Traditional Cloning Techniques Research Articles

Bioengineering a Cadmium Sensing Green Fluorescent Protein based Whole-Cell Biosensor from Pseudomonas aeruginosa

Heavy metal toxicity remediation is a major issue due to the increase in industrial waste production, with cadmium being one of the major pollutants. An approach involving homologous cloning was made to bioengineer a microbial cadmium biosensor from a strain of Pseudomonas aeruginosa. The promoter pCadR from P. aeruginosa was cloned into a vector pEGFP-N2. Gibson assembly cloning method was chosen considering the several advantages it holds over the traditional cloning techniques. Escherichia coli DH5 alpha strain was used as the host cell, which on sensing cadmium, produced fluorescence using the reporter gene called green fluorescent protein (GFP). The clone, pEGFP-N2CadR, was subjected to increasing concentrations of cadmium chloride to determine the sensitivity. It was observed that pEGFP-N2CadR responded well to micromolar concentrations of cadmium chloride, and hence it may be used to detect low concentrations of cadmium. To determine the specificity of the sensor, it was also tested with lead nitrate and copper sulfate solutions. It was determined that the biosensor had non-specific interactions with other metals. The interaction of the promoter with the metals was weak as compared to previous studies, and this was attributed to slight variations and mutations observed in the promoter sequence following subsequent rounds of sequencing. As the fluorescent intensities of the sensor in response to the metals were not highly distinguishable, this biosensor was not classified as an effective cadmium sensor. Further studies for determining the promoter interaction and affinity towards various metals at varying concentrations are required to validate the results obtained.

A Practical Comparison of Ligation-Independent Cloning Techniques

The precise assembly of specific DNA sequences is a critical technique in molecular biology. Traditional cloning techniques use restriction enzymes and ligation of DNA in vitro, which can be hampered by a lack of appropriate restriction-sites and inefficient enzymatic steps. A number of ligation-independent cloning techniques have been developed, including polymerase incomplete primer extension (PIPE) cloning, sequence and ligation-independent cloning (SLIC), and overlap extension cloning (OEC). These strategies rely on the generation of complementary overhangs by DNA polymerase, without requiring specific restriction sites or ligation, and achieve high efficiencies in a fraction of the time at low cost. Here, we outline and optimise these techniques and identify important factors to guide cloning project design, including avoiding PCR artefacts such as primer-dimers and vector plasmid background. Experiments made use of a common reporter vector and a set of modular primers to clone DNA fragments of increasing size. Overall, PIPE achieved cloning efficiencies of ∼95% with few manipulations, whereas SLIC provided a much higher number of transformants, but required additional steps. Our data suggest that for small inserts (<1.5 kb), OEC is a good option, requiring only two new primers, but performs poorly for larger inserts. These ligation-independent cloning approaches constitute an essential part of the researcher's molecular-tool kit.

A series of TA-based and zero-background vectors for plant functional genomics.

With the sequencing of genomes from many organisms now complete and the development of high-throughput sequencing, life science research has entered the functional post-genome era. Therefore, deciphering the function of genes and how they interact is in greater demand. To study an unknown gene, the basic methods are either overexpression or gene knockout by creating transgenic plants, and gene construction is usually the first step. Although traditional cloning techniques using restriction enzymes or a site-specific recombination system (Gateway or Clontech cloning technology) are highly useful for efficiently transferring DNA fragments into destination plasmids, the process is time consuming and expensive. To facilitate the procedure of gene construction, we designed a TA-based cloning system in which only one step was needed to subclone a DNA fragment into vectors. Such a cloning system was developed from the pGreen binary vector, which has a minimal size and facilitates construction manipulation, combined with the negative selection marker gene ccdB, which has the advantages of eliminating the self-ligation background and directly enabling high-efficiency TA cloning technology. We previously developed a set of transient and stable transformation vectors for constitutive gene expression, gene silencing, protein tagging, subcellular localization analysis and promoter activity detection. Our results show that such a system is highly efficient and serves as a high-throughput platform for transient or stable transformation in plants for functional genome research.

Evaluation of Internal Standards in a Competitive Nucleic Acid Sequence-Based Amplification Assay

An end-point quantitative nucleic acid sequence-based amplification (NASBA) reaction with two exogenous internal standards for the detection of the model analyte E. coli clpB mRNA was developed and statistically analyzed. Electrochemiluminescence was chosen as a highly sensitive detection means allowing careful evaluation of the internal standards used. The two internal standards examined had been designed previously using a novel and rapid NASBA-based method. Initially, each standard was used separately in a NASBA reaction; subsequently, two internal standards were added into one reaction at different concentrations. The accuracy and precision of the data obtained were analyzed using linear and multiple regression analysis. In the case of single-standard reactions, the accuracy was >95% and the precision >98.5%. In the case of double-standard reactions, the accuracy increased to >97%. With a single internal standard, 3 orders of magnitude of target sequence could be quantified; using three different concentrations of one internal standard, the dynamic range increased to 5 orders of magnitude. In both cases, a detection limit as low as 0.14 pg of target sequence was obtained. In the case of double-internal standard reactions, a dynamic range with 5 orders of magnitude and a detection limit of 1.76 pg was determined. The high-performance quality of the internal standards was assumed to be in part due to the unique synthesis process using two NASBA reactions rather than traditional cloning techniques.

Descobrindo Genes no Século XXI: Enfoque na Área de Onco-Endocrinologia

A área de endocrinologia genética e oncológica tem sido alvo de enorme avanço nos anos recentes. A descoberta de genes responsáveis por neoplasias hereditárias nas últimas décadas representou uma fonte importante de informações concernentes à avaliação de risco, prevenção e aconselhamento genético. Neste particular, a caracterização do gene responsável pela neoplasia endócrina múltipla tipo 2 (MEN 2) representou a "pedra angular" para o desenvolvimento do campo de oncogenética clínica. Portanto, estima-se que o estudo genético e funcional das neoplasias hereditárias será igualmente capaz de liderar o avanço para um melhor manuseio clínico e terapêutico destas doenças. Um dos grandes desafios do futuro reside em se entender o intrincado mecanismo de interação entre genes e proteínas no controle do desenvolvimento e regulação dos diferentes sistemas biológicos. Uma das conseqüências mais antecipadas deste avanço é a sua aplicação para o tratamento específico e "individualizado" de todas as doenças humanas. Esta breve revisão tratará de aspectos gerais que envolvem o processo de identificação de novos genes e sua associação com condições clínicas específicas. As técnicas clássicas de clonagem serão apresentadas ao lado de estratégias modernas de identificação e análise de genes. O papel da bioinformática no Projeto Genoma Humano e o imenso potencial que esta informação traz para acelerar o processo de caracterização de novos grupos de genes serão brevemente discutidos.