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R D Blake

Publications and source records attributed to R D Blake.

At least 37 records · Page 2Linked to original sources
PubMed1986

Distribution and evolution of sequence characteristics in the E. coli genome.

The mean (G + C) composition (51.0%) and standard deviation (+/- 3.8%) of published DNA sequences accounting for 10% of the E. coli genome is in excellent agreement with the principal overall distribution determined by high resolution melting. While differences in base and neighbor characteristics are small and uniform throughout all regions of the genome, it is found that the (G + C) content of sequences varies in segmented fashion within boundaries corresponding to coding (53% G + C) and noncoding (46% G + C) regions; with variances in the latter being six-fold greater than in coding regions. The variance in different regions shows a strong negative dependence on (G + C) content of the region, reflecting the condition that A-T and G-C base pairs are preferred neighbors of A-T and C-G pairs, respectively; with the bias increasing with decreasing (G + C) content. Neighbor analysis indicates the most extreme positive biases occur in AA, TT, GC and CG throughout all regions, but particularly in noncoding regions. Extraordinary numbers of oligomeric strings of (A)n, etc., are the further consequence of this bias. These and other characteristics point to the existence of inherent biases in neighbor frequencies levied during replication or repair, and which reflect, in turn, neighbor influences during mutation. The bias in codon usage noted by Grantham and others is seen here as due, in part, to the adaptation of coding sequences to this microenvironment through selection among synonymous codons so as to preserve inherent neighbor biases.

Base Composition↗
PubMed1985

Spectral analysis for base composition of DNA undergoing melting.

A microcomputer-controlled spectrophotometer is described for obtaining the base composition of melting domains in DNA from derivative melting curves. Values have been determined for the differential molar extinction coefficients for the A-T and G-C base pair at the three wavelengths most useful for spectral analysis of base composition, 260, 270 and 282 nm. The average RMS error for these values was 29 l(mol X cm)-1 for the melting of 14 DNA specimens ranging in base composition from 0-0.72 F(G + C). A precision of approximately 1% in base composition of domains is possible. Such analysis is useful for confirming or establishing assignments of domains to particular subtransitional features in high resolution melting curves.

Base Composition↗
PubMed1985

Delineation of coding areas in DNA sequences through assignment of codon probabilities.

Codon usage tables have been produced for E. coli, yeast, human, and mouse. The nonrandom employment of codons allows assignment of probability values to trinucleotides in any DNA sequence. These values represent the probability that a given trinucleotide is used as a codon in the organism from which the table is derived. For the graphical delineation of coding areas in DNA sequences, a probability is assigned to each trinucleotide equal to its frequency in the codon table. Averaging and smoothing procedures then greatly enhance the detectability of areas of high average codon probability and better represent the mean codon probability. These manipulations increase graphical clarity without altering the overall magnitude of probabilities. Averaging introduces an error of less than 0.5% between "raw" and smoothed data. This graphical delineation of coding sequences does not depend on the presence of punctuation, ribosomal binding sites, etc: moreover the delineation of introns and exons is also possible.

Base Sequence↗
PubMed1984

Degrees of divergence in the E. coli genome from correlations between dinucleotide, trinucleotide and codon frequencies.

Oligonucleotide and codon frequencies have been determined in published sequences of E. coli DNA totaling 103,100bp with 18,459 reading frame trinucleotides; corresponding to 2.5% of the total genome. Dinucleotide frequencies are in excellent agreement with those determined by nearest neighbor chemical analysis, indicating the computer count of a limited sampling to be a good representation of the overall frequencies in total genomic DNA. The distinctive nonrandom codon pattern is found to be uniformly distributed and contributes to a distinctive nonrandom oligonucleotide pattern; enabling correlations between frequency levels to be extended beyond reading frame sequences. Correlation analysis indicates a surprisingly high degree of correlation everywhere in the genome. Coefficients of correlation between oligonucleotide frequencies overall and those in specific segments vary as follows: primary strands of individual coding sequences greater than 0.9 greater than lambda DNA greater than noncoding, non-RNA greater than phi X174 DNA greater than complementary strands greater than RNA genes congruent to 0.6 greater than transposon-insertion elements greater than T7DNA much greater than eukaryotic sequences congruent to 0. It is concluded that this high degree of oligonucleotide and codon correspondence in E. coli reflects the widespread distribution of remnants of an early and slowly changing codon pattern that has been continually dispersed by duplication-divergence processes, leading to the present genome.

Base Composition↗
PubMed1984

Analysis of the codon bias in E. coli sequences.

Fifty-three gene sequences from E. coli containing 18,288 reading frame triplets have been characterized according to the nature and level of average codon preference. The distribution of average preferences is bimodal, with approximately half the genes using an average of only 36 codons, and the remainder just 42 codons. There is a high correlation between the level of codon bias, the tRNA population and the abundance of protein product, indicating biased patterns are exploited by the cell for the production of widely different levels of gene product. This relationship is especially striking in genes involved in the production of components for transcription and translation. Overall, the genes for these processes generate some five-fold more protein than the average in the genome, and use about five fewer codons. The very high codon bias found in the RNA polymerase gene thus provides a simple, autogenous mechanism for the coordinate synthesis of these components and RNA polymerase. A surprisingly high level of codon probability is also found in triplets of the complement of coding sequences. This is apparently due to the evolutionary dispersion of coding sequences and/or the requirement for increased levels of secondary structure in messenger RNAs.

Base Sequence↗
PubMed1982

Statistical significance of symmetrical and repetitive segments in DNA.

Methods of computer analysis for the recurrence of symmetrical and repetitive elements in large numbers of DNA sequences are described, together with derivations of appropriate quantitative criteria for the evaluation of the statistical significance of these elements in DNAs of different base composition. Examples of some extraordinary variations in the occurrence of symmetrical and repetitive elements are provided, many of which are new. Special consideration is devoted to a determination of the statistical significance of a two-fold palindrome at the origin of replication. A computer search of 14 independently determined DNA sequences containing an origin of replication locus indicates each contains a large two-fold palindrome. The average length of this palindrome is 28 +/- 6 base pairs, of which 22 contribute to the palindromic symmetry. The probability of occurrence of such a palindrome is only 1/26000, while the probability of occurrence in all 14 different species is (1/26000).

Animals↗
PubMed1978

Spectral analysis of high resolution direct-derivative melting curves of DNA for instantaneous and total base composition.

Derivative melting profiles of DNA have been obtained directly by recording the difference in absorbance between two identical solutions maintained at a small constant temperature differential. This deltaA is monitored continuously with increasing temperature in a ratio recording spectrophotometer. Resolution of complex hyperfine structure in the profiles of small homogeneous viral DNAs appears to be significantly better than has been produced by various numerical methods of differentiation. In addition, a spectral method has been modified that permits easy analysis for DNA base composition from the ratio of derivative melting curves obtained at 282 and 260 nm. Eight bacterial and three vertebrate DNAs have been analyzed for total base composition from the product of the instantaneous base composition at small temperature intervals (0.05 degrees C) throughout the entire melting region and the integrated area of the 282 nm profile. The results are in excellent agreement with values determined by traditional methods.

Bacillus subtilis↗
PubMed1976

Thermal unfolding of yeast glycine transfer RNA.

In the present investigations the molecular unfolding of yeast tRNA(Gly) has been studied by a combination of nuclear magnetic resonance spectroscopy, melting techniques, and relaxation kinetics. From these studies the following pathway of unfolding was found. In a coupled melting transition the tertiary, the DHU, and the anticodon structure are disrupted. This is followed by the melting of the acceptor arm, while the T psi C arm, which only contains G-C pairs, melts out last. Interestingly, during the first melting transition a new structure not belonging to the original cloverleaf structure is formed. The thermodynamic and kinetic parameters of the melting transitions were determined and are discussed in relation to earlier work. The present nuclear magnetic resonance (NMR) experiments as well as earlier studies show that the ring current calculations based on the cloverleaf structure provide a good first-order interpretation of the NMR spectra of tRNA.

Base Sequence↗