Fluorometric assay of DNA in cartilage explants using Hoechst 33258

A simple two-step fluorometric assay of DNA in cartilage explants, utilizing the bisbenzimidazole dye Hoechst 33258, is described. Cartilage explants were prepared for assay by digestion with papain. Aliquots of the digest were mixed with dye solution, and the fluorescence emission measured. The enhancement in fluorescence of dye was specific for DNA, as demonstrated by 97% sensitivity to DNase and resistance to RNase. In addition, little or no interference was caused by non-DNA tissue components, since DNA caused an equal enhancement in fluorescence independent of the presence of papain-digested cartilage. By performing the assay on isolated chondrocytes, the cellular content of DNA was computed to be 7.7 pg per chondrocyte. The assay was stable for at least 2 h and sensitive to as little as 6 ng of DNA or equivalently less than 1000 cells. This procedure offers advantages over other established DNA assays of cartilage and may be especially useful in metabolic studies of cartilage explants.

A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells

The c-myc gene product is a nuclear protein expressed in a wide variety of cell types. It has been implicated in the control of normal cell growth as well as transformation, but its exact function is unknown. When the human promyelocytic leukaemia cell line HL60 is treated with retinoic acid, the cells differentiate into granulocytes, and there is a reduction in steady state c-myc RNA of more than 10-fold. Nuclear runoff assays show that this reduction is caused by a corresponding decrease in the transcription of exon 2. However, only a minor decrease in exon 1 transcription is observed upon differentiation. In undifferentiated HL60 cells there is an approximately 3-fold molar excess of exon 1 transcription over exon 2, and this excess increases to about 15-fold in differentiated cells. This observation suggests that a major component of c-myc transcriptional down-regulation in HL60 cells is at the level of elongation rather than at the level of initiation. The position of the elongation block was mapped to the region of the boundary between exon 1 and intron 1. During HL60 differentiation, a DNase I hypersensitive site in the chromatin about 300 bases downstream of the 5' end of of intron 1 increases in intensity relative to other sites, possibly reflecting events associated with the termination of transcription. Our runoff analysis also revealed transcription of both strands immediately upstream of exon 1 in HL60 cells. The sense strand transcription of this region produces a novel c-myc RNA which initiates several hundred bases upstream of the previously defined promoters and is found in a variety of cell types.

Crystalline desoxyribonuclease; isolation and general properties; spectrophotometric method for the measurement of desoxyribonuclease activity

A crystalline enzyme capable of digesting thymus nucleic acid (desoxyribonucleic acid) has been isolated from fresh beef pancreas. The enzyme called "desoxyribonuclease" is a protein of the albumin type. Its molecular weight is about 60,000 and its isoelectric point is near pH 5.0. It contains about 8 per cent tyrosine and 2 per cent tryptophane. It is readily denatured by heat. The denaturation is reversible if heated in dilute acid at pH about 3.0. The digestion of thymus nucleic acid by crystalline desoxyribonuclease is accompanied by a gradual increase in the specific absorption of ultraviolet light by the acid. The spectrophotometric measurement of the rate of increase in the light absorption can be conveniently used as a general method for estimating desoxyribonuclease activity. Details are given of the method for isolation of crystalline desoxyribonuclease and of the spectrophotometric procedure for the measurement of desoxyribonuclease activity.

Interferon-induced nuclear factors that bind a shared promoter element correlate with positive and negative transcriptional control

Human alpha- and beta-interferons (IFNs) stimulate rapid but transient increases in transcription from a set of previously quiescent genes. Protein synthesis is not required for initial stimulation, but duration of the response is limited to a few hours by a process requiring synthesis of new proteins. An IFN-stimulated response element (ISRE) was identified 5' to an inducible gene by deletion analysis and point mutagenesis, and sequence comparisons with other promoters defined the consensus element YAGTTTC(A/T)YTTTYCC. Two classes of IFN-inducible nuclear factors were found that bind to the ISRE. The most rapidly induced factor appeared without new protein synthesis, whereas a second factor required active protein synthesis for its appearance and maintenance. The kinetics of appearance and loss of these binding activities correlate with the activation and repression of IFN-stimulated genes. These different IFN-activated or induced factors may bind sequentially to the same essential promoter element to first increase and then repress transcription.

Two protein-binding sites in chromatin implicated in the activation of heat-shock genes

The resistance to exonuclease digestion of two regions of chromatin at the 5' end of heat-shock genes in Drosophila implies they have protein bound to them. The pattern of resistance before and after induction of gene expression suggests that heat-shock genes are activated by the sequential binding of at least two protein factors.

Chromatin structure of endogenous retroviral genes and activation by an inhibitor of DNA methylation

The transcriptionally active ev-3 and inactive ev-1 endogenous retrovirus loci in chick cells differ in that ev-3 is undermethylated, preferentially sensitive to DNase I digestion, and contains nuclease hypersensitive sites in each of its two long terminal repeats. Transient exposure of cells to 5-azacytidine, a cytosine analogue which cannot be methylated at the 5 position, results in the hypomethylation and transcriptional activation of ev-1, as well as the acquisition of at least one nuclease-hypersensitive site within the chromosomal domain of ev-1.

The sequence specificity of homeodomain-DNA interaction

The Drosophila developmental gene, engrailed, encodes a sequence-specific DNA binding activity. Using deletion constructs expressed as fusion proteins in E. coli, we localized this activity to the conserved homeodomain (HD). The binding site consensus, TCAATTAAAT, is found in clusters in the engrailed regulatory region. Weak binding of the En HD to one copy of a synthetic consensus is enhanced by adjacent copies. The distantly related HD encoded by fushi tarazu binds to the same sites as the En HD, but differs in its preference for related sites. Both HDs bind a second type of sequence, a repeat of TAA. The similarity in sequence specificity of En and Ftz HDs suggests that, within families of DNA binding proteins, close relatives will exhibit similar specificities. Competition among related regulatory proteins might govern which protein occupies a given binding site and consequently determine the ultimate effect of cis-acting regulatory sites.

DNA structural variations in the E. coli tyrT promoter

X-ray studies have established that the structure of a right-handed, Watson-Crick double helix can change from place to place along its length as a function of base sequence. The base pairs transmit deformations out to the phosphate backbone, where they can then be recognized by proteins and other DNA-binding reagents. Here we have examined at single-bond resolution the interactions of three commonly used nucleases (DNAase I, DNAase II, and copper-phenanthroline) with a DNA of natural origin, the 160 bp tyrT promoter. All three of these reagents seem sensitive to DNA backbone geometry rather than base sequence per se. Their sequence-dependent patterns of cleavage provide evidence for structural polymorphism of several sorts: global variation in helix groove width, global variation in radial asymmetry, and local variation in phosphate accessibility. These findings explain how sequence zones of a certain base composition, or purine-pyrimidine asymmetry, can influence the recognition of DNA by protein molecules.

The twisted circular form of polyoma viral DNA

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