Cyclization of eucaryotic deoxyribonucleic acid fragments

doi:10.1016/0022-2836(70)90012-4

Journal of Molecular Biology

Volume 51, Issue 3, 14 August 1970, Pages 621-622, IN5-IN7, 623-632

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Abstract

Highly purified, shear-broken fragments of DNA extracted from certain eucaryotes (salmon, trout, Necturus, calf thymus and others) can form circles and circular structures by either “folding” or “slipping”. Procaryotic DNA fragments (from T7 bacteriophage, Escherichia coli and Bacillus subtilis) do not form circles or circular structures by this treatment. “Folding” involves partial degradation with exonucleases (exonuolease III or λ exonuclease) and annealing. Up to 35% of all Necturus DNA fragments seen in the electron microscope are folded into circular structures. The same treatment applied to trout and salmon sperm DNA fragments results in about 20% circular structures. “Slipping” involves chain separation and subsequent annealing. In this case circular structures are easy to find, but their frequency cannot be estimated because much of the DNA remains denatured and invisible.

We conclude that a large fraction of the eucaryotic genomes that we have studied is composed of regions containing tandemly-repeating sequences. At this time it is not known whether or not these tandemly-repeating regions function in the genetic sense (to specify amino acid sequences). Either way this question is resolved, the finding that such a large fraction of the euearyotic chromosome is constructed in this manner raises some paradoxical questions.

References (27)

J.A. Abelson et al.
J. Mol. Biol
(1966)
D.D. Brown et al.
J. Mol. Biol
(1968)
D.D. Brown et al.
J. Mol. Biol
(1968)
E. Burgi et al.
J. Mol. Biol
(1961)
E. Burgi et al.
Virology
(1966)
H.G. Callan
J. Cell. Sci
(1967)
H.G. Callan et al.
Phil. Trans. Roy. Soc. B
(1960)
R.W. Davis et al.
W.G. Flamm et al.
J. Mol. Biol
(1969)
W.G. Flamm et al.
J. Mol. Biol
(1969)

A.D. Hershey et al.

J.W. Little

J. Biol. Chem

(1967)

Y. Miyazawa et al.

J. Mol. Biol

(1965)

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Historical overview
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Chloroplast DNA Replication in Chlamydomonas reinhardtii
1981, International Review of Cytology
Chlamydomonas reinhardtii occupies a central position in cytoplasmic inheritance because it is the simplest organism that contains a chloroplast and non-Mendelian inheritance. Being unicellular and heterothallic, Chlamydomonas can be handled in the laboratory with the same ease as bacteria and yeast. The vegetative, haploid life cycle and the diploid meiotic sexual cycle can be physiologically controlled in large synchronous populations to facilitate either cell cycle biochemistry or genetic analysis. This chapter discusses the replication of the chloroplast DNA in vivo. Chloroplast replication usually is initiated 1–3 hours after the onset of the light period and continues for six hours, whereas nuclear DNA synthesis is initiated 2–3 hours into the dark period and continues for six hours. If cell division results in the production of four daughters, then two rounds of replication of chloroplast DNA synthesis precede two rounds of nuclear DNA synthesis. Both DNAs replicate by a semiconservative mechanism. Chlamydomonas does not appear to have dark repair reactions, so the chloroplast chromosome is stable over the entire cell cycle
Genetic analysis of chloroplast DNA in chlamydomonas
1977, Advances in Genetics
This chapter focuses on genetic analysis and correlated physical studies of the chloroplast DNA of Chlamydomnas, particularly those aspects of the subject that have progressed in the past few years. Genetic analysis based on segregation and recombination has been carried out with biparental zygotes, either of spontaneous origin or UV-induced. A comparison of results from zygotes of bath types has been discussed. The chapter investigates (1) the events affecting cytoplasmic gene markers occurring in the zygote, and the distribution of cytogenes to the four meiotic products; (2) the events occurring in the first few mitotic doublings, examining each doubling independently by means of pedigree analysis; and (3) the events occurring over the range of doublings required before most of the heterozygous genes had segregated, examined in liquid cultures of zoospore clones. The chapter also presents an overall picture of the segregation and recombinational behavior of the linked set of chloroplast genes that had been investigated. Supporting data, including the results of a set of 25 multigene crosses have been included. The principal conclusions reached from the analysis of the 25 crosses listed in the chapter are: (1) Chloroplast genes of Chlamydomonas show maternal inheritance and can be identified by the transmission pattern. (2) Exceptional zygotes are of two types: biparental zygotes that transmit the chloroplast genome from both parents; and paternal zygotes, in which the maternal complement is lost. (3) Zoospores from biparental zygotes are usually, heterozygous for the entire genome, and are referred to as cytohets. The chapter discusses the frequencies of simultaneous coconversions of two or more genes that provide valuable mapping data.
Underreplication of repetitive DNA in polyploid cells of Pisum sativum
1976, Experimental Cell Research
Organization of highly repeated sequences in mouse main-band DNA
1976, Journal of Molecular Biology
Renaturation analysis shows that the main CsCl density band of mouse DNA (at 400 bases mol. wt) contains a minimum of four second-order kinetic components: non-repetitive DNA; two major classes of repeated DNA, called “moderately repeated” and “highly repeated”, each comprising 8 to 16% of the genome; and a minor sub-class of the highly repeated DNA, about 0·5% of the genome with a satellite-like complexity. The highly repeated main-band sequences are isolated from high molecular weight DNA (12,000 bases) by renaturation to low C₀t§ and hydroxyapatite chromatography. This DNA is spread for electron microscopy by the formamide isodenaturing technique. Most of the bimolecular renaturation products show interspersion of renatured and single-stranded regions. The renatured regions average about 700 base-pairs in length, most being in the range of 200 to 1000. On molecules where two or more renatured regions. The renatured regions average about 700 base-pairs in length, most being in the range of 200 to 1000. On molecules where two or more renatured regions can be identified, they are separated by a wide range of distances averaging 1800 bases. A minority fraction (about 12% by weight) of the bimolecular renaturation products shows no evidence of interspersion, and may consist of tandemly repeated sequences.
The renaturation rate of the highly repeated DNA fraction (at initial mol. wts of 6000 and 12,000 bases) is studied before and after shearing the DNA to low molecular weight. The kinetic complexity of the interspersed, single-stranded DNA that is attached to renatured, highly repeated DNA is thereby determined. Most of the unrenatured DNA contains highly repeated sequences similar in complexity to the sequences that renatured at low C₀t. Only about 20% of the interspersed DNA has a low repetition frequency, approximately non-repetitive. We conclude that about 15% of the mouse main-band DNA contains highly repeated sequences, most of which are organized as permuted tandem repeats. About 5% of the non-repetitive DNA of mouse is interspersed with this fraction of the genome. This model of sequence organization differs from those that have been demonstrated for more moderately repeated sequences of higher organisms, where much more non-repetitive DNA is interspersed with the repeated sequences.
Premelting Changes in DNA Conformation
1976, Progress in Nucleic Acid Research and Molecular Biology
This chapter discusses that Deoxyribonucleic acid (DNA) premelting has been demonstrated under conditions preceding thermal, acidic, and alkaline denaturation of aqueous DNA solutions. Certain signs of premelting changes have been discussed to arise from the addition of organic solvent to DNA solution. It thus appears that premelting might be as general a phenomenon as DNA melting itself. However, whereas melting is an event, related rather to the entire DNA molecule, premelting is more limited to the small portions of the DNA molecule that differ from the predominating part of the molecule. The chapter also emphasizes that the structure of doublestranded nucleic acids is so complicated and the possibilities of structural changes is so great that at the present time, no substantial progress can be made on the basis of the results obtained with only a single experimental technique. For further achievements in this field, it will be necessary to study well-defined nucleic acid samples using various methods differing in principle. Besides the studies of nucleic acids in solution, it could be useful to extend research to conditions simulating in some respects conditions existing in vivo. The chapter summarizes the results of DNA studies in a region to which, until recently, relatively little attention has been devoted.

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^☆: One of us (B. A. H.) was the recipient of a National Institutes of Health Post-doctoral Fellowship no. 5-F02-CA41226-02 from the National Cancer Institute and another (C. S. L.) is a Fellow of the Jane Coffin Childs Memorial Fund for Medical Research.

^†: Present address: Biology Division, Oak Ridge National Laboratory, Oak Ridge, Tenn. U.S.A.

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Journal of Molecular Biology

Abstract

References (27)

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

Virology

J. Cell. Sci

Phil. Trans. Roy. Soc. B

J. Mol. Biol

J. Mol. Biol

J. Biol. Chem

J. Mol. Biol

Cited by (66)

Historical overview

Chloroplast DNA Replication in Chlamydomonas reinhardtii

Genetic analysis of chloroplast DNA in chlamydomonas

Underreplication of repetitive DNA in polyploid cells of Pisum sativum

Organization of highly repeated sequences in mouse main-band DNA

Premelting Changes in DNA Conformation

Journal of Molecular Biology

Cyclization of eucaryotic deoxyribonucleic acid fragments☆

Abstract

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

Virology

J. Cell. Sci

Phil. Trans. Roy. Soc. B

J. Mol. Biol

J. Mol. Biol

J. Biol. Chem

J. Mol. Biol