Effect of ethylene glycol, urea, and N-methylated glycines on DNA thermal stability: the role of DNA base pair composition and hydration

The accumulation of the cosolutes ethylene glycol, urea, glycine, sarcosine, and glycine betaine at the single-stranded DNA surface exposed upon melting the double helix has been quantified for DNA samples of different guanine-cytosine (GC) content using the local-bulk partitioning model [Record, M. T., Jr., Zhang, W., and Anderson, C. F. (1998) Adv. Protein Chem. 51, 281-353]. Urea and ethylene glycol are both locally accumulated at single-stranded DNA relative to bulk solution. Urea exhibits a stronger affinity for adenine (A) and thymine (T) bases, leading to a greater net dehydration of these bases upon DNA melting; ethylene glycol local accumulation is practically independent of base composition. However, glycine, sarcosine, and glycine betaine are not necessarily locally accumulated at single strands after melting relative to bulk solution, although they are locally accumulated relative to double-stranded DNA. The local accumulation of glycine, sarcosine, and glycine betaine at single strands relative to double-stranded DNA decreases with bulk cosolute molality and increases with GC content for all N-methylated glycines, demonstrating a stronger affinity for G and C bases. Glycine also shows a minimum in melting temperature T(m) at 1-2 m for DNA samples of 50% GC content or less. Increasing ionic strength attenuates the local accumulation of urea, glycine, sarcosine, and glycine betaine and removes the minimum in T(m) with glycine. This attenuation in local accumulation results in counterion release during the melting transition that is dependent on water activity and, hence, cosolute molality.     

The relationship of DNA base composition and individual protein composition in micro-organisms

Summary To investigate the dependence of protein composition on DNA base composition, a set of data on individual proteins with known amino acid compositions from a spectrum of bacterial species has been compiled. It is found that similar relationships of amino acid frequency to G + C content exist for these proteins as for the bulk proteins studied by Sueoka (1961). The data are analysed by linear and cubic regression, and a measure of the proportions of A + T-rich and G + C-rich codons in the underlying messenger RNAs is put forward. The theoretical limits on the G + C content of coding DNA are discussed, and inference are made about the various selective forces acting on DNAs of different G + C contents.     

Taxonomy ofKluyveromyces: evaluation of DNA base composition

The DNA base composition of 19 strains ofKluyveromyces was calculated from the thermal denaturation temperature (Tm) of their DNA. The % GC ranged from 33 to 45, with a bimodal repartition. It may be inferred that the intrageneric variation is too weak to discriminate two genera. However, two groups can be distinguished on the base of % GC and two other criteria of classification. associated with the Centre National de la Recherche Scientifique. The authors are indebted to Professor Dr. J. De Ley for his advice on the thermal-denaturation technique and to Mrs. Billon-Grand for her skilful technical assistance.     

DNA base composition ofKlebsiella rubiacearum

The base composition of pure DNA from a strain of a nitrogen-fixing leaf-nodule bacterium was determined. The mean molar (guanine + cytosine) composition of 55.5% is in agreement with previous conclusions that this bacterium belongs in the genusKlebsiella.     

The topography of lambda DNA: polyriboguanylic acid binding sites and base composition

The positions of the ten poly(rG) binding sites on the two strands of λ DNA have been determined with the aid of the families of overlapping DNA fragments described in the preceding paper and the DNA of deletion mutants. Nine sites are on the r-strand ^‡: two are located in the right half, 0·84 ± 0·03 and 0·91 ± 0·02 molecular length unit from the left end; and seven are evenly distributed within 0·4 unit from the left end. The tenth site is on the l-strand, 0·60 ± 0·03 unit from the left end. Another site was mapped on the r-strand of the bio segment of Escherichia coli DNA found in λ bio variants; the l-strand of this segment contains no sites.     

DNA base composition of yellowErwinia strains

DNA base composition, expressed as % GC, was determined in 34 strains of yellow-pigmentedErwinia-like organisms from plant, animal and human origin. Organisms calledErwinia herbicola (Graham and Hodgkiss, 1967) have a % GC in the narrow range 55.0 to 56.5, with the exception of strain G 146 which has 58.6% GC. They include the formerBacterium herbicola, Erwinia lathyri, Bacterium typhi flavum and the Muraschi isolates,Erwinia milletiae with 55.8 % falls within the % GC range of theHerbicola group,Erwinia ananas is at the lower end of the group with 54.8 ± 0.4 % GC andErwinia uredovora still lower at 53.7 ± 0.7 % GC. These data and the compositional distribution of the DNA fragments do not exclude the inclusion of these organisms into the genusErwinia.     

The genome of Plasmodium falciparum. I: DNA base composition.

Some structural properties of the DNA of Plasmodium falciparum were studied thoroughly using several techniques. Its G+C content was found to be extremely low (17-19%), the lowest reported for a living organism. The DNA seems to be composed only of the four major bases as no methylated bases were detected. This DNA had a Tm value of 62.5 degrees C and its denaturation profile showed no marked intramolecular heterogeneity.     

On the hydration of DNA. II. Base composition dependence of the net hydration of DNA

The dependence of the net hydration of DNA on its base composition has been measured by density gradient ultracentrifugation of three DNA's in a series of cesium and lithium salt solutions of different water activities. Extrapolation to zero water activity showed the dependence of the partial specific volume on base composition to be very small for CsDNA and aero for LiDNA. At least 99% of the dependence of buoyant density on base composition can be accounted for on the basis of a differential hydration, with a mole of adenine–thymine pairs binding about 2 moles more water than a mole of guanine–cytosine pairs in CsCl.     

Modulation of the B-A transition of DNA by potential antitumor antibiotics. Influence of the base composition of DNA

The B-A transition of DNA in oriented films of DNA-drug complexes is more or less restricted as a consequence of drug binding as revealed by infrared linear dichroism. A fraction of DNA is irreversibly locked into the B form. This behavior is described by the number of DNA base pairs "frozen" in the B form by one drug molecule. This quantity is dependent on the DNA sequence the drug is attached to. In this paper, drug complexes of oriented films of NaDNA with a GC content of 42% from calf thymus and a GC-rich DNA from Micrococcus lysodeikticus were compared. The restriction of the B-A transition of DNA complexes with two intercalating antibiotics, aclacinomycin A and violamycin BI, is not severely influenced by the base composition of DNA. By contrast, the strong groove binding oligopeptide antibiotics netropsin and distamycin A are much less effective to restrict the B-A transition of GC-rich DNA than of AT-rich DNA. This finding is in agreement with previous results by other methods which support a model based upon a strong preference of AT clusters by these two non-intercalating drugs.     

DNA base composition and taxonomy of someAcinetobacter strains

The DNA base composition of a group of numerically analyzed acinetobacters was determined. Seven strains ofAcinetobacter anitratus appear to form a homogeneous group with S>90% and ca. 42.1 % GC.A. Iwoffii is less homogeneous. Most of the strains have around 46.6 % GC and a broad compositional distribution with 2=3.8 C. Two other small groups have a % GC of 44.8±0.3 and 42.1±1 % GC. The DNA characteristics of the latter group are indistinguishable fromA. anitratus-DNA. ThreeAlcaligenes faecalis strains have 58.8 % GC. Numerical analysis suggests that they might be related toBordetella bronchiseptica, but the % GC of the latter (69.5) shows that the relationship is only remote.     

DNA base composition and adansonian analysis of mycobacteria

The contents of guanine and cytosine (GC) in DNA were determined in 20 strains of rapidly growing mycobacteria, 18 of which were originally classified as 8 different species and 2 were not defined. The values of GC expressed in molar percentage varied between 63.3 and 67.9 and agreed generally, as well as individually in the various species, with data reported in the literature for the genusMycobacterium (60.8–73.0% GC). In addition to the determination of GC in DNA, 20 mycobacteria were tested for various physiological and biochemical characteristics (a total of 82 characters were processed). Adansonian analysis was applied to establish similarity between individual pairs of microorganisms as to their phenotypic expression. All the mycobacteria used were divided into 6 groups (group 2 was subdivided into 3 sub-groups) of phylogenetically related organisms with a high percentage of similarity (S≤70%) and with great similarity in the GC content in DNA (±1% GC).     

The quick approximation of DNA base composition from absorbancy ratios

The approximate base composition of pure deoxyribonucleic acid (DNA) can be quickly estimated from the absorbancy ratio E₂₆₀/E₂₈₀ in 0.1n acetic acid according to the empirical relation % GC=168.6–87.4 (E₂₆₀/E₂₈₀), valid in the range 40 to 70% GC (molar per cent guanine ... cytosine). The method is only accurate to within + 3% GC. It can be used when a quick, rough estimate of DNA base composition is required, e.g., to check the correct taxonomic position of new isolates or to give an approximation of the melting point T_m or buoyant density of an unknown DNA sample. The method can not be recommended for distinguishing between two genera with closely related % GC values, or for finer distinction within one genus.