Separation of B. subtilis DNA into complementary strands. 3. Direct analysis.

Rudner, Rivka; Karkas, John D.; Chargaff, Erwin

doi:10.1073/pnas.60.3.921

Cited by 173 publications

(121 citation statements)

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“…Since then scientists have gathered very strong evidence for its general validity (8). Nevertheless, there are exceptions to the rule (7,9,12,14). However, as reported here, there seem to be none if the genome size exceeds 100 kb.…”

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confidence: 67%

“…Discovered almost 40 years ago (7,8), before any sequence data were available, the rules continue to stimulate the search for their unknown underlying mechanism (6,(9)(10)(11)(12)(13). Obviously, base pairing does not provide one because the nucleotides of each single strand of a duplex are already paired with the nucleotides on their opposite strands and need not pair with any other on their own strand.…”

mentioning

confidence: 99%

“…Chargaff discovered it in 1968 after separating the genome of Bacillus subtilis into separate strands and analyzing the nucleotide contents of each single-strand preparation (7,8). Since then scientists have gathered very strong evidence for its general validity (8).…”

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confidence: 99%

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Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions

Albrecht‐Buehler

2006

Proc. Natl. Acad. Sci. U.S.A.

101

103

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Chargaff's second parity rules for mononucleotides and oligonucleotides (C II mono and C II oligo rules) state that a sufficiently long (>100 kb) strand of genomic DNA that contains N copies of a monoor oligonucleotide, also contains N copies of its reverse complementary mono-or oligonucleotide on the same strand. There is very strong support in the literature for the validity of the rules in coding and noncoding regions, especially for the C II mono rule. Because the experimental support for the C II oligo rule is much less complete, the present article, focusing on the special case of trinucleotides (triplets), examined several gigabases of genome sequences from a wide range of species and kingdoms including organelles such as mitochondria and chloroplasts. I found that all genomes, with the only exception of certain mitochondria, complied with the C II triplet rule at a very high level of accuracy in coding and noncoding regions alike. Based on the growing evidence that genomes may contain up to millions of copies of interspersed repetitive elements, I propose in this article a quantitative formulation of the hypothesis that inversions and inverted transposition could be a major contributing if not dominant factor in the almost universal validity of the rules.chloroplasts ͉ genomics ͉ mitochondria ͉ base composition ͉ oligonucleotide composition

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Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions

Albrecht‐Buehler

2006

Proc. Natl. Acad. Sci. U.S.A.

101

103

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“…[2][3][4] in Table 2) came from strains that are known to be hosts for phages yielding DNA readily separable into complementary strands, as has been mentioned. Whether this is more than a coincidence cannot be said, nor whether it is significant that these strains are also spore-forming.…”

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confidence: 99%

Separation of Microbial Deoxyribonucleic Acids Into Complementary Strands

Rudner

Karkas

Chargaff

1969

Proc. Natl. Acad. Sci. U.S.A.

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Abstract.-DNA preparations from seven bacterial species and from the E. coli phage T4 can, after denaturation with alkali, be separated chromatographically into two distinct components (L and H) through intermittent gradient elution from methylated albumin kieselguhr columns. The direct chemical analysis of the L and H fractions isolated from DNA specimens of the AT type shows them to exhibit a high degree of complementarity; but despite a bias in the distribution of purines and pyrimidines, either fraction contains equimolar quantities of 6-amino and of 6-keto nucleotides. In the L and H components derived from DNA of the equimolar and GC types, the distribution bias appears limited to guanine and cytosine. It is suggested that the L and H fractions represent the complementary DNA strands.As we reported recently,1-3 denaturated DNA of Bacillus subtilis can be separated by a technique of intermittent gradient elution from a column of methylated albumin kieselguhr (MAK), into two fractions, designated, by virtue of their buoyant densities, as L (light) and H (heavy). Taking into account some of the requirements that genuine strands deriving from a native DNA duplex must fulfill,4 we concluded (on the basis of evidence bearing on the biological activity, nucleotide composition, and temperature-absorbance behavior) that the two fractions isolated from B. subtilis DNA represented indeed such complementary strands. They could be annealed together easily, thereby regaining considerable secondary structure as shown by transforming activity and hypochromicity; they were in their nucleotide composition strictly complementary so that the adenine content of fraction L was equivalent to the thymine content of fraction H, the guanine of L to the cytosine of H, etc.; the greater abundance of purines in fraction L was matched by that of pyrimidines in fraction H. As would be expected of genuine strands,4 the molar sums of A + T and of G + C did not vary in the two fractions5 and were identical with those found in the native DNA, and this was, therefore, also true of the dissymmetry ratio A + T/G + C; but the preparations also exhibited an unexpected regularity, which would not have been predicted for a single strand, namely, the equality of the 6-amino and the 6-keto nucleotides, A + C and G + T.We were naturally interested in the generality of these observations and in their biological meaning with respect to template functions, etc. While the latter problem will be taken up in a subsequent paper, we present here evidence that denatured DNA from seven microbial species and from bacteriophage T4, representing DNA varieties of the AT, GC, and equimolar types, can be separated on MAK columns into two distinct and reproducible chromatographic 152

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“…Chargaff's second parity rule (Rudner et al, 1968;Forsdyke and Mortimer, 2000), is also true for the chromosomes. Even when applied to oligomers, the Chargaff's second parity rule still holds true, i.e., in the whole single-stranded sequence of chromosome, number of an oligomer is almost equal to that of its reverse complement.…”

Section: Science Publicationsmentioning

confidence: 99%

The Bacterial Chromosomal Sequence and Related Issues

Phan

Nguyễn

2013

American Journal of Virology

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There has been a rapid increasing in the number of bacterial genomes that are completely sequenced recently. However, nucleotide arrangement in bacterial chromosome is still not clear, though it is known that the chromosomal strand is symmetric as a whole but asymmetric locally. The unequal distribution of adenine and thymine as well as cytosine and guanine in the local genomic sequences has been suggested to be associated with transcription and replication. In the bacterial chromosome, distribution of nucleotides in the leading and lagging strands, which interact with the structurally asymmetric DNA polymerase during replication process, has also been reported to be biased. Recent studies on changing the nucleotide sequence of bacterial chromosomes have revealed the importance of nucleotide arrangement in chromosome, which exerts influences on success of the chromosome engineering experiments. This review highlights common properties of bacterial chromosomal sequences with related issues involved in the nucleotide arrangement in chromosome, emphasizing that arrangement of nucleotides in chromosome regarding local strand asymmetry and chromosomal strand symmetry needs to be made clear so as to help in experimental design for effectiveness in changing chromosomal sequences or creating artificial chromosomes.

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Separation of B. subtilis DNA into complementary strands. 3. Direct analysis.

Cited by 173 publications

References 3 publications

Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions

Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions

Separation of Microbial Deoxyribonucleic Acids Into Complementary Strands

The Bacterial Chromosomal Sequence and Related Issues

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