An apparatus for studying the thermal transition of nucleic acids at high resolution

The nonequilibrium character of DNA melting: effects of the heating rate on the fine structure of melting curves

To investigate the effects of heating rate on the DNA melting profile and to test the predictions of the theory of slow relaxation processes in DNA melting (1) concerning these effects, we obtained differential melting curves for the Bsp I C1 fragment of T7 DNA (1461 bp) and the Sma I-Eco RI fragment of Col E1 DNA (1291 bp) at heating rates of 0.05 and 0.5 deg/min. At low ionic strength (0.02 M Na+) the heating rate has been shown to affect the position of the third peak in melting curve for C1 fragment. According to the melting maps (2), this peak corresponds to the unwinding of the section between the end of the molecule and the region already melted. At high ionic strength (0.2 M Na+), when the melting of this DNA is reversible (3), the position of the peaks does not depend on the heating rate. In the case of the Col E1 DNA fragment the heating rate affects, as might be expected from the melting maps (4), only the last peak, as the melting of the last section is always nonequilibrium. The results of the study are in good qualitative agreement and in satisfactory quantitative agreement with the theoretical predictions (1).

Correlation between thermal stability maps and genetic maps of double-stranded DNAs

The positional correlation of boundaries of cooperatively melting regions with boundaries of protein coding regions and mere open reading frames, and with cleavage sites of restriction enzymes and S1 nuclease are statistically examined for phi X174, G4, fd, SV40, BKV, and polyoma DNAs. A statistically significant correlation does exist in the case of boundaries of protein coding regions, but none is detected for boundaries of mere open reading frames or cleavage sites of restriction enzymes and S1 nuclease. The significant correlation disappears when the cooperativity of melting of the DNA double strand decreases to a nonphysiological condition. The result presents the first evidence showing that a physical property of DNAs correlates with their biological function.

Thermotropic state transition in isolated platelet membranes studied by Raman spectroscopy

The thermotropic state transition of the lipids in isolated platelet membranes has been studied by Raman spectroscopy in the temperature range from -3 degrees C to +45 degrees C using the (C-H) stretching vibrations, carotenoid(s) vibrations at 1530 cm-1 and 1160 cm-1, as well as the skeletal optical vibrations. 1. The increase of temperature causes a decrease in intensity of the 2885 cm-1 band relative to the 2855 cm-1 one. The evaluation of the ratio I2885/I2855 as a function of temperature indicates a double thermotropic state transition of platelet membrane lipids: the first one near 5 degrees C and the second near 17.5 degrees C. 2. The ratio I1530/I1160 shows that the intensity variations in the carotenoid(s) peaks follow the second lipid transition. Thus, it seems that the platelet membrane carotenoid(s) might be linked to the lipids which undergo transition near 17.5 degrees C. 3. The spectral changes in the skeletal optical range suggest a considerable proportion of all trans chains in the membrane lipids at lower temperatures whereas gauche structures seem to be introduced at higher temperatures.

Genetic and physical characterization of a segment of yeast mitochondrial DNA involved in the control of genetic recombination

Genetic recombination between the 3 RIB (ribosomal) loci of yeast mitochondrial DNA is under the control of a mitochondrial locus named omega (with alleles omega+ and omega-) which is tightly linked to the RIBI locus. We have attempted to elucidate the molecular mechanisms(s) involved by using rho- mutants with similar (RIBI+ RIB2+ RIB3(0) genotype but different recombination properties in rho- x rho+ crosses. These were obtained through pedigree analysis and their mitochondrial DNAs were mapped on a high resolution physical map of the RIB section that had been built by analysis of thermal denaturation profiles and electron microscopy of partially denatured molecules. By comparison of physical and genetic data it can be shown that possession of the omega+ allele by the rho- cell is not sufficient for its expression in crosses, some additional DNA segments(s) in the ribosomal region being needed. This result and several features of the rho+ x rho- crosses are discussed in the light of current concepts in mitochondrial genetics of yeast and the recently discovered fact that omega+ and omega- strains differ by the presence of a 1000 base pairs insertion in the former.

Fine structure in the thermal denaturation of DNA: high temperature-resolution spectrophotometric studies

Fine structures which appear in the optical melting profile of DNA are examined from both the experimental and theoretical aspects. After a brief historical survey of the DNA melting experiments during the pre-fine-structure era in Section II, the high temperature-resolution experimental techniques which are essential to the investigation of fine structure are described in Section III. Then, the current status of the high-resolution study is reviewed first by a phenomenological description of the melting profile (Section IV) and then of the refolding profile (Section V), where a general idea about the cooperatively melting region and several factors affecting it is given. Sections VI and VII are devoted to the review of current theoretical works. Several well-established theoretical frameworks which correlate the base sequence with the melting phenomena are examined in terms of their rigorousness and usefulness. The molecular thermodynamic parameters concerning the DNA melting which have been evaluated by several research groups are compared and discussed. Finally, in Section VIII, current ideas on the correlation between the fine structure and genetic functions and genetic maps are reviewed. Some future problems relating to the fine structure are also discussed.

Lack of correlation between affinity of the tRNA for the aminoacyl-tRNA synthetase and aminoacylation capacity as studied with modified tRNAPhe

The interactions of several modified yeast tRNAPhe [tRNAPhe lacking 7-methylguanine; a fragment comprising about 3/4 of the whole molecule: tRNAPhe (18--76); tRNAPhe (18--76) lacking 7-methylguanine] with yeast phenylalanyl-tRNA synthetase were studied. Upon excision of the 5'-quarter of the tRNAPhe molecule, the residual fragment still tightly binds to the synthetase, but can no longer by aminoacylated. Surprisingly, upon removal of the 7-methylguanine base at position 46 in this fragment, althought the affinity drops by a factor 10, a significant aminoacylation is restored. These results are discussed in terms of molecular flexibility and a model is proposed for tRNA-enzyme interaction, involving multisite recognition.

The 1360 bp long basic repeat unit of calf satellite I DNA contains GC rich nucleus of about 140 bp

Fine melting profiles of calf satellite I DNA and its fragments obtained after digestion with endoR.EcoRI and endoR.AluI nucleases were investigated. It is shown that the 1360 bp basic repeat unit of calf satellite I DNA contains an about 140 bp long GC rich nucleus. It is localized on the 600 bp restriction fragment obtained after digestion of 1360 bp fragment with endoR.AluI nuclease. The main part of satellite I DNA melts as loops between such GC rich nuclei which strongly influence the melting properties of this satellite. There exist significant differences between the thermal stabilities of fragments containing many nuclei, one nucleus and those in which such nucleus is absent.

Numerical analysis of thermal denaturation of nucleic acids

Denaturation of DNA molecules by stepwise incrementation of the temperature leads to melting profiles showing a fine structure, composed of individual melting modes. A method is described by which quantitative physical information brought by the modes can be extracted from the melting profile. Related problems such as data editing and smoothing are also discussed.

Saltatory thermal denaturation of double-stranded viral RNAs

The double-stranded RNAs from bacteriophage phi6 and the replicative form of mengovirus denature upon heating in a series of abrupt steps which resemble the subtransitions (thermalites) observed within the high resolution profiles of small, naturally occurring DNA molecules. Such RNA thermalites are approximately an order of magnitude narrower than typical thermal subtransitions of nominally single-stranded RNA. We conclude that the same features of nucleotide sequence that give rise to cooperative denaturation in DNA genomes are to be found also in RNA genomes. Thus, high resolution thermal denaturation profiles are useful for characterizing double-stranded RNA molecules as well as native DNA in the size range of common viruses. A medium containing dimethylsulfoxide was required to lower the Tm of the RNA samples to a satisfactory temperature range. For double-stranded RNA in 50% dimethylsulfoxide, the dependence of Tm on G . C composition was greater than that of DNA in the same medium and also greater than that of double-stranded RNA in an aqueous medium. The fact that RNA thermalites are broader than DNA thermalites and that the melting temperature of double-stranded RNA has a greater dependence on base composition than that of DNA, indicates that at least one of the thermodynamic parameters for double helix formation in RNA is different from that in DNA.

Biological effects and repair of damage photoinduced by a derivative of psoralen substituted at the 3,4 reaction site: photoreactivity of this compound and lethal effect in yeast

A newly synthesized linear psoralen derivative, 3-carbethoxypsoralen is shown to bind to yeast nucleic acids after 365 nm light treatment. As compared to 8-methoxypsoralen, a well-known bifunctional furocoumarin, 3-carbethoxypsoralen exhibits a high photoaffinity for DNA in vivo. Both compounds bind and photoreact more efficiently in vivo than in vitro. In contrast to 8-methoxypsoralen, 3-carbethoxypsoralen does not form cross-links in yeast DNA as demonstrated by heat denaturation-reassociation studies at least in the range of doses used. Thus 3-carbethoxypsoralen reacts as a monofunctional compound. Wild-type cells of Saccharomyces cerevisiae are 6 times more resistant to 3-carbethoxypsoralen than to 8-methoxypsoralen plus 365 nm light treatment in terms of lethal effect. In comparison to angelicin, another monofunctional (but angular) furocoumarin, 3-carbethoxypsoralen is more photoreactive. When the photoaffinity for DNA of 8-methoxypsoralen and 3-carbethoxypsoralen are considered in relation to photoinduced cell killing, it is clear that monoadducts are very efficiently repaired in wild-type cells. In contrast to the additivity obtained with 8-methoxypsoralen, a synergistic interaction of the two different repair pathways blocked by the rad2 and the rad9 mutation is observed after 3-carbethoxypsoralen plus 365 nm light. Dark holding experiments show that the excision repair function which is present in wild-type and rad9-4 cells is important for dark recovery.

Recombined molecules of mitochondrial DNA obtained from crosses between cytoplasmic petite mutants of Saccharomyces cerevisiae: the stoichiometry of parental DNA repeats within the recombined molecule

We have studied recombination between repetitive mitochondrial DNAs from cytoplasmic petite mutants of Saccharomyces cerevisiae. Mitochondrial DNA was isolated from two parental p- mutants, carrying respectively the CR and the ER mitochondrial genetic markers, and from two p- CRER diploid genetic recombinants. These two recombinants, obtained from the same parental petites, differ in their degrees of suppressiveness. The p- mitochondrial DNAs were analyzed by DNA-DNA hybridization, high resolution melting and reassociation kinetics. It was found that the repeating unit of the CR parental p- DNA is 3 to 4 times longer than that of the ER parent. There is very little sequence homology between these two p- mitochondrial DNAs and almost all parental sequences are integrated into the recombined molecules. Mitochondrial DNA from both types of recombinants seems to contain the two parental repeating units in the ratio 1:1.

Transcription of chromatin from mouse fibroblasts

Chromatin purified from mouse fibroblasts can be fractionated after shearing by sedimentation in a sucrose gradient into an extended "light" and a compact "heavy" component. Further purification of these classically described components can be achieved by a second cycle of centrifugation of the light and heavy components through an equilibrium density gradient of metrizamide. The light component purified from sucrose gradient sediments faster (peak I) on metrizamide than its heavy counterpart (peak II). Template activity for DNA directed RNA synthesis in the presence of E. coli RNA polymerase is negligible in peak II but very pronounced in the peak I fraction. The difference in template activity appears to be connected with differences in propagation rather than initiation rates. Comparison of gel electrophoresis patterns of proteins indicate that the active subcomponent includes high molecular weight components not present in the inactive one, but that its histone content is somewhat lower. Using a very highly sensitive automatic recording apparatus for the measurement of melting profiles, no clear cut difference has been observed in the behaviour of active and inactive chromatin subcomponents nor in that of their total DNA.