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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Base Composition

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Disease relevance of Base Composition

  • SPI2 has a lower G+C content than that of the remainder of the Salmonella genome and is flanked by genes whose products share greater than 90% identity with those of the E. coli ydhE and pykF genes [1].
  • This investigation was designed to explore transfer RNA (TRNA) methyltransferase activity, urinary excretion levels of tRNA degradation products, and tRNA base composition in normal monkeys and in those with hepatocellular carcinomas induced by N-nitrosodiethylamine [2].
  • Our comparison of the Escherichia coli UvrABC endonuclease incision of a variety of specific cross-link sequences in a single natural DNA fragment showed that DNA base composition determines which of two cross-linked DNA strands will be incised [3].
  • The predicted orf 253 gene sequence showed a significantly lower GC content than the surrounding intron and lysin gene sequences, and the predicted protein shared a motif with endonucleases found in phages from both gram-positive and gram-negative bacteria [4].
  • In the capsid region of the most highly modified virus construct, the effective number of codons used (N(C)) fell from 56.2 to 29.8, the number of CG dinucleotides rose from 97 to 302, and the G+C content increased from 48.4% to 56.4% [5].

High impact information on Base Composition

  • In fact, this latter property, which is dependent upon salt concentration and nucleotide base composition, is a major factor influencing whether ssDNA interacts with all four or only two SSB subunits, which in turn determines the type of intertetramer positive cooperativity [6].
  • Thermal stability was measured by hydroxyapatite thermal chromatography, S1 nuclease resistance after heating in a solvent which neutralizes the effect of DNA base composition, and spectrophotometric melting [7].
  • To explain these observations, it has been proposed that the base composition at the centre of the operator affects the affinity of the operator for repressor by altering the ease with which operator DNA can undergo the torsional deformation necessary for complex formation [8].
  • The gene is unusual in that its base composition is nearly 90 percent adenine plus thymine [9].
  • These data suggest, therefore, that in addition to base composition, other factors are involved in the production of chromosome banding by chromomycin A3 and olivomycin [10].

Chemical compound and disease context of Base Composition


Biological context of Base Composition


Anatomical context of Base Composition


Associations of Base Composition with chemical compounds


Gene context of Base Composition

  • The identification of GSCL required a genomic sequence-based approach because of its restricted expression and high GC content [31].
  • Because of low steady-state levels of BCR mRNA and the high GC content (78%) of the promoter region, definitive mapping of transcription start sites required artificial amplification of BCR promoter-directed transcripts [32].
  • Gene conversion and GC-content evolution in mammalian Hsp70 [33].
  • Branchiostoma mtDNA lacks a vertebrate-like control region; its largest noncoding region (129 nt) is unremarkable in sequence or base composition, and its location between ND5 and tRNAG differs from that usually found in vertebrates [34].
  • The GC content at synonymous third codon positions (GC3s) of the Amy1-type genes was higher than that of the Amy3-type genes [35].

Analytical, diagnostic and therapeutic context of Base Composition


  1. Identification of a virulence locus encoding a second type III secretion system in Salmonella typhimurium. Shea, J.E., Hensel, M., Gleeson, C., Holden, D.W. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  2. Composition, associated tissue methyltransferase activity, and catabolic end products of transfer RNA from carcinogen-induced hepatoma and normal monkey livers. Lakings, D.B., Waalkes, T.P., Borek, E., Gehrke, C.W., Mrochek, J.E., Longmore, J., Adamson, R.H. Cancer Res. (1977) [Pubmed]
  3. DNA base composition determines the specificity of UvrABC endonuclease incision of a psoralen cross-link. Jones, B.K., Yeung, A.T. J. Biol. Chem. (1990) [Pubmed]
  4. Widespread distribution of a group I intron and its three deletion derivatives in the lysin gene of Streptococcus thermophilus bacteriophages. Foley, S., Bruttin, A., Brüssow, H. J. Virol. (2000) [Pubmed]
  5. Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region. Burns, C.C., Shaw, J., Campagnoli, R., Jorba, J., Vincent, A., Quay, J., Kew, O. J. Virol. (2006) [Pubmed]
  6. Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities. Lohman, T.M., Ferrari, M.E. Annu. Rev. Biochem. (1994) [Pubmed]
  7. The single-copy DNA sequence polymorphism of the sea urchin Strongylocentrotus purpuratus. Britten, R.J., Cetta, A., Davidson, E.H. Cell (1978) [Pubmed]
  8. Dependence of the torsional rigidity of DNA on base composition. Fujimoto, B.S., Schurr, J.M. Nature (1990) [Pubmed]
  9. The unusual varl gene of yeast mitochondrial DNA. Butow, R.A., Perlman, P.S., Grossman, L.I. Science (1985) [Pubmed]
  10. Simultaneous production of Q and R bands after staining with chromomycin A3 or olivomycin. Prantera, G., Bonaccorsi, S., Pimpinelli, S. Science (1979) [Pubmed]
  11. RNAs of influenza A, B, and C viruses. Ritchey, M.B., Palese, P., Kilbourne, E.D. J. Virol. (1976) [Pubmed]
  12. Evidence for effect of random genetic drift on G+C content after lateral transfer of fucose pathway genes to Escherichia coli K-12. Aoyama, K., Haase, A.M., Reeves, P.R. Mol. Biol. Evol. (1994) [Pubmed]
  13. Vole agent identified as a strain of the trench fever rickettsia, Rochalimaea quintana. Weiss, E., Dasch, G.A., Woodman, D.R., Williams, J.C. Infect. Immun. (1978) [Pubmed]
  14. Clostridium hydroxybenzoicum sp. nov., an amino acid-utilizing, hydroxybenzoate-decarboxylating bacterium isolated from methanogenic freshwater pond sediment. Zhang, X., Mandelco, L., Wiegel, J. Int. J. Syst. Bacteriol. (1994) [Pubmed]
  15. Spectrophotometric characteristics of cholera phage phi2 DNA. Chaudhuri, K., Maiti, M. J. Gen. Virol. (1980) [Pubmed]
  16. The chicken beta 2-microglobulin gene is located on a non-major histocompatibility complex microchromosome: a small, G+C-rich gene with X and Y boxes in the promoter. Riegert, P., Andersen, R., Bumstead, N., Döhring, C., Dominguez-Steglich, M., Engberg, J., Salomonsen, J., Schmid, M., Schwager, J., Skjødt, K., Kaufman, J. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  17. Characterization of the 5' flanking region of the human D1A dopamine receptor gene. Minowa, M.T., Minowa, T., Monsma, F.J., Sibley, D.R., Mouradian, M.M. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  18. A dinucleotide deletion in the ankyrin promoter alters gene expression, transcription initiation and TFIID complex formation in hereditary spherocytosis. Gallagher, P.G., Nilson, D.G., Wong, C., Weisbein, J.L., Garrett-Beal, L.J., Eber, S.W., Bodine, D.M. Hum. Mol. Genet. (2005) [Pubmed]
  19. Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance. Sémon, M., Mouchiroud, D., Duret, L. Hum. Mol. Genet. (2005) [Pubmed]
  20. Complex events in the evolution of the human pseudoautosomal region 2 (PAR2). Charchar, F.J., Svartman, M., El-Mogharbel, N., Ventura, M., Kirby, P., Matarazzo, M.R., Ciccodicola, A., Rocchi, M., D'Esposito, M., Graves, J.A. Genome Res. (2003) [Pubmed]
  21. Enzymological characterization of KB cell DNA polymerase-alpha. Regulation of template binding by nucleic acid base composition. Fisher, P.A., Chen, J.T., Korn, D. J. Biol. Chem. (1981) [Pubmed]
  22. Oligodeoxynucleotides containing palindrome sequences with internal 5'-CpG-3' act directly on human NK and activated T cells to induce IFN-gamma production in vitro. Iho, S., Yamamoto, T., Takahashi, T., Yamamoto, S. J. Immunol. (1999) [Pubmed]
  23. Preferential stimulation of human lymphocytes by oligodeoxynucleotides that copy DNA CpG motifs present in virulent genes of group A streptococci. Chatellier, S., Kotb, M. Eur. J. Immunol. (2000) [Pubmed]
  24. Serine-palmitoyl transferase activity in cultured human keratinocytes. Holleran, W.M., Williams, M.L., Gao, W.N., Elias, P.M. J. Lipid Res. (1990) [Pubmed]
  25. Taxonomic study of Corynebacterium Group ANF-1 strains: Proposal of Corynebacterium afermentans sp. nov. containing the subspecies C. afermentans subsp. afermentans subsp. nov. and C. afermentans subsp. lipophilum subsp. nov. Riegel, P., de Briel, D., Prévost, G., Jehl, F., Monteil, H., Minck, R. Int. J. Syst. Bacteriol. (1993) [Pubmed]
  26. Isolation and characterization of a novel ribonucleoprotein particle: large structures contain a single species of small RNA. Kedersha, N.L., Rome, L.H. J. Cell Biol. (1986) [Pubmed]
  27. Nick-translation of metaphase chromosomes: in vitro labeling of nuclease-hypersensitive regions in chromosomes. Kuo, M.T., Plunkett, W. Proc. Natl. Acad. Sci. U.S.A. (1985) [Pubmed]
  28. Base composition-independent hybridization in tetramethylammonium chloride: a method for oligonucleotide screening of highly complex gene libraries. Wood, W.I., Gitschier, J., Lasky, L.A., Lawn, R.M. Proc. Natl. Acad. Sci. U.S.A. (1985) [Pubmed]
  29. Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Woodside, M.T., Behnke-Parks, W.M., Larizadeh, K., Travers, K., Herschlag, D., Block, S.M. Proc. Natl. Acad. Sci. U.S.A. (2006) [Pubmed]
  30. Analysis of the mouse Dhfr/Rep-3 major promoter region by using linker-scanning and internal deletion mutations and DNase I footprinting. Smith, M.L., Mitchell, P.J., Crouse, G.F. Mol. Cell. Biol. (1990) [Pubmed]
  31. The DiGeorge syndrome minimal critical region contains a goosecoid-like (GSCL) homeobox gene that is expressed early in human development. Gottlieb, S., Emanuel, B.S., Driscoll, D.A., Sellinger, B., Wang, Z., Roe, B., Budarf, M.L. Am. J. Hum. Genet. (1997) [Pubmed]
  32. Characterization of the BCR promoter in Philadelphia chromosome-positive and -negative cell lines. Shah, N.P., Witte, O.N., Denny, C.T. Mol. Cell. Biol. (1991) [Pubmed]
  33. Gene conversion and GC-content evolution in mammalian Hsp70. Kudla, G., Helwak, A., Lipinski, L. Mol. Biol. Evol. (2004) [Pubmed]
  34. Complete sequence, gene arrangement, and genetic code of mitochondrial DNA of the cephalochordate Branchiostoma floridae (Amphioxus). Boore, J.L., Daehler, L.L., Brown, W.M. Mol. Biol. Evol. (1999) [Pubmed]
  35. Phylogeny and the evolution of the Amylase multigenes in the Drosophila montium species subgroup. Zhang, Z., Inomata, N., Cariou, M.L., Da Lage, J.L., Yamazaki, T. J. Mol. Evol. (2003) [Pubmed]
  36. A rare branch-point mutation is associated with missplicing of fibrillin-2 in a large family with congenital contractural arachnodactyly. Maslen, C., Babcock, D., Raghunath, M., Steinmann, B. Am. J. Hum. Genet. (1997) [Pubmed]
  37. Ribosomal genes in Physarum polycephalum: transcribed and non-transcribed sequences have similar base compositions. Steer, W.M., Molgaard, H.V., Bradbury, E.M., Matthews, H.R. Eur. J. Biochem. (1978) [Pubmed]
  38. Purification of synthetic oligodeoxyribonucleotides by ion-exchange high-performance liquid chromatography. Scanlon, D., Haralambidis, J., Southwell, C., Turton, J., Tregear, G. J. Chromatogr. (1984) [Pubmed]
  39. Characterization of minute differences between genomes of strains of Penicillium nalgiovense using subtractive suppression hybridization without cloning. Harms, C., Käse, M., Hildebrandt, A. Lett. Appl. Microbiol. (2002) [Pubmed]
  40. Structural basis of polyamine-DNA recognition: spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy. Deng, H., Bloomfield, V.A., Benevides, J.M., Thomas, G.J. Nucleic Acids Res. (2000) [Pubmed]
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