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

• The base compositions of the RNAs of influenza A, B, and influenza C virus are almost identical and comparative analysis on polyacrylamide gels shows that the genome of influenza C/GL/1167/54 virus, like that of the RNAs of influenza A and B viruses, is segmented [11].
• Evidence for effect of random genetic drift on G+C content after lateral transfer of fucose pathway genes to Escherichia coli K-12 [12].
• The base ratio (molar percent guanine plus cytosine) of its deoxyribonucleic acid was shown to be 39, which was identical to the base ratio of the deoxyribonucleic acid of Rochalimaea quintana tested simultaneously [13].
• The DNA base composition of the type strain is 35.5 mol% guanine plus cytosine, whereas the DNA base compositions of the type strains of Clostridium sticklandii and Clostridium aminovalericum are 33 and 33.5 mol% guanine plus cytosine, respectively, as determined by a chemical method [14].
• Purified preparations of cholera bacteriophage phi2 were treated with cold phenol and the nucleic acid examined for its hydroxyapatite chromatographic pattern, thermal denaturation profile, base composition and mol. wt [15].

Biological context of Base Composition

• The chicken beta 2-microglobulin gene has a similar genomic organization but smaller introns and higher G+C content than mammalian beta 2-microglobulin genes [16].
• The promoter region lacks a TATA box and a CAAT box, is rich in G+C content, and has multiple putative binding sites for transcription factor Sp1 [17].
• The ankyrin erythroid promoter is a member of the most common class of mammalian promoters which lack conserved TATA, initiator or other promoter cis elements and have high G+C content, functional Sp1 binding sites and multiple transcription initiation sites [18].
• We reassessed this issue by examining in human and mouse the correlation between gene expression and GC-content, using different measures of gene expression (EST, SAGE and microarray) and different measures of GC-content [19].
• The four genes within PAR2 have been proposed to constitute two zones with different base ratios and transcription, one of which was added recently to the X chromosome [20].

Anatomical context of Base Composition

• Enzymological characterization of KB cell DNA polymerase-alpha. Regulation of template binding by nucleic acid base composition [21].
• The changes of base composition inside or outside the palindrome sequence altered its activity: The homooligo-G-flanked GACGATCGTC was the most potent IFN-gamma inducer for NK cells [22].
• Despite low GC content in GAS DNA, the emm1 gene encoding the streptococcal M1 protein contained a relatively high frequency of TTCG(T/C), TCGTCG and (G/A)TCGT motifs that preferentially stimulated human lymphocytes [23].
• In summary, we have found that cultured human neonatal keratinocytes contain unusually high levels of serine-palmitoyl transferase activity, and that the substrate specificity of keratinocyte SPT may determine the base composition of epidermal sphingolipids [24].
• We have determined the cell wall composition, guanine-plus-cytosine (G+C) contents of the DNA, rRNA gene restriction patterns, and the levels of DNA-DNA relatedness of 11 strains identified biochemically as Centers for Disease Control (CDC) Corynebacterium group absolute nonfermenter 1 (Corynebacterium group ANF-1) [25].

Associations of Base Composition with chemical compounds

• Another major species of Mr 37,000 has been identified as a species of small RNA of unusual base composition (adenosine 12.0%, guanosine 29.7%, uridine 30.9%, and 27.4% cytidine), which migrates as a single species in urea PAGE between the 5S and 5.8S ribosomal standards, containing approximately 140 bases [26].
• Base composition analyses showed that the labeled DNA was highly enriched in guanine and adenine residues, suggesting that the nick-translation reaction was asymmetrical and the strand enriched in purine was preferentially translated [27].
• This technique, which uses tetramethylammonium chloride, is especially helpful whenever a highly complex library is screened with a pool of oligonucleotide probes, which usually vary widely in base composition [28].
• We measured 20 different hairpin sequences with quasi-random stem sequences that were 6-30 bp long, polythymidine loops that were 3-30 nt long, and stem GC content that ranged from 0% to 100% [29].
• The mouse dihydrofolate reductase (Dhfr) promoter region is buried within a CpG island (a region rich in unmethylated CpG dinucleotides), has a high G+C content, and lacks CAAT and TATA elements [30].

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

• Sequence analysis of genomic DNA revealed an unusual base composition for intron 30 and identified the mutation, a g-26t transversion, in the vicinity of the splicing branch-point site in intron 30 [36].
• The base compositions of the fragments were determined by analytical centrifugation in CsCl or in CsCl with netropsin [37].
• Synthetic oligodeoxyribonucleotides ranging from 11 to 37 nucleotides in length and with varying base compositions, prepared by both the phosphotriester and phosphite procedures, have been purified by ion-exchange high-performance liquid chromatography on Whatman Partisil 10/SAX columns using phosphate buffer gradients [38].
• Combined with a special two-dimensional polyacrylamide gel electrophoretic technique the usual background was eliminated from the prospective foreign polymerase chain reaction fragments according to their base composition (Müller et al. 1981) [39].
• Structural basis of polyamine-DNA recognition: spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy [40].

References