Spectral analysis on the melting fine structure of is lambda DNA and T2 DNA

Optically induced microfluidic reconfiguration

Reconfigurable systems, like the field-programmable gate array in electronics, have numerous advantages including cost, adaptability, robustness, and security. Despite this, few other chip-based technologies have developed equivalently ubiquitous reconfiguration methods. As a first step to applying this paradigm to channel-based microfluidics, we present here a rapid optofluidic technique to create, move, and remove arbitrary solid regions in a microfluidic flow simply by illumination with an optical pattern. While other techniques have shown the ability to manipulate individual particles using spatial light modulation, we demonstrate here the ability to create reconfigurable flow pathways and build morphable channel structures. These structures can be modified on the order of seconds using a combined photothermal and thermo-rheological effect. In addition to characterizing the effect, we also apply this technique to create dynamic traps for biomolecules, and demonstrate trapping of λ-DNA molecules and nanoparticles, with a 25 fold suppression of diffusion.

Stability distribution in the phage lambda-DNA double helix: a correlation between physical and genetic structure

Statistical analyses on the positional correlation of physical-stability and base-sequence distribution maps with genetic map are made for the whole DNA (48502 bases) of lambda-phage. The susceptibility to a double-helix unfolding perturbation and the fraction of the transient opening of a particular region of the double helix are adopted to define this physical stability. The principal features obtained are: A) The DNA double strand of protein coding regions is found to have homostabilizing propensity around a defined stability which is characteristic to each individual gene. B) The stability of the double helix in non-protein coding region fluctuates, on average over the whole region, more than that in protein coding region. C) Boundary regions of protein coding and non-protein coding regions are regions of high stability-fluctuation. Stability especially fluctuates at the protein-coding-region side of the boundary. Contrary to the quiet feature of the interior part of protein coding region rather noisy part exists at its edge. D) One frequently opening region coincides with the attaching site for the site specific recombination between phage and bacterial DNA. There are two possible ways to explain the noisy feature in the stability distribution in non-protein coding regions: 1) The region has been used as the locus of recombination as evolution took place. Thus DNAs which were homostabilized around a different value characteristic to each individual DNA, have been joined there many times, so that the noise has accumulated as a remnant of evolutional history; and/or 2) the base-composition homogenizing or double-helix homostabilizing mechanism does not work in unneeded region such as non-protein coding region or introns. Since corresponding characteristics have been found in our previous analyses on other viral and globin-gene DNAs, the rules mentioned above may be comprehensively extended to other DNAs.

Preferential reaction of the carcinogen N-acetoxy-2-acetylaminofluorene with satellite DNA

The carcinogens N-acetoxy-2-acetylaminofluorene (N-acetoxy-AAF) and N-hydroxy-2-aminofluorene (N-hydroxy-AF) were incubated with calf thymus DNA to determine if reaction occurred preferentially with discrete regions within the DNA. Derivative melting profiles indicated that both compounds decreased satellite transitions and that N-acetoxy-AAF depressed the melting of higher temperature regions. These data suggest that N-acetoxy-AAF reacted to a greater extent with G + C-rich regions and, because the resulting adduct disrupted the helix, the cooperativity of melting decreased. Reaction of N-acetoxy-AAF with purified satellite III DNA confirmed the preferential interaction of this carcinogen with G + C-rich regions as compared to main component DNA. The derivative melting profile of lambda DNA in the presence of actinomycin D further demonstrated that this type of analysis can detect preferential interactions with specific DNA sequences.

Dual-mode computer processing for high resolution DNA thermal denaturation experiments

Two modes of data processing are appropriate in conducting high resolution thermal denaturation experiments (thermal increments of 0.05 degrees or closer). In the first mode, a general purpose microcomputer provides on-line services important to the control and monitoring of the initial experiment, including control of the spectrophotometer and heater, the recording of data, and the display of current hyperchromicities and approximate first derivatives. A subsequent microcomputer program then reads the recorded data files and carries out accurate calculations of derivative denaturation profiles and the estimate of the statistical error of the first derivative at each point. The data collection program handles three samples at a time and was designed to provide optimal results in thermal denaturation experiments with a single-beam spectrophotometer.

Separation of random fragments of DNA according to properties of their sequences

The separation of DNA fragments by electrophoresis at high temperature in a denaturing gradient is independent of the length of the fragments. We have suggested that the basis of fragment separation is that each DNA molecule undergoes partial melting as it encounters a concentration of denaturants sufficient to melt its least stable sequence, while other sequences remain double stranded; in the partially melted configuration, DNA can continue migration only slowly. This model is consistent with the observation that fragments of lambda phage DNA cleaved by different restriction endonucleases reach the same final depth in the gel if they contain the same least-stable sequence. A unique set of bands is produced from the electrophoresis of randomly fragmented DNA; this would be expected if there were a limited number of melting centers occupying discrete genetic loci. An intact DNA molecule penetrates about as deeply into the gel as the uppermost band after fragmentation; this would be expected only if the least-stable sequence controls the final depth of the whole molecule.

Structural changes in the glutamine-chargeable Escherichia coli transfer RNA-Trp produced by chemical modification with sodium bisulfite

Glutamine-mischargeable tRNA produced by sodium bisulfite-treated Escherichia coli tRNA-Trp was isolated by dihydroxyboryl-cellulose affinity column chromatography. This tRNA was shown to have dual specificity tryptophan and glutamine, and, when charged with either amino acid, bound to ribosomes in response to the non-sense codon UAG but not in response to the tryptophan codon UGG. The results were consistent with the reported properties of Su+7 tRNA. The bisulfite-treated tRNA-Trp migrated as two bands during polyacrylamide gel electrophoresis. The faster moving band (band I) coincided with that of untreated tRNA-Trp. The slower moving band (band II) coincided with the glutamine-chargeable tRNA-Trp. Su+7 tRNA behaved like band II tRNA upon gel electrophoresis. Nucleotide sequence analysis showed that a cytidine-uridine transition occurred at the 1st or the 2n position of the anitcodon of band II tRNA. Band I and band II tRNAs differed from each other in their thermal melting profiles. It is suggested that the single base change in the anticodon is responsible for the altered conformation of band II tRNA.

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.

Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis

When double helical DNA is exposed to conditions favoring partial melting in polyacrylamide gels, its electrophoretic mobility undergoes a sharp cooperative transition, resulting in a large reduction in mobility. In the present experiments, where the transition is effected at a uniform temperature of 60 degrees C in a concentration gradient of a urea-formamide mixture, each Eco RI fragment of lambda or E. coli DNA exhibits the mobility transition at a characteristic concentration of the denaturant. The sudden retardation of fragments moving toward higher denaturant concentration in the gradient results in a pattern of sharpened zones in order depending upon nucleotide sequence, rather than size, and only very slightly dependent upon the time after the last fragment has been retarded. When combined with length-dependent electrophoresis in agarose in the perpendicular direction, this system provides a two-dimensional separation of fragments. The resolving power of the system is demonstrated by the clear resolution of over 250 fragments of the Eco RI digest of E. coli DNA. Corresponding fragments from an isogenic lambda lysogen of E. coli are found in the same positions, and additional fragments unique to the lysogen are evident.

Measurement of the differential melting profile of a promoter-containing fragment of T7 DNA by means of a microspectrophotometer

A double-beam microspectrophotometer with a 5 microliter cell has been used to study denaturation of DNA in an aqueous solution. This instrument enables measurement of high-resolution differential melting profiles simultaneously at several wavelengths with 0.5 to 1 microgram of DNA. Therefore it becomes possible to study nucleic acids which are difficult to obtain in large amounts. The techniques have been employed to measure the differential melting profiles of T7 DNA and of a fragment of this DNA 1000 base pairs long which contains the four early promoters.

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.

A spectroscopic and electron microscopic examination of the highly condensed DNA structures formed by denaturation in Mg(ClO4)2

1. Thermal denaturation in 1.5 M Mg(ClO4)2 of the DNA from bacteriophage lambda results in four well-separated subtransitions, as monitored by the accompanying increase in absorbance. The midpoint of the hyperchromic spectrum is significantly lowered compared to either 1.5 M MgCl2 or 3.0 M NaClO4. 2. The first two subtransitions are associated with the melting of the A . T-richest regions of the lambda DNA, as revealed by electron micrographs following fixation with formaldehyde. 3. Commencing with the third subtransition, an unusual DNA structure is observed in electron micrographs. In this structure the A . T-rich half of the molecule appears completely condensed, whereas the G . C-rich half remains native. 4. During the fourth subtransition DNA molecules condense completely and eventually aggregate to form extremely high molecular weight particles containing centers of electron density. Tendrils of DNA, primarily duplex, radiate outward from these centers. 5. The aggregation may be reversed by the removal of magnesium. The intramolecular condensation may be at least partly reversed by increasing the Mg(ClO4)2 concentrations to saturating levels.

Spectral analysis of high resolution direct-derivative melting curves of DNA for instantaneous and total base composition

Derivative melting profiles of DNA have been obtained directly by recording the difference in absorbance between two identical solutions maintained at a small constant temperature differential. This deltaA is monitored continuously with increasing temperature in a ratio recording spectrophotometer. Resolution of complex hyperfine structure in the profiles of small homogeneous viral DNAs appears to be significantly better than has been produced by various numerical methods of differentiation. In addition, a spectral method has been modified that permits easy analysis for DNA base composition from the ratio of derivative melting curves obtained at 282 and 260 nm. Eight bacterial and three vertebrate DNAs have been analyzed for total base composition from the product of the instantaneous base composition at small temperature intervals (0.05 degrees C) throughout the entire melting region and the integrated area of the 282 nm profile. The results are in excellent agreement with values determined by traditional methods.

Location of the cooperative melting regions in bacteriophage fd DNA

Differential melting profiles of the linear replicative form (RF-III) DNA of bacteriophage fd, of the fragments obtained by the restriction endonuclease R.HinHI and of those obtained by R.Hga were investigated. With these results a physical map which locates the cooperative melting regions on the DNA was constructed, and compared with the genetic map.