Accurate scanning of the BssHII endonuclease in search for its DNA cleavage site

A facilitated diffusion mechanism has been proposed to account for the kinetic efficiency with which restriction endonucleases are able to locate DNA recognition sites. Such a mechanism involves the initial formation of a nonspecific complex upon collision of the protein with the DNA, with the subsequent diffusion of the protein along the DNA helix until either a recognition site is located or the protein dissociates into solution. Protein translocation may be facilitated by either sliding along the DNA, hopping to nearby sites, or intersegment transfer over larger distances. Previous analyses of the manner in which restriction enzymes cleave DNA substrates did rule out the latter mechanism. To discriminate between protein sliding or scanning and protein hopping, we designed a unique DNA template with three overlapping, mutually exclusive recognition sites for the BssHII endonuclease. Analysis of the cleavage pattern demonstrated efficient usage of both external sites, whereas the centrally located site was not efficiently cleaved. These results confirm that linear diffusion of the BssHII enzyme occurs by scanning along the DNA. Furthermore, the scanning enzyme was found to stop and cleave at the first site encountered. Thus, a sliding restriction endonuclease recognizes cleavage sites with high fidelity, without skipping of potential sites.

Requirements for DNA strand transfer during reverse transcription in mutant HIV-1 virions

Retroviruses convert their RNA genome into a DNA form by means of reverse transcription. According to the current model of reverse transcription, two strand transfer reactions are needed to synthesize a full-length DNA genome. Because reverse transcription is initiated close to the 5' end of the RNA genome, the first strand transfer translocates the minus-strand cDNA to the 3' end of the viral genome. This jump is facilitated by the presence of a perfect repeat element (R) at both ends of a retroviral genome. Strand transfer has been extensively studied in in vitro systems with purified reverse transcriptase enzyme (RT) and nucleic acid donor and acceptor templates. In this study, we set out to test several parameters of the strand transfer reaction as it occurs in cells infected with the human immunodeficiency virus (HIV-1). We constructed mutant HIV-1 genomes with 3' R acceptor sequences that were specifically altered either in length or structure. Analysis of the replication characteristics of the mutant viruses indicates that repeats much shorter than the wild-type 97-nucleotides R region can efficiently act as acceptors during reverse transcription. Furthermore, the introduction of excessively stable hairpin structures within the 3' R element did only marginally affect the strand transfer efficiency. We also analysed the DNA forms inherited upon infection of cells with HIV-1 templates with multiple 3' R copies. These experiments indicate that various 3' R repeats can serve as acceptor during minus-strand DNA transfer.

A sensitive promoter assay based on the transcriptional activator Tat of the HIV-1 virus

We developed a sensitive vector system for the analysis of weak promoter activities. This promoter assay is based on the transcriptional activator protein, Tat, of human immunodeficiency virus type 1 (HIV-1). High-level expression of HIV requires activation in trans by Tat of the promoter in the long terminal repeat (LTR). Here we describe the construction of a promoterless pTat vector. Foreign promoter elements can be inserted upstream from the tat gene, and expression of Tat protein is measured in trans on a co-transfected LTR-CAT reporter plasmid. We show that this binary system is more sensitive than standard pCAT reporter assays.

Intracellular analysis of in vitro modified HIV Tat protein

Human immunodeficiency viruses HIV-1 and HIV-2 encode a Tat protein that specifically activates transcription from the viral long terminal repeat. To characterize the properties of the Tat proteins, we have expressed them in Escherichia coli. The purified Tat protein was biochemically analyzed and tested for activity upon electroporation into human cell lines. This protein electroporation was used for the intracellular analysis of in vitro modified Tat protein. Our results indicate that the transcriptionally active form of the Tat protein is a monomer. Furthermore, we found that Tat activity is dramatically inhibited by preincubation of the protein with strongly reducing agents. In contrast, no inhibitory effect was measured upon incubation with metal-chelating reagents. These results suggest that the cysteine residues of Tat are involved in the formation of intramolecular disulfide bonds.