Nucleotide Composition

GTP hydrolysis by Ras, which is considerably slow, has been analyzed, usually by single turn-over measurements. Ras is loaded with GTP by incubation of Ras (being in the GDP form after preparation) with a large excess of GTP in the presence of EDTA, which leads to faster dissociation of the nucleotide. After change of buffer and removal of excess nucleotide, aliquots are taken at certain time intervals and the nucleotide composition is analyzed with the help of filter binding assays or HPLC. Series of experiments with mutations in the neighbor-... 

We have started examining nucleotide compositional strand asymmetries in transcribed regions of human sequences [36]. We have computed the 5ta and 5gc skews [Eq. (1)] for intron sequences since, in contrast to exonic sequences, they can be considered as weakly selected sequences. For each gene, we have concatenated all the introns in a unique sequence (see Section II.A). The distributions of the TA and GC skews, computed on the 14,854 intro-containing... 

The relative numbers of these pyrimidine dimers formed depend upon the nucleotide composition of the DNA. Setlow and Carrier examined dimer formation in DNA from three microorganisms whose DNA had differing A-T contents. The composition of the DNA, and... 

Maga, J. A., McNeill, J. G. (1986). Nucleotide composition of incubated potatoes from five potato Solanum tuberosum) cultivars. Lebensmittel-Wissenschaft Technologies 19, 31-33. 

Amino acid Observed frequency of incorporation (Lys = 100) Tentative assignment for nucleotide composition of corresponding codon Expected frequency of incorporation based on assignment (Lys = 100)... 

These designations of nucleotide composition contain no information on nucleotide sequence (except, of course, AAA and CCC). 

Melting temperatures (Tm) of DNA molecules with different nucleotide compositions. (At a wavelength of 260 nm, single-stranded DNA has a higher relative absorbance than does double-stranded DNA.)... 

A body of chemical information that proved vital to understanding DNA structure came from Erwin Chargaff s analyses of the nucleotide composition of duplex DNAs from various sources (table 25.1). Although the base compositions varied over a wide range, Chargaff found that within the DNA of each source that he examined, the amount of A was very nearly equal to the amount of T, and the amount of G was very nearly equal to the amount of C. The C is present as both unmodified C and, to a lesser extent, 5-methyl-cytosine, which results from postreplicative... 

Using DNA fragments of various origins, nucleotide compositions, and lengths (maximum of x 3 kb), we observed mutation frequencies of 0.93 0.06% per... 

Williams TT, Odom DT, Barton JK. Variation in DNA charge transport with nucleotide composition and sequence. J Am Chem Soc 2000 122 9048-9. 

To evaluate molar masses from equilibrium runs it is necessary to know (very accurately) the value of the partial specific volume of the species. The partial spedfic volumes of proteins and nucleic acids are not dependent on conformation so they can be evaluated from the amino acid or nucleotide composition (Laue et al. 1992). A satisfactory working value for proteins is v = 0.735 10-3 m3 kg-1. Partial specific volumes can also be measured by comparison of equilibrium runs carried out in H20, D20 and H280, using the different densities of the three isotopic forms of water. 

Pd. occultum, with the highest optimal growth temperature (>100°C), exhibits the highest G-i-C content (62%), for the next group of organisms, growing at 95-100 C, the G-i-C contents lie in the range of 38-46%. Thus, one can infer that factors other than nucleotide composition of the DNA determine its thermal stability. Examples of... 

For the open reading frames, the nucleotide compositions were also correlated with the optimal growth temperatures. No direct relationship was observed between G-t-C content and temperature. However, as illustrated in Fig. 2, the G+C content of the protein-coding... 

Fig. 1. Dependence of the nucleotide compositions of the large rRNAs on the optimal growth temperature of the organisms listed in Table 3. The bacterial rRNAs from Eschericia coli, Bacillus stearothermophilus and Fervidobacterium nodosum were used to cover the lower temperature range.

Fig. 2. Dependence of the nucleotide composition of the protein-coding regions on the G-C contents of the genomes (listed in Table 3) for S. acidocaldarius, S. solfataricus, SSVl plasmid, Tc. celer, Tp. acidophilum, TTVl virus, Ag. fulgidus, Mt.fervidus, M. thermoautotrophicum and Me. vannielii.

Its main limitations are that it is not usually the best method for small oligonucleotides (n < 10), it does not distinguish nucleotide composition differences clearly, -and it is difficult to scale up for preparative use. It is widely used for analytical and small scale preparative separations because it is quick, sensitive and has high resolving power. Very little specialised apparatus is required and routine fractionation can be carried out by a technician. 

The nucleotide composition of oligonucleotides is usually measured by digesting the oligonucleotide to its constituents, in the form of nucleotides, nucleosides or bases and then estimating the proportion of each substance in the mixture either directly or by separating and estimating the components. Alkali, acid and enzyme digestion are commonly used. 

---