Structural uniqueness of lactose operator

Hairpin Structure-forming Propensity of the (CCTG·CAGG) Tetranucleotide Repeats Contributes to the Genetic Instability Associated with Myotonic Dystrophy Type 2

The genetic instabilities of (CCTG.CAGG)(n) tetranucleotide repeats were investigated to evaluate the molecular mechanisms responsible for the massive expansions found in myotonic dystrophy type 2 (DM2) patients. DM2 is caused by an expansion of the repeat from the normal allele of 26 to as many as 11,000 repeats. Genetic expansions and deletions were monitored in an African green monkey kidney cell culture system (COS-7 cells) as a function of the length (30, 114, or 200 repeats), orientation, or proximity of the repeat tracts to the origin (SV40) of replication. As found for CTG.CAG repeats related to DM1, the instabilities were greater for the longer tetranucleotide repeat tracts. Also, the expansions and deletions predominated when cloned in orientation II (CAGG on the leading strand template) rather than I and when cloned proximal rather than distal to the replication origin. Biochemical studies on synthetic d(CAGG)(26) and d(CCTG)(26) as models of unpaired regions of the replication fork revealed that d(CAGG)(26) has a marked propensity to adopt a defined base paired hairpin structure, whereas the complementary d(CCTG)(26) lacks this capacity. The effect of orientation described above differs from all previous results with three triplet repeat sequences (including CTG.CAG), which are also involved in the etiologies of other hereditary neurological diseases. However, similar to the triplet repeat sequences, the ability of one of the two strands to form a more stable folded structure, in our case the CAGG strand, explains this unorthodox "reversed" behavior.

Kilo-sequencing: an ordered strategy for rapid DNA sequence data acquisition

A strategy for rapid DNA sequence acquisition in an ordered, nonrandom manner, while retaining all of the conveniences of the dideoxy method with M13 transducing phage DNA template, is described. Target DNA 3 to 14 kb in size can be stably carried by our M13 vectors. Suitable targets are stretches of DNA which lack an enzyme recognition site which is unique on our cloning vectors and adjacent to the sequencing primer; current sites that are so useful when lacking are Pst, Xba, HindIII, BglII, EcoRI. By an in vitro procedure, we cut RF DNA once randomly and once specifically, to create thousands of deletions which start at the unique restriction site adjacent to the dideoxy sequencing primer and extend various distances across the target DNA. Phage carrying a desired size of deletions, whose DNA as template will give rise to DNA sequence data in a desired location along the target DNA, may be purified by electrophoresis alive on agarose gels. Phage running in the same location on the agarose gel thus conveniently give rise to nucleotide sequence data from the same kilobase of target DNA.

Junction between Z and B conformations in a DNA restriction fragment: evaluation by Raman spectroscopy

Raman vibrational spectra were obtained from two DNA restriction fragments and the DNA polymer (dG-dC)n . (dG-dC)n in 0.01 and 4.5 M NaCl. One fragment contained 95 base pairs (bp) of the Escherichia coli lactose operator-promoter region (95-bp fragment). The other fragment consisted of the 95-bp region flanked by 26 and 32 bp of dC-dG sequences and BamHI ends (157-bp fragment). In 0.01 M NaCl all three DNAs have Raman spectra characteristic of a right-handed B conformation. The high salt spectrum of the 95-bp fragment is also characteristic of a B conformation. However, the spectrum of the 157-bp fragment in 4.5 M NaCl shows major intensity changes from the 0.01 M NaCl spectrum. These changes are also observed in the high salt spectra of (dG-dC)n . (dG-dC)n and are correlated with the presence of a left-handed Z conformation. Comparisons between the high salt Raman spectra of the 157-bp fragment and spectra calculated from (dG-dC)n . (dG-dC)n and the 95-bp fragment indicated that essentially all of the dC-dG regions in the 157-bp fragment are in the Z conformation and a large part (approximately 80%) of the 95-bp region no longer has a B-type backbone vibration. However, this non-B-DNA-like character of the central region is not indicated by base vibrations.

Temperature mediated variation of DNA secondary structure in (A.T) clusters; evidence by use of the oligopeptide netropsin as a structural probe

The titration viscometric investigation of the multi-mode interaction of netropsin (Nt) with (A.T) clusters of NaDNA12 and NH4DNA10 has been extended to different temperatures. The position of two boundaries on the r-scale (r= [Nt]bound/[DNA-P]) with increasing temperature steadily (rI/II) or more abruptly (rO/I) shifts to lower values. For the most (A.T) rich Nt-binding sites of modes (O), (I) and (II) this observation suggests the existence of an equilibrium between different DNA secondary structures with a different translation per base pair. The mode specific changes delta L1Nt of DNA contour length as induced by one Nt molecule proved to be almost independent of temperature. Concomitant stiffening effects increase with decreasing temperature, contrary to initial expectation. Conformational variability of (A.T) clusters may represent an essential feature in specific or selective DNA-protein interaction.

Purification and characterization of an endonuclease specific for apurinic sites in DNA from a permanently established mouse plasmacytoma cell line

An endonuclease specific for apurinic sites in double stranded DNA has been purified 373-fold from the nuclei of mouse plasmacytoma cells (line MPC-11). The enzyme is free of any detectable amounts of aspecific nucleases. The enzyme does not act on methylated or OsO4-treated DNA. However, high doses of UV-light and gamma-rays render the DNA slightly susceptible to endonucleolytic attack, which is believed to be due to depurination of depyrimidination caused by the treatment. The molecular weight of the enzyme is determined to be 28,000 and its apparent Km of the purified enzyme is calculated to be 2.7 nM apurinic sites. The activity is not absolutely dependent upon the presence of Mg2+ in the assay mixture although metal chelating agents such as sodium citrate and EDTA abolish the activity completely. The nuclease was stimulated by moderate concentrations of potassium chloride optimizing at 50 mM, and higher concentrations inhibiting the activity. The pH optimun for the reaction was 9.5.

The DNA . tyrocidine complex and its dissociation in the presence of gramicidin D

The peptide antibiotic tyrocidine affects transcription in vitro by interfering with the initiation process. The complex formed between tyrocidine and native DNA is stable against nucleolytic enzymes. It is sensitive to variations in the salt concentration. Protection of DNA as a function of the tyrocidine concentration follows a curve suggesting cooperative binding of tyrocidine to DNA. The complex formation at low tyrocidine concentrations is accompanied by the presence of single stranded regions of unknown length. With single-stranded DNA, tyrocidine forms a complex which is relatively insensitive to high salt concentrations. Both native and single-stranded DNAs of the complexes become digestible in the presence of gramicidin D, another peptide antibiotic. Breakdown of the complex as a function of the gramicidin D concentration follows a curve which is the reverse of cooperative binding. Gramicidin D acts more effectively on single-stranded rather than on double-stranded DNA . tyrocidine complexes. The DNA . tyrocidine complex, which is broken down by formamide and dimethyl sulfoxide is stabilized by gramicidin D. The implications of these results are discussed with respect to a possible recognition of DNA sequences by tyrocidine and the interaction between DNA, tyrocidine and gramicidin D.

Iodination as a probe for small regions of disrupted secondary structure in double-stranded DNAs

Conditions were established where the thallium-catalyzed iodination of random coil DNA proceeded 100-200 times faster than for native DNA. This reaction was explored as a probe for localized regions of disrupted base pairs in duplex DNA. A heteroduplex was constructed between DNA fragments produced by Hind II + III cleavage of phi80 plac DNA and phi80 plac DNA containing the Ll deletion (73 nucleotides in length). This heteroduplex incorporated twelve times as much iodine as the parent homoduplex fragments. Hence the technique could reveal the presence of a few (two or more) nonpaired cytosines, if they existed within an otherwise helical DNA fragment 789 base pairs long. Iodination studies were performed on superhelical SV40 DNA and on linear lambdaplac DNA. Analysis of the relative amount of iodine in restriction endonuclease fragments of these DNA's revealed the absence of localized single-stranded regions.

Preparative fractionation of DNA restriction fragments by reversed phase column chromatography

Reversed phase column chromatography on RPC-5 resin was used to fractionate milligram quantities of DNA fragments generated by restriction endonucleases. Fractionation was on the basis of size, the presence or absence of sticky ends, and at least one as yet undertermined property.

Coumerimycin A1: A preferential inhibitor of replicative DNA synthesis in Escherichia coli. II. In vivo characterization

In vitro inhibitions by coumermycin A1 of DNA and RNA synthesis in toluenized cells were studied. In a sensitive strain, 50% inhibitions of replication and transcription were observed at 0.035 and 0.600 mug/ml, respectively. DNA synthesis in a toluenized-resistant mutant was 50% inhibited at 0.140 mug/ml of coumermycin A1, whereas RNA synthesis was unaffected at all concentrations tested. Studies with a mixture of toluenized-sensitive and -resistant bacteria ruled out the presence of a diffusable activator or inhibitor of coumermycin A1 action. Density label studies with toluenized pol A+ and pol A- strains indicated that replicative DNA synthesis was specifically inhibited, in agreement with the in vivo studies in the preceding paper of this issue (Ryan, M. J. (1976), Biochemistry 15). Highly purified Escherichia coli DNA polymerase III and RNA polymerase both were inhibited by this antibiotic. However, the high concentrations necessary for these inhibitions suggest that they are not biologically relevant. No interaction between DNA and coumermycin A1 was observed with the following analytical procedures: ultraviolet difference spectra, DNA absorbance-temperature transitions, equilibrium buoyant density centrifugation, and DNA cross-linking determinations.

Coumermycin A1: A preferential inhibitor of replicative DNA synthesis in Escherichia coli. I. In vivo characterization

Coumermycin A1, an antibiotic related to novobiocin, inhibited nucleic acid synthesis in intact Escherichia coli with replication being slightly more sensitive to this drug than transcription. The ultraviolet-induced repair synthesis of DNA was only partially inhibited under conditions where replication was eliminated by coumermycin A1. Inhibition of protein synthesis was a secondary effect. Coumermycin A1-resistant E. coli were isolated and the mutation was mapped near dnaA. Chromatography of crude protein extracts of sensitive and resistant bacteria on drug affinity columns implicated a soluble protein of approximately 37,000 molecular weight as the target site for coumermycin A1. Depending on the medium used, this antibiotic had either a bacteriocidal or a bacteriostatic effect on E. coli. Results showed that the effect of coumermycin A1 cannot be explained by the degradation of DNA under bacteriocidal growth conditions.

Structure of Caulobacter deoxyribonucleic acid

The deoxyribonucleic acid of the dimorphic bacterium Caulobacter crescentus contains a component that renatures with rapid, unimolecular kinetics. This component was present in both swarmer and stalked cells and exhibited the sensitivity to endonuclease S1 expected for hairpin loops. Double-stranded side branches between 100 and 600 nucleotide pairs in length were visible in electron micrographs of rapidly reassociating deoxyribonucleic acid isolated by hydroxyapatite chromatography. No extrachromosomal elements were found in spite of systematic attempts to detect their presence. These results indicate that the rapidly reassociating fraction derives from inverted repeat sequences within the chromosome and not from cross-links or plasmids. We estimate that there are approximately 350 inverted repeat regions per Caulobacter genome. The kinetic complexity of Caulobacter deoxyribonucleic acid, however, is no greater than that of other bacteria.

Iodination of DNA. Studies of the reaction and iodination of papovavirus DNA

Iodination of DNA by the reaction originally described by S. L. Commerford ((1971), Biochemistry 10, 1993) is extremely sensitive to the secondary structure of the DNA. Cytidines in denatured simian virus 40 (SV40) DNA react at a slightly slower rate than free cytidine monophosphate; hydrogen-bonded cytidines in SV40 form I DNA are iodinated considerably more slowly; elimination of the negative supercoils in form I DNA by conversion to form II or form III reduces reactivity even further. The residual reactivity of form II or form III duplex DNA is not due to preferential iodination of unpaired cytidines near phosphodiester bond breaks; rather iodination occurs throughout the molecule. Cytidine monophosphate has been used as a model for DNA, to enable spectral measurements of its reaction with iodine and T1C13. At temperatures above 42 degrees C and at pH 5.0, formation of 5-iodocytidine is limited by the rate of formation of an intermediate, probably 5-iodo-6-hydroxydihydrocytidine. At lower temperatures, the conversion of intermediate to product is rate limiting, but can be accelerated by lowering the pH. By appropriate adjustment of pH, or temperature, the formation of intermediate or its conversion to product can be accelerated. Iodination destabilizes the DNA duplex. Iodocytosines in SV40 DNA are preferentially removed by S1 nuclease. Heavily iodinated DNA does not reassociate normally, but DNA with only 5-10% of its cytosines iodinated appears to reassociate with normal kinetics, if duplex formation is measured by hydroxylapatite chromatography. Conditions are described to permit preparation of DNA, which reassociates normally, having a specific activity of 10(8) cpm/mug.

Inverted repeat sequences in the Drosophila genome

The properties of inverted repeat (foldback) sequences in Drosophila melanogaster DNA have been studied by HAP chromatography and electron microscope methods. Electron microscope observations show that there is a broad distribution of lengths of the duplex regions of the inverted repeats from very short to greater than 15 kb, with number and weight average values of 1.35 kb and 5.0 kb respectively. About 20% of the inverted repeats are separated by a single-strand spacer with lengths too short to observe, but the other 80% have spacers, P, with lengths ranging from 0.5 kb to greater than 30 kb. The number average and weight average spacer lengths for the total sample are 2.7 kb and 6.1 kb. With respect to the lengths of the spacers, P, between inverted repeats, the Drosophila genome differs from that of most organisms which have been studied where the spacers P are mostly too short to be measured. EM and HAP studies suggest that the average center-to-center spacing between sets of inverted repeats is 40-80 kb. The HAP studies show that there is a broad range of thermal stabilities for the duplexes formed by reassociation of inverted repeat sequences. Kinetic analysis shows that all of the frequency components of the Drosophila genome are present in the inverted repeats, the loops P, and the flanking sequences. There is a somewhat larger proportion of middle repetitive DNA in those inverted repeat duplexes which are resistant to digestion by Mung Bean Endonuclease I. These enzyme resistant duplexes comprise about 3% of the entire genome. It is estimated that there are approximately 2000-4000 inverted repeat pairs in the entire genome.