Variation In Base Composition Research Articles

Enhanced graphic matrix analysis of nucleic acid and protein sequences.

The enhanced graphic matrix procedure analyzes nucleic acid and amino acid sequences for features of possible biological interest and reveals the spatial patterns of such features. When a sequence is compared to itself the technique shows regions of self-complementarity, direct repeats, and palindromic subsequences. Comparison of two different sequences, exemplified by immunoglobulin kappa light chain genes, by using colored graphic matrices showed domains of similarity, regions of divergence, and features explainable by transpositions. Analysis of mouse constant domain immunoglobulin sequences revealed self-complementary regions that can be used to fold the molecule into a structure consistent with electron microscopic observations. Computer translation of nucleic acid sequences into all possible amino acid sequences followed by graphic matrix analysis provides a way to detect the most likely protein encoding regions and can predict the correct reading frames in sequences in which splicing patterns are not defined. Application of this technique to regions of simian virus 40 and polyoma virus demonstrates the frames of translation and shows the agreement of sequences determined in separate laboratories with different virus isolates. The graphic matrix technique can also be used to assemble fragmentary sequences during determination, to display local variations in base composition, to detect distant evolutionary relationships, and to display intragenic variation in rates of evolution.

Plasmids in two cyanobacterial strains

FEBS LettersVolume 107, Issue 1 p. 165-168 Full-length articleFree Access Plasmids in two cyanobacterial strains Devorah Friedberg, Devorah Friedberg Department of Microbiological Chemistry, The Hebrew University-Hadassah Medical School, Jerusalem, IsraelSearch for more papers by this authorJulie Seijffers, Julie Seijffers Department of Microbiological Chemistry, The Hebrew University-Hadassah Medical School, Jerusalem, IsraelSearch for more papers by this author Devorah Friedberg, Devorah Friedberg Department of Microbiological Chemistry, The Hebrew University-Hadassah Medical School, Jerusalem, IsraelSearch for more papers by this authorJulie Seijffers, Julie Seijffers Department of Microbiological Chemistry, The Hebrew University-Hadassah Medical School, Jerusalem, IsraelSearch for more papers by this author First published: November 01, 1979 https://doi.org/10.1016/0014-5793(79)80487-1Citations: 10AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL References 1 R.Y. Stanier, G. Cohen-Bazire, Ann. Rev. Microbiol., 31, (1971), 225– 274. 2 M. Herdman, M. Janvier, J.B. Waterbury, R. Rippka, R.Y. Stanier, J. Gen. Microbiol., 111, (1979), 63– 71. 3 R. Rippka, J. Deruelles, J.B. Waterbury, M. Herdman, R.Y. Stanier, J. Gen. Microbiol., 111, (1979), 1– 61. 4 M. Herdman, M. Janvier, R. Rippka, R.Y. Stanier, J. Gen. Microbiol., 111, (1979), 73– 85. 5 Y. Asato, H.S. Ginoza, Nature New Biol., 244, (1973), 132– 133. 6 T.M. Roberts, K.E. Koths, Cell, 9, (1976), 551– 557. 7 R.D. Simon, J. Bacteriol., 136, (1978), 414– 418. 8 R.H. Lau, W.F. Doolittle, J. Bacteriol., 137, (1979), 648– 652. 9 S.F. Delaney, M. Herdman, N.G. Carr, R.A. Lewin Genetics of Blue—Green Algae (1976), Univ. Calif. Press Berkeley 7– 28. 10 E. Padan, Ann. Rev. Plant Physiol., 30, (1979), 27– 40. 11 A. Zehnder, P.R. Gorham, Can. J. Microbiol., 6, (1960), 645– 660. 12 A. Oren, E. Padan, J. Bacteriol., 133, (1978), 558– 563. 13 P. Guerry, D.J. Leblanc, S. Falkow, J. Bacteriol., 116, (1973), 1064– 1066. 14 J.G. Sutcliffe, Nucleic Acids Res., 5, (1978), 2721– 2728. 15 J.A. Meyers, D. Sanchez, L.P. Elwell, S. Falkow, J. Bacteriol., 127, (1976), 1527– 1537. 16 Y. Cohen, B.B. Jorgensen, E. Padan, M. Shilo, Nature, 257, (1975), 489– 492. 17 R.D. Davis, M. Simon, N. Davidson, Methods Enzymol., 21, (1971), 413– 428. Citing Literature Volume107, Issue1November 01, 1979Pages 165-168 ReferencesRelatedInformation

High resolution chromosome analysis: one and two parameter flow cytometry

Isolated mammalian chromosomes have been quantitatively classified by high resolution flow cytometry. Chinese hamster chromosomes stained with 33258 Hoechst and excited in the UV showed a fluorescence distribution in which the 14 types of Chinese hamster chromosomes were resolved into 16 groups seen as distinct peaks in the distributions. Chinese hamster chromosomes were also stained with both 33258 Hoechst (HO) and chromomycin A3 (CA3); the two dye contents were measured by selective excitation in the UV and at 458 nm in a dual beam flow cytometer. The resulting two parameter distribution (HO versus CA3) showed 10 chromosome groups1. Human strain LLL 761 chromosomes stained with HO and excited in the UV showed a fluorescence distribution in which the 23 types of human chromosomes were resolved into 12 groups. Human chromosomes stained with both HO and CA3 and measured in the dual beam flow cytometer produced two parameter fluorescence distributions which showed 20 groups. The chromosomes associated with each group were determined by quinacrine banding analysis of sorted chromosomes and by DNA cytophotometry of preidentified metaphase chromosomes. The relative HO and CA3 stain content and frequency of occurrence of chromosomes in each group were determined from the fluorescence distributions and compared to the results from DNA cytophotometry. The chromosome to chromosome variations in HO and CA3 staining are attributed to variations in chromosomal base composition.

Mechanisms of chromosome banding. IX. Are variations in DNA base composition adequate to account for quinacrine, Hoechst 33258 and daunomycin banding?

Prior studies on subfractions of mouse and Kangaroo rat DNA have suggested that variations in base concentration within a given genome may not be great enough to account for Q-banding. To examine this with another species, calf DNA was subfractionated by CsCl ultracentrifugation into GC-rich satellites and the main band DNA was further fractionated into AT-rich, intermediate and GC-rich portions. The effect of varying concentrations of these DNAs on quinacrine and Hoechst 33258 fluorescence was examined. Although with both compounds there was less fluorescence in the presence of the GC-rich satellites than main band fractions, these results per se did not answer the question of whether the variation in base composition alone was adequate to account for chromosome banding. To answer this the fluorescence observed in the presence of DNA of a given base composition was related to the fluorescence observed in the presence of DNA of 40% GC content (F/F40). This allowed the derivation of a term B which indicated the relative change in fluorescence per 1% change in base composition of DNA. To determine the percent change in fluorescence observed in Q-banding, the photoelectric recordings of Caspersson et al. (1971) were used. From these data we conclude: 1. Quinacrine is twice as sensitive to changes in base composition as Hoechst 33258. 2. Variation in the base content of DNA along the base content of DNA along the chromosome is sufficient to account for most Q-banding, except possibly for some of the extremes of quinacrine fluorescence. This was further examined with daunomycin. Even though daunomycin gives good fluorescent banding, DNAs varying in base composition from 100 to 40% GC content all resulted in the same relative fluorescence of 0.03. However, in the presence of poly (dA-dT) the relative fluorescence was 0.85, indicating a great sensitivity to very AT-rich DNA. This suggests that with daunomycin and possibly other fluorochromes, stretches of very AT-rich DNA may be more important in fluorescent banding than simple variation in mean base composition.

Determination of the molecular weights of RNAs by low-speed sedimentation equilibrium: 16 S ribosomal RNA as a model compound

Problems associated with the determination of molecular weights of ribonucleic acids by sedimentation equilibrium have been investigated, using the sodium salt of 16 S ribosomal RNA from Escherichia coli as a model system, for which a chemical molecular weight has been computed from the sequence data (Fellner et al. , 1972; Fellner & Zimmermann, 1974) . It is shown that 16 S rRNA solutions exhibit significant interaction, probably in the form of a reversible dimerization. The sedimentation equilibrium procedure of Rowe & Rowe (1970 a,b ) is used to remove both interaction and non-ideality terms resulting in an estimated ideal molecular weight of 5·21 ± 0·11 × 10 5 for the monomeric species, based upon a partial specific volume &-v = 0·523 cm 3 ·g −1 determined using a Digital Density meter. This molecular weight value agrees well with the computed formula weight (5·33 ± 0·05 × 10 5 ), and implies that even for a polyelectrolyte such as a nucleic acid, &-v , measured conventionally, is a satisfactory parameter so far as hydrodynamic measurements are concerned. The partial specific volumes at 5°C of the sodium salts of poly(U), poly(A) and poly(U)·poly(A) have been measured and found to be closely similar (0·527, 0·531 and 0·529 cm 3 ·g −1 , respectively), and do not differ significantly from that of 16 S rRNA; suggesting that variation in base composition and secondary structure of RNAs has little effect on &-v , under defined conditions of temperature, ionic strength and counter-ion composition. A new method for measuring the absolute fringe displacement in the interference patterns obtained at sedimentation equilibrium has been developed and applied in this study (see Appendix).

Mechanisms of chromosome banding. V. Quinacrine banding.

A series of biochemical investigations were undertaken to determine the mechanism of Q-banding. The results were as follows: 1. In agreement with previous studies, highly AT-rich DNA, such as poly(dA)-poly(dT), markedly enhanced quinacrine fluorescence while GC containing DNA quenched fluorescence. These effects persisted at DNA concentrations comparable to those in the metaphase chromosome. 2. Studies of quinacrine-DNA complexes in regard to the hypochromism of quanacrine, DNA Tm, DNA viscosity, and equilibrium dialysis, indicated the quinacrine was bound be intercalation with relatively little sid binding. 3. Single or double stranded nucleotide polymers, in the form of complete or partial helices, were 1000-fold more effective in quenching than solutions of single nucleotides, suggesting that base stacking is required for quenching. 4. Studies of polymers in the A conformation, such as transfer RNA and DNA-RNA hybrids, indicated that marked base tilting does not affect the ability of nuclei acids to cause quenching or enhancement of quinacrine fluorescence. 5. Salts inhibit the binding of quinacrine to DNA. 6. Spermine, polylysine and polyarginine, which bind in the small groove of DNA, inhibited quinacrine binding and quenching, while histones, which probably bind in the large groove, had little effect. This correlated with the observation that removal of histones with acid has no effect on Q-banding. 7. Mouse liver chromatin was separated into five fractions. At concentrations of quinacrine from 2 times 10-6 to 2 times 10-5 M all fractions inhibited to varying degrees the ability of the chromatin DNA to bind quinacrine and quench quinacrine fluorescence. At saturating levels of quinacrine two fractions, the 400 g pellet (rich in heterochromatin) and a dispersed euchromatin supernatant fraction, showed a decreased number of binding sites for quinacrine. These two fractions were also the richest in non-histone proteins. 8. DNA isolated from the different fractions all showed identical quenching of quinacrine fluorescenc. 9. Mouse GC-rich, mid-band, AT-rich, and satellite DNA, isolated by CsCL AND Cs-2SO-4-Ag+ centrifugation all showed identical quenching of quinacrine fluorescence, indicating that within a given organism, except for very AT or GC-rich satellites, the variation in base composition is not adequate to explain Q-banding. We interpret these results to indicate that: (a) quinacrine binds to chromatin by intercalation of the three planar rings with the large group at position 9 lying in the small groove of DNA, (b) most pale staining regions are due to a decrease binding of quinacrine, and (c) this inhibition of binding is predominately due to non-histone proteins.

Polyoma DNA Replication: Location of the Origin in Different Virus Strains

In virus-infected or transformed cells, polyoma expresses a large number of functions. Attempts to understand these in relation to the structure of the virus DNA have until recently been limited by our knowledge of polyoma DNA anatomy and nucleotide sequence. Methods such as denaturation mapping, based on the variation of base composition in different regions of the DNA, provide some information, but they are limited by the small size and circularity of the molecule (Follet and Crawford 1968). Cleavage by restriction endonucleases, which cut the DNA at specific nucleotide sequences, provide both better reference points on the DNA and the means for physical separation of different regions. Here we have made use of a variety of restriction enzymes in conjunction with other techniques to provide information on the mode of DNA replication and on the positions in the molecule at which replication starts and finishes.

Optical studies of complexes of quinacrine with DNA and chromatin: implications for the fluorescence of cytological chromosome preparations.

The fluorescence and circular dichroism of quinacrine complexed with nucleic acids and chromatin were measured to estimate the relative magnitudes of factors influencing the fluorescence banding patterns of chromosomes stained with quinacrine or quinacrine mustard. DNA base composition can influence quinacrine fluorescence in at least two ways. The major effect, evident at low ratios of quinacrine to DNA, is a quenching of dye fluorescence, correlating with G-C composition. This may occur largely prior to relaxation of excited dye molecules. At higher dye/DNA saturations, which might exist in cytological chromosome preparations stained with high concentrations of quinacrine, energy transfer between dye molecules converts dyes bound near G-C base pairs into energy sinks. In contrast to its influence on quinacrine fluorescence, DNA base composition has very little effect on either quinacrine binding affinity or the circular dichroism of bound quinacrine molecules. The synthetic polynucleotides poly(dA-dT) and poly(dA)-poly(dT) have a similar effect on quinacrine fluorescence, but differ markedly in their affinity for quinacrine and in the circular dichroism changes associated with quinacrine binding. Quinacrine fluorescence intensity and lifetime are slightly less when bound to calf thymus chromatin than when bound to calf thymus DNA, and minor differences in circular dichroism between these complexes are observed. Chromosomal proteins probably affect the fluorescence of chromosomes stained with quinacrine, although this effect appears to be much less than that due to variations in DNA base composition. The fluorescence of cytological chromosome preparations may also be influenced by fixation effects and macroscopic variations in chromosome coiling.

Deoxyribonucleic acid base composition in the taxonomy of Staphylococcus.

Twenty-four strains of Staphylococcus aureus, including eight known mutants of S. aureus and strains growing under a variety of environmental conditions or exposed to a number of physical and chemical agents, maintained a remarkably narrow range of guanine plus cytosine (GC) content (32.4 to 35.1%). The wide range of GC content (30.7 to 40%) reported in the literature was due to the variety of methods and calculations used rather than to any substantial variation in base composition. The UV-2 "mutant" (ATCC 13680) with a GC content of 67.6% reported to be derived from S. aureus (ATCC 13679) was a species of Corynebacterium. The data presented were consistent with the concept that base composition changes only to a very slight degree by mutation.

Recognition of DNA bse sequencedifferences among vertebrates.

UNLIKE the wide variation of DNA base composition found in bacteria, higher organisms tend to have a restricted average base composition, (vertebrates ∼ 42 moles per cent guanine + cytosine)1. Thus physical methods such as thermal denaturation or equilibrium density gradient sedimentation, which are useful in distinguishing bacterial DNAs2, do not discriminate to any extent among vertebrate DNAs, excluding the question of satellite bands. Phylogenetic relationships among bacteria, based on other criteria, are largely borne out by DNA–DNA hybridization3. While the latter technique can discriminate among distantly related higher organisms4 it can be applied with only limited confidence to more closely related vertebrates.

The ribonucleic acid of axons and myelin sheaths from Mauthner neurons

Axons and myelin sheaths from the paired giant Mauthner neuron were isolated from fixed spinal cords of the goldfish by means of micromanipulation. Isolated cells were extracted with ribonuclease and the extracts were investigated for RNA content and composition using ultramicrochemical procedures. The following results were obtained. 1. 1. RNA is present in axons and myelin sheaths of Mauthner neurons. 2. 2. The amount of RNA per unit fibre-length is of the same order for axon and myelin sheath. 3. 3. The concentration of RNA for axons and myelin sheaths per fixed volume compared to that of the nerve cell body is 10 and 40 times lower, respectively. 4. 4. The total amount of RNA in the axon is estimated to be 4 times greater than that of the cell body. 5. 5. The RNA of axons and myelin sheaths shows great variations in base composition and differs distinctly from ribosomal RNA, in contrast to the RNA of nerve cell bodies.

Variation in base composition of ribonucleic acid in Escherichia coli.

Variation in base composition of ribonucleic acid in Escherichia coli.

Variation and heterogeneity of base composition of deoxyribonucleic acids: A compilation of old and new data

A compilation of the previously accumulated data as well as some new results on the base composition of DNA from various organisms reveals some general features of its variation and heterogeneity: Among bacteria the mean guanine-cytosine (G-C) content of DNA varies approximately from 25 to 75%, and this extends over the range of the mean G-C content of DNA of higher organisms. Phylogenetic relations may be reflected in the mean G-C content. The distribution of G-C content of the DNA molecules of an organism is generally unimodal and the range is relatively narrow. If the mean G-C contents of DNA of two species are different by 10% in bacteria, there are few DNA molecules of the same G-C content common to the two species. The small heterogeneity of the base composition among the DNA molecules of an organism seems to be true for smaller regions within molecules. Each point is discussed with respect to its genetic implication.

Luminescent Barium and Magnesium Halophosphates

Uranium is the principal useful activator in magnesium and barium halophosphates, giving rise to efficient and fairly saturated yellow‐green luminescence. Barium chlorophosphate U, in particular, shows a strong emission peaking at 5300 Å under both short and long ultraviolet excitation. Details of absorption characteristics and variations in base composition are discussed briefly.