of ATP caged with [7-(diethylamino)coumarin-4-yl]methyl (DEACM) for light-controlled in vitro transcription reactions. Polymerization is blocked when DEACM is bonded to the gamma phosphate group of the ATP molecule. Controlled light irradiation releases ATP and transcription is initiated. In order to provide full control over the process, conditions involved in substrate release, nucleotide availability after release and the effect of the released coumarin in RNA polymerization were assessed in further detail. Together, our data provide the first direct evidence of control over enzymatic polymerization of nucleic acids through light. This approach may provide researchers with a unique tool for the study of biological processes at a molecular level.

Giestas, L, Ferreira {GNM }, Baptista {PV}, Lima {JC}. 2008. Multiplexed spectral coding for simultaneous detection of DNA hybridization reactions based on FRET, aug. Sensors and Actuators B: Chemical. 134:146–157., Number 1: Elsevier Abstract

Fluorescence resonance energy transfer (FRET) is widely used in spectral codification of information at the molecular level, and can be used to generate several layers of information on a DNA chip. We used two oligonucleotides (probes) labeled with different donor (harvesting) molecules in hybridization experiments with complementary oligonucleotides labeled with four different acceptors (targets). By looking at the fluorescence response of the sample after {"}specific{"} excitation of each donor molecule (by {"}specific{"} we mean a wavelength where one of the donors is predominantly excited), we inspected the possibility t o identify the complementary oligonucleotide hybridized to the probe, in mixtures containing two donor probe/acceptor target pairs. In most samples (13 out of the 16 possible), it is trivial to identify the complementary target that is hybridized to the excited donor probe in the mixtures. The major limitations of the chosen system arise when very different concentrations of donor probe/acceptor target pairs are present in the same sample. (C) 2008 Elsevier B.V. All rights reserved.

de Martins, {RFP}, Baptista P, Silva {LB}, Raniero L, c}alo Dória G{\c, Franco R, Fortunato E. 2008. Identification of unamplified genomic DNA sequences using gold nanoparticle probes and a novel thin film photodetector, may. Journal of Non-Crystalline Solids. 354:2580–2584., Number 19-25: Elsevier Abstract

This paper describes a novel colorimetric method for detection of nucleic acid targets in a homogeneous format with improved sensitivity by means of a system based on the combination of a tunable monochromatic light source and an amorphous/nanocrystalline silicon photodetector that detects color and light intensity changes undergone by samples/assays containing tailored gold nanoparticles probes. This new low cost, portable, fast and simple optoelectronic platform, with the possibility to be re-used, permits detection of at least 400 fentomole of specific DNA sequences without target or signal amplification and was applied to the rapid detection of human pathogens in large variety of clinical samples such as Mycobacterium tuberculosis.

Miscellaneous

Tavares, {JRRF}, Baptista {PMRV}, Doria {GMRPDF}, Flores {AODL}. 2008. Colorimetric method and kit for the detection of specific nucleic acid sequences using metal nanoparticles functionalized with modified oligonucleotides, nov. 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.

Martins, {RFDP}, Baptista {PMRV}, Fortunato {EMC}. 2008. 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, mar. 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.

Martins, {RFDP}, Pedro {MRVB}, Fortunato {EMC}. 2008. 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, mar. 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.

Tavares, {JRRF}, Baptista {PMRV}, Dória {GMRPDF}, de Flores {AOL}. 2008. Método colorimétrico e estojo de detec{\c c}ão de sequências específicas de ácidos nucleicos através de nanopartículas metálicas funcionalizadas com oligonucleótidos modificados, nov. 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.