Intact yeast cells treated with alkali cations took up plasmid DNA. Li+, Cs+, Rb+, K+, and Na+ were effective in inducing competence. Conditions for the transformation of Saccharomyces cerevisiae D13-1A with plasmid YRp7 were studied in detail with CsCl. The optimum incubation time was 1 h, and the optimum cell concentration was 5 x 10(7) cells per ml. The optimum concentration of Cs+ was 1.0 M. Transformation efficiency increased with increasing concentrations of plasmid DNA. Polyethylene glycol was absolutely required. Heat pulse and various polyamines or basic proteins stimulated the uptake of plasmid DNA. Besides circular DNA, linear plasmid DNA was also taken up by Cs+-treated yeast cells, although the uptake efficiency was considerably reduced. The transformation efficiency with Cs+ or Li+ was comparable with that of conventional protoplast methods for a plasmid containing ars1, although not for plasmids containing a 2 microns origin replication. Images

Transformation of intact yeast cells treated with alkali cations.

Construction and characterization of a class of multicopy plasmid cloning vehicles containing the replication system of miniplasmid P15A are described. The constructed plasmids have cleavage sites within antibiotic resistance genes for a variety of commonly employed site-specific endonucleases, permitting convenient use of the insertional inactivation procedure for the selection of clones that contain hybrid DNA molecules. Although the constructed plasmids showed DNA sequence homology with the ColE1 plasmid within the replication region, were amplifiable by chloramphenicol or spectinomycin, required DNA polymerase I for replication, and shared other replication properties with ColE1, they were nevertheless compatible with ColE1. P15A-derived plasmids were not self-transmissible and were mobilized poorly by Hfr strains; however, mobilization was complemented by the presence of a ColE1 plasmid within the same cell.

Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid.

The discovery of specific restriction endonucleases (Smith and Wilcox 1970) made possible the isolation of discrete molecular fragments of naturally occurring DNA for the first time. This capability was crucial to the development of molecular cloning (Cohen et al. 1973); and the combination of molecular cloning and endonuclease restriction allowed the synthesis and isolation of any naturally occurring DNA sequence that could be cloned into a useful vector and, on the basis of flanking restriction sites, excised from it. The availability of a large variety of restriction enzymes (Roberts 1985) has significantly extended the utility of these methods. The de novo organic synthesis of oligonucleotides and the development of methods for their assembly into long double-stranded DNA molecules (Davies and Gassen 1983) have removed, at least theoretically, the minor limitations imposed by the availability of natural sequences with fortuitously unique flanking restriction sites. However, de novo synthesis, even with automated equipment, is not easy; it is often fraught with peril due to the inevitable indelicacy of chemical reagents (Urdea et al. 1985; Watt et al. 1985; Mullenbach et al. 1986), and it is not capable of producing, intentionally, a sequence that is not yet fully known. We have been exploring an alternative method for the synthesis of specific DNA sequences (Fig. 1). It involves the reciprocal interaction of two oligonucleotides and the DNA polymerase extension products whose synthesis they prime, when they are hybridized to different strands of a DNA template in a relative orientation such that their extension products overlap. The method consists of repetitive cycles of denaturation, hybridization, and polymerase extension and seems not a little boring until the realization occurs that this procedure is catalyzing a doubling with each cycle in the amount of the fragment defined by the positions of the 5' ends of the two primers on the template DNA, that this fragment is therefore increasing in concentration exponentially, and that the process can be continued for many cycles and is inherently very specific. The original template DNA molecule could have been a relatively small amount of the sequence to be synthesized (in a pure form and as a discrete molecule) or it could have been the same sequence embedded in a much larger molecule in a complex mixture as in the case of a fragment of a single-copy gene in whole human DNA. It could also have been a single-stranded DNA molecule or, with a minor modification in the technique, it could have been an RNA molecule. In any case, the product of the reaction will be a discrete double-stranded DNA molecule with termini corresponding to the 5' ends of the oligonucleotides employed. We have called this process polymerase chain reaction or (inevitably) PCR. Several embodiments have been devised that enable one not only to extract a specific sequence from a complex template and amplify it, but also to increase the inherent specificity of this process by using nested primer sets, or to append sequence information to one or both ends of the sequence as it is being amplified, or to construct a sequence entirely from synthetic fragments.

Specific Enzymatic Amplification of DNA In Vitro: The Polymerase Chain Reaction

When intact cells of Saccharomyces cerevisiae were treated with alkali cations or thiol compounds, the cells gained the ability to take up plasmid DNAs. The transformation efficiencies of yeast cells treated with alkali cations was greatly influenced by both the kind and concentration of cation used. The transformation efficiency also varied depending on the yeast strain. Polyethylene glycol was indispensable for the transformation. The uptake of plasmid DNAs into the yeast cells was found only in the presence of this polymer. Based on these results, the properties of transformation of intact yeast cells treated with alkali cations or thiol compounds were discussed.

Transformation of intact yeast cells treated with alkali cations or thiol compounds

Molecular self-assembly presents a `bottom-up' approach to the fabrication of objects specified with nanometre precision. DNA
 molecular structures and intermolecular interactions are particularly
 amenable to the design and synthesis of complex molecular objects. We
 report the design and observation of two-dimensional crystalline forms
 of DNA that self-assemble from synthetic DNA double-crossover
 molecules. Intermolecular interactions between the structural units are
 programmed by the design of `sticky ends' that associate according to
 Watson-Crick complementarity, enabling us to create specific periodic
 patterns on the nanometre scale. The patterned crystals have been
 visualized by atomic force microscopy.

https://issg.cs.duke.edu/courses/spring04/cps296.4/papers/WLWS98.pdf

Design and self-assembly of two-dimensional DNA crystals

The construction of new plasmid DNA species by in vitro joining of restriction endonuclease-generated fragments of separate plasmids is described. Newly constructed plasmids that are inserted into Escherichia coli by transformation are shown to be biologically functional replicons that possess genetic properties and nucleotide base sequences from both of the parent DNA molecules. Functional plasmids can be obtained by reassociation of endonuclease-generated fragments of larger replicons, as well as by joining of plasmid DNA molecules of entirely different origins.

https://www.pnas.org/content/pnas/70/11/3240.full.pdf

Construction of Biologically Functional Bacterial Plasmids In Vitro

By means of agarose-gel electrophoresis, endonuclease R.EcoRI-generated fragments of DNA from various viruses were separated, their molecular weights were determined, and complete or partial fragment maps for lambda, phi80, and hybrid phages were constructed.

Analysis of endonuclease R-EcoRI fragments of DNA from lambdoid bacteriophages and other viruses by agarose-gel electrophoresis.

Fragments of amplified Xenopus laevis DNA, coding for 18S and 28S ribosomal RNA and generated by EcoRI restriction endonuclease, have been linked in vitro to the bacterial plasmid pSC101; and the recombinant molecular species have been introduced into E. coli by transformation. These recombinant plasmids, containing both eukaryotic and prokaryotic DNA, replicate stably in E. coli. RNA isolated from E. coli minicells harboring the plasmids hybridizes to amplified X. laevis rDNA.

https://www.pnas.org/content/pnas/71/5/1743.full.pdf

Replication and transcription of eukaryotic DNA in Escherichia coli.

Populations of Escherichia coli, initiated with a single clone and maintained for long periods in glucose-limited continuous culture, developed extensive polymorphisms. In one population, examined after 765 generations, two majority and two minority types were identified. Stable mixed populations were reestablished from the isolated strains. Factors involved in the development of this polymorphism included differences in the maximum specific growth rate and in the transport of glucose, and excretion of metabolites by some clones which were utilized by minority clones.

https://www.genetics.org/content/genetics/116/3/349.full.pdf

Evolution of Escherichia coli during Growth in a Constant Environment

Escherichia coli has two primary pathways for glutamate synthetase-glutamate synthase pathway is known to be essential for synthesis at low ammonium concentrations and for regulation of the glutamine pool, but the necessity for glutamate dehydrogenase (GDH) has been uncertain. The results of competition experiments between the wild type and a GDH-deficient mutant during nutrient-limited growth and of direct enzyme measurements suggest that GDH is used in glutamate synthesis when the cell is limited for energy (and carbon) but ammonium and phosphate are present in excess, while the glutamine synthetase-glutamate synthase pathway is used when the cell is not under energy limitation. The use of alternative routes for glutamate synthesis implies that the energy cost of biosynthesis may be less when energy is limited than when energy is unlimited.

Robert B. Helling

Papers

Construction of Biologically Functional Bacterial Plasmids In Vitro

Analysis of endonuclease R-EcoRI fragments of DNA from lambdoid bacteriophages and other viruses by agarose-gel electrophoresis.

Replication and transcription of eukaryotic DNA in Escherichia coli.

Evolution of Escherichia coli during Growth in a Constant Environment

Why does Escherichia coli have two primary pathways for synthesis of glutamate