Structural Insights into the HIV-1 Minus-strand Strong-stop DNA.

An essential step of human immunodeficiency virus type 1 (HIV-1) reverse transcription is the first strand transfer that requires base pairing of the R region at the 3'-end of the genomic RNA with the complementary r region at the 3'-end of minus-strand strong-stop DNA (ssDNA). HIV-1 nucleocapsid protein (NC) facilitates this annealing process. Determination of the ssDNA structure is needed to understand the molecular basis of NC-mediated genomic RNA-ssDNA annealing.

RNA SHAPE chemistry with aromatic acylating reagents.

As chemical methods for RNA secondary structure determination, SHAPE chemistry (selective 2'-hydroxyl acylation analyzed by primer extension) has been developed to specifically target flexible nucleotides (often unpaired nucleotides) independently to their purine or pyrimidine nature. In order to improve the specificity of acylating reagents towards unpaired nucleotides, we have explored the reactivity of symmetric anhydrides, acyl fluorides, active esters like succinimidyl ester and cyanomethyl esters for 2'-O-acylation reaction. Among the tested compounds, only the acyl fluoride 4 showed a low reactivity (compared to NMIA).

Dynamic interactions of the HIV-1 Tat with nucleic acids are critical for Tat activity in reverse transcription.

The HIV-1 transactivator of transcription (Tat) protein is thought to stimulate reverse transcription (RTion). The Tat protein and, more specifically, its (44-61) domain were recently shown to promote the annealing of complementary DNA sequences representing the HIV-1 transactivation response element TAR, named dTAR and cTAR, that plays a key role in RTion. Moreover, the kinetic mechanism of the basic Tat(44-61) peptide in this annealing further revealed that this peptide constitutes a representative nucleic acid annealer.

Intrinsic nucleic acid dynamics modulates HIV-1 nucleocapsid protein binding to its targets.

HIV-1 nucleocapsid protein (NC) is involved in the rearrangement of nucleic acids occurring in key steps of reverse transcription. The protein, through its two zinc fingers, interacts preferentially with unpaired guanines in single-stranded sequences. In mini-cTAR stem-loop, which corresponds to the top half of the cDNA copy of the transactivation response element of the HIV-1 genome, NC was found to exhibit a clear preference for the TGG sequence at the bottom of mini-cTAR stem.

Structural determinants of TAR RNA-DNA annealing in the absence and presence of HIV-1 nucleocapsid protein.

Annealing of the TAR RNA hairpin to the cTAR DNA hairpin is required for the minus-strand transfer step of HIV-1 reverse transcription. HIV-1 nucleocapsid protein (NC) plays a crucial role by facilitating annealing of the complementary hairpins. To gain insight into the mechanism of NC-mediated TAR RNA-DNA annealing, we used structural probes (nucleases and potassium permanganate), gel retardation assays, fluorescence anisotropy and cTAR mutants under conditions allowing strand transfer.

Structural insights into the cTAR DNA recognition by the HIV-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC.

An essential step of the reverse transcription of the HIV-1 genome is the first strand transfer that requires the annealing of the TAR RNA hairpin to the cTAR DNA hairpin. HIV-1 nucleocapsid protein (NC) plays a crucial role by facilitating annealing of the complementary hairpins. Using nuclear magnetic resonance and gel retardation assays, we investigated the interaction between NC and the top half of the cTAR DNA (mini-cTAR).

Structural and dynamic characterization of the upper part of the HIV-1 cTAR DNA hairpin.

First strand transfer is essential for HIV-1 reverse transcription. During this step, the TAR RNA hairpin anneals to the cTAR DNA hairpin; this annealing reaction is promoted by the nucleocapsid protein and involves an initial loop-loop interaction between the apical loops of TAR and cTAR. Using NMR and probing methods, we investigated the structural and dynamic properties of the top half of the cTAR DNA (mini-cTAR).

Structural requirements for nucleocapsid protein-mediated dimerization of avian leukosis virus RNA.

The avian leukosis virus (ALV) belongs to the alpha group of retroviruses that are widespread in nature. The 5'-untranslated region of ALV genome contains the L3 element that is important for virus infectivity and the formation of an unstable RNA dimer in vitro. The L3 sequence is predicted to fold into a long stem-loop structure with two internal loops and an apical one.

Specific interactions between HIV-1 nucleocapsid protein and the TAR element.

During retroviral reverse transcription, the minus-strand strong-stop DNA (ss-cDNA) is transferred to the 3' end of the genomic RNA and this requires the repeat (R) sequences present at both ends of the genome. In vitro, the human immunodeficiency virus type 1 (HIV-1) R sequence can promote DNA strand transfer when present in ectopic internal positions. Using HIV-1 model systems, the R sequences and nucleocapsid protein (NC) were found to be key determinants of ss-cDNA transfer.

Cellular resistance to the antitumor DNA topoisomerase II inhibitor S16020-2: importance of the N-[2(Dimethylamino)ethyl]carbamoyl side chain.

The new olivacine derivative S16020-2 (NSC-659687) is a DNA topoisomerase II inhibitor endowed with a remarkable antitumor activity against various experimental tumors. In vitro physicochemical properties of this compound, in particular its interaction with DNA and DNA topoisomerase II, were very similar to those of ellipticine derivatives, except for a strictly ATP-dependent mechanism of cleavable complex induction. From the Chinese hamster lung fibroblast cell line DC-3F, a subline resistant to S16020-2, named DC-3F/S16, was selected by adding stepwise increasing concentrations of the drug to the cell growth medium.

In vitro and in vivo pharmacological characterizations of the antitumor properties of two new olivacine derivatives, S16020-2 and S30972-1.

S16020-2, a new olivacine derivative and a topoisomerase II inhibitor, has recently entered clinical trials. New analogues and derivatives have been synthesized from the S16020-2 compound. Preliminary data indicate that S30972-1, one of these S16020-2 derivatives, may exhibit a comparatively higher level of antitumor potency associated with an improved therapeutic index than does S16020-2.

Mutations in three subdomains of the carboxy-terminal region of collagen type X account for most of the Schmid metaphyseal dysplasias.

We have used the polymerase chain reaction and single strand conformation polymorphism (SSCP) methods to analyse the COL10A1 gene, which encodes collagen type X, in DNA samples from patients with metaphyseal dysplasia type Schmid (SMCD) and other related forms of metaphyseal dysplasia. Five cases of SMCD were sporadic and three others were familial. Abnormal SSCP profiles were observed in six instances.

Non-collagenous protein screening in the human chondrodysplasias: link proteins, cartilage oligomeric matrix protein (COMP), and fibromodulin.

A gel-electrophoretic screening for link proteins, cartilage oligomeric matrix protein (COMP), and fibromodulin abnormalities was performed in fetuses, newborn infants, and children with various types of chondrodysplasia. Microdissected freeze-dried sections of upper tibial growth cartilage were extracted with 4M guanidinium chloride in the presence of proteolysis inhibitors. After dialysis against 8M urea, the extracts were submitted to stepwise ion-exchange chromatography to separate the large proteoglycans (aggrecans) from the other components.

The epidermal growth factor-like domain of the large proteoglycans from articular cartilage (aggrecans). Estimate of content at different ages and in osteoarthritis.

Sequencing of cDNA clones has shown that the carboxy terminal domain of the core protein of large proteoglycans (aggrecans) from human cartilage contains an epidermal growth factor-like (EGF-like) domain which is alternatively spliced. In a previous study it was found that the domain of the translated protein can be recognized by polyclonal antibodies to mouse EGF. A competitive enzyme-linked immunoabsorbent (ELISA) assay has been developed to evaluate the EGF-like domain content of aggrecans at various ages and in osteoarthritis.

Immunological detection of the EGF-like domain of the core proteins of large proteoglycans from human and baboon cartilage.

Recent data from the literature have shown that cDNA clones for the carboxyterminal domain of the core protein of large proteoglycan monomers from human cartilage contain an EGF-like domain, which appears to undergo alternative splicing. In the present study we have found that articular proteoglycans from human and baboon separated on agarose flat-bed gels and blotted onto nitrocellulose react with a rabbit antiserum to mouse EGF. In addition both forms of the proteoglycans (band I and band II) seen on these gels are reactive.

Age-related changes in small proteoglycans of low buoyant density of human articular cartilage.

Proteoglycans extracted from articular cartilage of large joints of humans aged 4, 11, 70 and 75, were fractionated on associative density gradients. The top fraction (A3) was purified by ion-exchange chromatography and subsequent gel filtration on Sepharose CL 4B in 4 M GuCl, 0.5% Triton x 100.

The protein core of the largest proteoglycan monomer of articular cartilage. Gel electrophoretic pattern and tryptophanyl peptide bond cleavage.

The largest proteoglycan monomer of baboon (Papio papio) articular cartilage was isolated and the protein rich core was obtained after chondroitinase AC II and keratanase digestions. On SDS-PAGE the core yielded a single band with apparent Mr of 290,000. Tryptophanyl peptide bond cleavage of the core with N-chlorosuccinimide/urea gave 4 peptides with apparent Mr of 105,000, 66,000, 62,000 and 56,000

Proteoglycan electrophoresis on horizontal submerged polyacrylamide-agarose gels.

A method of proteoglycan electrophoresis on submerged horizontal polyacrylamide-agarose gels is described. Several preparations of purified proteoglycans extracted from fetal and young baboon articular cartilage and from mandibular dog-fish cartilage were analyzed. Discrete bands corresponding to proteoglycan monomers of different size were obtained.

Noncollagenous proteins in cartilage of normal subjects and patients with degenerative joint disease. A gel electrophoretic study.

Normal articular cartilage from subjects of various ages and cartilage from patients with degenerative joint disease were extracted with 4M guanidinium chloride. After dialysis against 8M urea pH 6.8, a 0.

Link-proteins and non-collagenous proteins from normal and chondrodysplastic cartilages.

Baboon and human articular and growth cartilage was extracted with 4M guanidinium chloride in the presence of proteolysis inhibitors. After dialysis against 8M urea pH 6.8 the proteins were separated from proteoglycans by ion-exchange chromatography.