Replication unit

In general, a given pair of chromosomes will replicate simultaneously and within a fixed portion of the S phase upon every replication. On a chromosome, clusters of replication units replicate coordinately. The na-mre of the signals that regulate DNA synthesis at these levels is unknown, but the regulation does appear to be an intrinsic property of each individual chromosome. 

Y. B. Yurov, and N. A. Liapunova, The units of DNA replication in the mammalian chromosomes evidence fora large size of replication units. Chromosoma 60, 253-267 (1977). 

N. A. Liapunova, Organization of replication units and DNA replication in mammalian cells as studied by DNA fiber radioautography. Int. Rev. Cytol. 154, 261-308 (1994). 

Yet again the conclusion can be drawn that all single-stranded RNA viruses are subject to similar restrictions with regard to information content. In nature there are no (single-stranded) RNA viruses whose replicative unit contains more than the order of 104 nucleotides. All larger viruses possess double-stranded nucleic acids or are composed of several... 

The first replicative units must have possessed considerably less information than the RNA viruses, which work with an optimized RNA-copying machinery. In the absence of efficiently adapted enzymes the accuracy of reproduction depends solely on the stability of the base pairs. Under these conditions the GC pair has a selective advantage over the AU pair of a factor of about 10. Model experiments show that for GC-rich polynucleotides the error rate per nucleotide can hardly be reduced below a value of 10-2. The first genes must accordingly have been polynucleotides with a chain length around 100 bases or less. 

Replicon. A genetic element that behaves as an autonomous replicating unit. It can be a plasmid, phage, or bacterial chromosome. 

DNA replication occurs only in the S phase. It occurs at many chromosomal origins, is bi-directional and semi-conservative. Sets of 20-80 replicons act as replication units that are activated in sequence. 

All of the regions of a chromosome are not replicated simultaneously. Rather, many replication eyes will be found on one part of the chromosome and none on another section. Thus replication origins are activated in clusters, called replication units, consisting of 20-80 origins. During S phase, the different... 

Fig. 3. Schematic picture of M/C interface structural models. A Cluster model with vacuum around it. B Dense M/C interface unit cell, physically corresponding to a superlattice or sandwich structure. C Slab model with vacuum between periodic images perpendicular to the interface. Physically, the structure corresponds to M/C thin films. The borders of the periodically replicated unit cells in B and C are shown with bold lines.

These two differential equations describe how selection acts on parts of the replicating unit. The equations are equivalent to the selection Eqn. (III. 15) in so far as no simplifying assumptions were made except the two concerning the structure of the mutation matrix Q. The interaction between the two parts of the polynucleotide occurs via the average rate constants Ajq, B,o, Aqj and Dqj as well as implicitly through the common average excess production ... 

Model focusing on the dynamics of replicating units (e.g., hypercycle). For a cell to grow effectively, there should be some positive feedback process to amplify the number of each molecular species. Such a positive feedback process leads to an autocatalytic process to synthesize each molecular species. For reproduction of a cell, (almost) all molecule species are somehow synthesized. Then, it would be possible to take a replication reaction from the beginning as a model. For example, consider a reaction... 

In the present chapter we mainly use the modeling of level 2. This class of model can be obtained by reducing from the level 1 model, by restricting our interest only to take into account of replicating units. In this sense, the model is a bit simpler than the level 1 model. On the other hand, it may not be suitable to discuss the condition for cell growth, since at the level 2 model, the supply of resource chemicals is automatically assumed, and one cannot discuss how transported chemicals are transformed into others. In the present chapter, we briefly refer to the level 1 model only at the end of Section V.D, to demonstrate the universality of our result, but for details see the original articles [15,26] on level 1 modeling. 

By the selection, DNA from a tube with a higher catalytic activity could be selected, but the variation by tubes is so small that the selection does not work. Hence deleterious mutations remain in the soup, and the self-replication activity will be lost by generations. In other words, the selection works because the number of information carriers in a replication unit (cell) is very small and is free from the statistical law of large numbers. 

Consequently, approximately one month is required for this DNA replication. Eukaryotic DNA synthesis is significantly faster than expected because each chromosome contains multiple replication units (replicons). 

Three aspects of the regulation of initiation of DNA synthesis are considered in this chapter the timing of DNA synthesis in the cell cycle, the structure of chromosomal replication units, and the role of the known enzymatic components of the cellular DNA synthesizing apparatus in ordering initiation in chromosomal replication units. 

The replicon model used to describe the regulation of DNA synthesis in prokaryote cells has influenced many concepts of the same process in eukaryote cells. Since the basis of this discussion will center around the limitations of the replicon model as applied to eukaryotes, several terms will be emphasized here. The term "replication unit used here refers to any stretch of DNA in a eukaryote chromosome which is replicated by the efforts of one growing point. The growing point is defined as any one site on a parental, double-standard DNA molecule where enzymatic activity results in the replication of both strands of parental DNA. 

The evidence that the DNA in a eukaryote chromosome is divided into a number of replication units comes from a number of sources. For example, there are autoradiographic studies of metaphase chromosomes from pulsedabeled cells in which multiple grain clusters in each chromosome suggest multiple sites of DNA synthesis (Taylor, 1960 lima-de-Faria, 1961 Painter, 1961 Stubblefield and Mueller, 1962 Moorhead and Defend , 1963 German, 1964 Hsu, 1964). Also eukaryote chromosomes synthesize DNA... 

There are a number of different reasons why non-DNA linkers have been considered necessary to hold DNA molecules in tandem arrangement in chromosomes. The most relevant of these to the regulation of DNA synthesis are as follows the presumption that replication units of DNA within a sin e chromosome cannot be directly connected to one another without interruption of the DNA double helix the need for a mechanism to relieve torsion of the DNA molecule, torsion developed in connection with semiconservative replication. The latter proposal that non-DNA linkers mi t serve to allow rotation of the DNA double helix during semiconservative replication is no longer considered valid since it has been repeatedly demonstrated that a single-stranded break in a DNA double helix allows the intact chain to serve as a swivel and release torsion within the molecule (Vlnograd and Lebowitz, 1966). 

Replication units in eukaryote cells may be contained then either in circular or linear molecules of DNA. The conclusion that is reached here is that replication units are separated only by deoxyribonucleotide sequences. This conclusion implies the existence in each replication unit of deoxyribonucleotide sequences which delineate regions where DNA synthesis is initiated. 

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