Heteroduplex formation and S1 digestion for mapping alternative splicing sites.

The identification of alternatively spliced transcripts has contributed to a better comprehension of developmental mechanisms, tissue-specific physiological processes and human diseases. Polymerase chain reaction amplification of alternatively spliced variants commonly leads to the formation of heteroduplexes as a result of base pairing involving exons common between the two variants. S1 nuclease cleaves single-stranded loops of heteroduplexes and also nicks the opposite DNA strand. In order to establish a strategy for mapping alternative splice-prone sites in the whole transcriptome, we developed a method combining the formation of heteroduplexes between 2 distinct splicing variants and S1 nuclease digestion. For 20 consensuses identified here using this methodology, 5 revealed a conserved splice site after inspection of the cDNA alignment against the human genome (exact splice sites). For 8 other consensuses, conserved splice sites were mapped at 2 to 30 bp from the border, called proximal splice sites; for the other 7 consensuses, conserved splice sites were mapped at 40 to 800 bp, called distal splice sites. These latter cases showed a nonspecific activity of S1 nuclease in digesting double-strand DNA. From the 20 consensuses identified here, 5 were selected for reverse transcription-polymerase chain reaction validation, confirming the splice sites. These data showed the potential of the strategy in mapping splice sites. However, the lack of specificity of the S1 nuclease enzyme is a significant obstacle that impedes the use of this strategy in large-scale studies.

Self-complementary sequences induce the formation of double-stranded filamentous phages.

The single strand nature of the filamentous phage (Ff) genome is currently one of the main drawbacks for their application as gene delivery vectors. In this work, by the incorporation of inverted self complementary sequences into the genome of Ff, we were able to convert single strand genome of Ff into double strand DNA structures. The presence of self complementary sequences in phage genome did not affect viral yields significantly, and the formation of double strands structures was successfully determined by a Mung Bean Nuclease resistance assay. Upon transfection into HEK293 cells, the double strand DNA structures showed to be readable by the transcriptional machinery of mammalian cells.

Horizontal transfer and hypovirulence associated with double-stranded RNA in Beauveria bassiana.

Beauveria bassiana strains from different hosts and geographic origins were assayed for the presence of double-stranded RNA (dsRNA). Two of them (15.4%) showed extra bands, with approximately 4.0-3.5 kb and 2-0.7 kb, respectively, after electrophoretic separation of undigested nucleic acids. Virus-like particles were approximately 28-30 nm diam. The dsRNA was maintained after conidiogenesis (vertical transmission) and was transmitted horizontally by hyphal anastomosis. Strains purged of dsRNA obtained after cycloheximide treatment showed increased conidial production when compared with strains carrying dsRNA particles. Bioassays demonstrated hypovirulence associated with dsRNA. The mean mortality against the insect Euschistus heros was reduced in strains containing dsRNA when compared with the isogenic dsRNA-free ones.

The binding of zinc(II) to Mung Bean Nuclease. A voltammetric study.

Binding of zinc to Mung Bean Nuclease was investigated by anodic stripping voltammetry and cyclic voltammetry. These methods rely on the direct monitoring of the oxidation current of zinc in the absence and presence of Mung Bean Nuclease. Titration curves of Zn(2+) with the enzyme were obtained in concentrations ranging from 1.08x10(-9) to 1.07x10(-8) M and 1.16x10(-8) to 1.04x10(-7) M. The acquired data were used to calculate the dissociation constant and the stoichiometry of the complex. The binding sites of zinc in the Mung Bean Nuclease molecule were investigated using cyclic voltammetry. Two types of binding sites for zinc were identified and were attributed to a mononuclear exposed zinc-binding site with catalytic function and to an inaccessible binuclear zinc-binding site with structural functions.

Nus A is involved in transcriptional termination on lambda tI.

The transcriptional terminator tI generates the 3'end of the integrase (int) gene transcript that is read from the lambda PI promoter in lambda phage. We have studied the factors that affect transcription termination in vitro and in vivo at the lambda tI terminator. In vitro transcriptional studies showed that tI is about 80% efficient in the presence of purified NusA protein, whereas it is only about 50% efficient in its absence. In vivo studies, where the readthrough transcript of lambda tI was measured by quantitative dot blot analysis, gave about 80% efficiency in wild-type strains, but only 60% in the nusA1 mutant strain at non-permissive temperatures. These results support the idea that termination at lambda tI in vivo involves interaction with the NusA factor.

Double-stranded RNA in the entomopathogenic fungus metarhizium flavoviride.

Bands of dsRNA were detected in five out of seven isolates of the entomopathogenic fungus Metarhizium flavoviride. The identity of these bands was proven by RNase and S1-nuclease treatments. The transference of dsRNA between isolates (from CG291 to CG442) was successfully carried out through forced heterokaryons. Isogenic strains, with or without dsRNA, were submitted to virulence tests against the grasshopper Rhammatocerus schistocercoides. In contrast to what has been found in some phytopathogenic fungi, these dsRNA fragments did not cause hypovirulence to M. flavoviride.