Fast assembly of non-thiolated DNA on gold surface at lower pH

In a typical protocol for attaching DNA to a gold electrode, thiolated DNA is incubated with the electrode at neutral pH overnight. Here we report fast adsorption of non-thiolated DNA oligomers on gold electrodes at acidic pH (i.e., pH ~3.0). The peak-to-peak potential difference and the redox peak currents in typical cyclic voltammetry of [Fe(CN)6]3- are investigated to monitor the attachment. Compared with incubation at neutral pH, the lower pH can significantly promote the adsorption processes, enabling efficient adsorption even in 30min. The adsorption rate is DNA concentration-dependent, while the ionic strength shows no influence. Moreover, the adsorption is base-discriminative, with a preferred order of A>C≫G, T, which is attributed to the protonation of A and C at low pH and their higher binding affinity to gold surface. The immobilized DNA is functional and can hybridize with its complementary DNA but not a random DNA. This work is promising to provide a useful time-saving strategy for DNA assembly on gold electrodes, allowing fast fabrication of DNA-based biosensors and devices. © 2013 Elsevier Inc.

Simple heuristics for the assembly line worker assignment and balancing problem

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Strain differentiation of Trichophyton rubrum by randomly amplified polymorphic DNA and analysis of rDNA nontranscribed spacer

Trichophyton rubrum is the most common pathogen causing dermatophytosis. Molecular strain-typing methods have recently been developed to tackle epidemiological questions and the problem of relapse following treatment. A total of 67 strains of T rubrum were screened for genetic variation by randomly amplified polymorphic DNA (RAPD) analysis, with two primers, 5'-d[GGTGCGGGAA]-3' and 5'-d[CCCGTCAGCA]-3', as well as by subrepeat element analysis of the nontranscribed spacer of rDNA, using the repetitive subelements TRS-1 and TRS-2. A total of 12 individual patterns were recognized with the first primer and 11 with the second. Phylogenetic analysis of the RAPID products showed a high degree of similarity (> 90 %) among the epidemiologically related clinical isolates, while the other strains possessed 60% similarity. Specific amplification of TRS-1 produced three strain-characteristic banding patterns (PCR types); simple patterns representing one copy of TRS-1 and two copies of TRS-2 accounted for around 85 % of all isolates. It is concluded that molecular analysis has important implications for epidemiological studies, and RAPID analysis is especially suitable for molecular typing in T. rubrum.

Road-killed wild animals: a preservation problem useful for eco-epidemiological studies of pathogens

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Two short peptides including segments of subunit A of Escherichia coli DNA gyrase as potential probes to evaluate the antibacterial activity of quinolones

Quinolones constitute a family of compounds with a potent antibiotic activity. The enzyme DNA gyrase, responsible for the replication and transcription processes in DNA of bacteria, is involved in the mechanism of action of these drugs. In this sense, it is believed that quinolones stabilize the so-called 'cleavable complex' formed by DNA and gyrase, but the whole process is still far from being understood at the molecular level. This information is crucial in order to design new biological active products. As an approach to the problem, we have designed and synthesized low molecular weight peptide mimics of DNA gyrase. These peptides correspond to sequences of the subunit A of the enzyme from Escherichia coli, that include the quinolone resistance-determining region (positions 75-92) and a segment containing the catalytic Tyr-122 (positions 116-130). The peptide mimic of the non-mutated enzyme binds to ciprofloxin (CFX) only when DNA and Mg2+ were present (Kd = 1.6 × 10 -6 m), a result previously found with DNA gyrase. On the other hand, binding was reduced when mutations of Ser-83 to Leu-83 and Asp-87 to Asn-87 were introduced, a double change previously found in the subunit A of DNA gyrase from several CFX-resistant clinical isolates of E. coli. These results suggest that synthetic peptides designed in a similar way to that described here can be used as mimics of gyrases (topoisomerases) in order to study the binding of the quinolone to the enzyme-DNA complex as well as the mechanism of action of these antibiotics. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd.

Estrutura populacional de Lutzomya longipalpis através da amplificação e sequenciamento do segmento ribossomal 12S de DNA mitocondrial

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Amplificação de DNA circulante para o diagnóstico da cisticercose bovina

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Condensação-psi do DNA: um estudo teórico e experimental

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Modelos de redes unidimensionais aplicados ao estudo termodinâmico do DNA

Pós-graduação em Biofísica Molecular - IBILCE

Detecção de DNA de micobactérias dos complexos M. tuberculosis e M. avium em amostras parafinadas de pacientes transplantados renais

Introduction: Tuberculosis (TB) is a granulomatous disease caused by Mycobacterium tuberculosis. The genus Mycobacteriumhas two different complexes: M. tuberculosis Complex and M. avium Complex. This is a global health epidemic and remains a major global health problem, besides, the clinical severity of TB is significantly higher in transplanted patients. The detection of these mycobacteria complexes in transplanted patients, by molecular methods, is fundamental for quick treatment of patients and can contribute for rapid and accuracy of diagnosis. Objective: To detect mycobacteria DNA of M. tuberculosis and M. avium Complexes in formalin fixed paraffin-embedded samples (FFPE) of two patients groups: non transplanted and transplanted. Materials and Methods: The study includes 40 FFPE biopsies separated in four groups: NTP – presence of epithelioid granuloma and positive ZN, non-transplanted patients – 9 samples; NTN - presence of epithelioid granuloma and negative ZN, non-transplanted patients – 10 samples; TP – positive ZN, transplanted patients – 9 samples; TN – negative ZN, transplanted patients – 7 samples. Sections were cut for DNA extraction. Samples were submitted to PCR for amplification of: a) β-actin, b) IS6110 insertion and c) IS1245 insertion. DNA evaluation was made by spectrophotometry and efficiency and PCR analysis was made by agarose gels under UV light. Results: In all samples processed, 97.1% were positive for human β-actin gene. In22.2% of NTP group were found the IS6110 insertion sequencebut the IS1245 wasn´t. In the NTN group was not found any sequence. In theTP group, 11.1% of the samples were positive for IS6110 and also 11,1% werepositive for IS1245. In the TN group, 14.3% of the samples were positive forIS6110 and for IS1245, 14.3% was also positive. Conclusion: Although factors such as DNA degradation after formalin fixation and paraffin embedding, were possible to detect DNA from the human gene ...