Kinetics of the middle and terminal phases of degradation of DNA by spleen acid DNAase

Silyl ether-coupled poly(epsilon-caprolactone)s with stepwise hydrolytic degradation profiles

Silyl ether-coupled poly(epsilon-caprolactone)s (PCLs) with stepwise degradation profiles were synthesized via the cross-dehydrocoupling polymerizations between 1,4-bis(dimethylsilyl)benzene (BDSB) and telechelic, diol-terminated PCL macromonomers. With the presence of 10 wt % palladium on activated carbon as the catalyst, the condensations between BDSB and diol-terminated PCL macromonomers having molecular weights of 1200, 2010, and 5500 g/mol were performed in toluene at 100 degrees C under argon. Hydrogen was eliminated as the condensate upon the formation of silyl ether bonds linking the PCL blocks, yielding within 24 h, silyl ether-coupled PCLs of molecular mass 7590, 29,900, and 29,500 g/mol, respectively. The characterization of each polymer included (1)H NMR, (13)C NMR, and (29)Si NMR spectroscopies, size exclusion chromatography (SEC), and differential scanning calorimetry. The hydrolytic degradation properties of the polymers in solution were studied, and the molecular weight reductions over time were monitored by SEC. The silyl ether linkages of the polymers underwent hydrolysis in the presence of mineral acids, whereas the PCL segments released from the cleavage of the labile silyl ether coupling unit did not undergo detectable molecular weight reduction over 15 days. In the presence of acetic acid, the silyl ether functionalities were cleaved with a half-life of 3 days; however, the PCL chain required reaction with trifluoroacetic acid to give a number-average molecular weight loss half-life of 4 days. The silyl ether-coupled PCLs underwent degradation in a gradient fashion, therefore, by a protocol that involved the addition of acetic acid for cleavage of the silyl ether functionalities, followed by further addition of trifluoroacetic acid to bring the hydrolysis of the silyl ether functionalities to completion and to trigger the degradation of PCL segments.

TMP-reactive autoantibodies in human SLE sera demonstrate thymine-dependent oligonucleotide specificity

Autoantibodies present in the sera of lupus patients and specific for single-stranded (ss) DNA were fractionated into subsets based upon their reactivity towards 5' nucleotide haptens. As evaluated by ELISA testing, antibodies retained by TMP-agarose bound to TMP-BSA and ssDNA but not to other nucleotide-BSA conjugates or to double-stranded (ds) DNA. Competition-inhibition studies further revealed that TMP-enriched oligo- and polynucleotides were the preferred antigens for these affinity purified antibodies. Similar assays with sequence- or size- defined oligonucleotides further implied that those oligonucleotides comprised entirely of TMP residues were most antigenic and that antigenicity increased with size (length). These results document the existence of a TMP-dependent oligonucleotide specificity among a diverse population of autoanti-ssDNA antibodies.

Location of specific messenger RNAs in Caenorhabditis elegans by cytological hybridization

We have developed an autoradiographic technique for detecting specific Caenorhabditis elegans messenger RNA molecules in situ by hybridization of labeled, cloned DNA probes to fixed tissue sections and squashes of embryos and adults. We report analyses with probes of actin and collagen gene sequences from a C. elegans genomic clone library. Hybridization is RNase sensitive and tissue specific. In adults the actin probe, which recognizes cytoplasmic as well as muscle actin mRNA, hybridizes strongly to muscle and distal gonad (ovary), somewhat less strongly to maturing oocytes, and weakly to intestine. The collagen probe hybridizes weakly to distal gonad and intestine and very strongly to subcuticular tissues, in particular to the hypodermal cells and syncytial cytoplasm of the lateral hypodermal ridges, which are the sites of cuticle synthesis. In embryos, hybridization to squashes indicates that actin message is present at fertilization, decreases during early cleavage, and then increases again during morphogenesis. By contrast, collagen message is absent until the 100-cell stage and then increases rapidly during morphogenesis. The number of cells labeled is consistent with the view that the collagen probe hybridizes to hypodermal precursor cells. We estimate that our present methods can detect messages representing about 0.2% or more of the total mRNA population, and increases in this sensitivity should be possible. Therefore, the cytological hybridization technique should be useful for determining temporal and spatial patterns of specific mRNA distributions during development, at least for abundant and moderately abundant messages.

An analysis of the bovine genome by density gradient centrifugation: fractionation in Cs2SO4/3,6-bis(acetatomercurimethyl)dioxane density gradient

The fractionation of calf thymus DNA by centrifugation in density gradients of Cs2SO4/BAMD, where BAMD = 3,6-bis(acetatomercurimethyl)dioxane, is described. A large-scale separation of (dG+dC)-rich DNA fractions has been obtained, allowing the relative amounts of minor and satellite components in the bovine genome to be precisely assessed.

Analysis of the breaking sites in the physical degradation of DNA

The 3'-termini of procaryotic and eucaryotic DNA fragments obtained by shearing, sonication and irradiation have been analyzed. Analysis of the 3'-ends of DNA fragments was done by 32-P-labeling with terminal transferase, hydrolysis of products by spleen DNAase and spleen exonuclease and separation of labeled 3'-terminal nucleotides on polyethyleneimine plates. In the case of sonication the deviation from DNA base composition of 3'-terminal nucleotides is very close to random for Escherichia coli and Haemophilius influenzae DNA, whereas for calf thymus, mouse and yeast mitochondrial DNAs a significant increase in dA and decrease in dC was observed. Shearing at high salt released random 3'-termini in E. coli DNA and 3'-termini with 4 to 6% deviation from base composition in calf thymus DNA. In the case of gamma-irradiation no real differences have been found between E. coli and calf thymus DNA and 3'-terminal nucleotide composition is very close to random. Mechanical breakage of eucaryotic DNA seems to release 3'-termini having a composition which differs slightly but significantly from the average base composition of the DNA.

The specificity of five DNAases as studied by the analysis of 5'-terminal doublets

The 5'-terminal dinucleotides released by five deoxyribonucleases (spleen acid DNase, snail acid DNase, pancreatic DNase, Escherichia coli endonuclease I and crab DNase) have been determined on E. coli DNA (51% dG & dC) digests having different average sizes (Pn) in the range 50 to 10. It has been shown that the composition of the 5'-terminal dinucleotide (a) is independent upon the degradation level, at least in the range explored; (b) is strongly different from the composition of E. coli DNA doublets, these differences being characteristic for each enzyme; (c) is very significantly different from the statistical composition of 5'-terminal dinucleotides, as calculated from the composition of 5'-terminal and penultimate nucleotides. A calculation of the statistical composition of the trinucleotides split by each enzyme, using the 3'-terminal nucleotide data in conjunction with the 5'-terminal dinucleotide results provided a qualitative "specificity spectrum" for each enzyme.

The specificity of a neutral deoxyribonuclease from Cancer pagurus

The recently isolated neutral deoxyribonuclease from crab (Cancer pagurus) testes has been characterized in its mode of action and its specificity. The enzyme is a typical endonuclease, forming 5'-phosphate oligonucleotides of large average size; after extensive digestion of calf thymus DNA over 75% of the fragments have a size larger than pentanucleotides and mononucleotides are absent. As far as specificity is concerned, thymidine is very abundant in the 5'-penultimate position (approximately 50%) and in the 3'-terminal position (37%) and almost absent in the 5'-terminal position (approximately 1%), the values quoted concerning Escherichia coli digests of average size (Pn) between 50 and 10.