E. coli DNA

B Guenther, R Onrust, A Sail, M O Donnell, J Kuriyan. Crystal structure of the 5 subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell 91 335-345, 1997. 

The renaturation rate of DNA is an excellent indicator of the sequence complexity of DNA. For example, bacteriophage T4 DNA contains about 2 X 10 nucleotide pairs, whereas Escherichia coli DNA possesses 4.64 X 10 . E. coli DNA is considerably more complex in that it encodes more information. Expressed another way, for any given amount of DNA (in grams), the sequences represented in an E. coli sample are more heterogeneous, that is, more dissimilar from one another, than those in an equal weight of phage T4 DNA. Therefore, it will take the E. coli DNA strands longer to find their complementary partners and reanneal. This situation can be analyzed quantitatively. 

E. Physical Methods and Analytical Techniques.—Nucleotide maps of enzymic digests of DNA have been obtained using the same ionophoretic techniques as have been developed for RNA digests. Pancreatic DNase and Neurospora crassa endonuclease produce very similar maps with E. coli DNA but this technique still awaits the discovery of specific DNases. 

There has been much recent interest in the role of zinc in activating cysteine residues to nucleophilic attack.542-545 Alkyl group transfer to coordinated cysteine residues occurs in a number of zinc proteins, such as Ada (the E. coli DNA repair protein) and the cobala-... 

Compound R R2 E. coli DNA gyrase E. coli H560 K. pneumoniae MGH-2 P. aeruginosa S. aureus UI-18 H-228 S. faecalis S. pneumoniae MGH-2 SV-1 S.pyogenes C203... 

Krogh, A., Mian, I. S., and Flaussler, D. (1994). A hidden Markov model that finds genes in E. coli DNA. Nucleic Acids Res. 22, 4768—4778. 

The formation of dimers other than thymine dimer in irradiated DNA has been recently reported by Setlow and Carrier,87 using E. coli DNA containing either labeled thymine (14C or tritium) or labeled cytosine (tritium). Three photoproducts could be isolated by chromatography of the acid hydrolysates of the irradiated DNA and were... 

Fig. 36. Percentage of radioactivity of the labeled base, in E. coli DNA that appears in the indicated photoproduct as a function of dose of 280-nm radiation. (O) TT/T ( ) UT/C or UT/T (A) CC/C. Each point represents the average of 5 determinations (Setlow and Carrier87).

M13mpl8 Filamentous E. coli DNA sequencing, mutagenesis, lac screening bacteriophage... 

Further reaction of 53 with diphenyl phosphate afforded a phospho-diester-bridged dinuclear magnesium(II) complex 54. The Mg-Mg distance of 4.11 A is comparable to similar distances in the Klenow fragment of E. coli DNA polymerase I (3.9 A) (39), rat DNA polymerase j8 (4 A) (46), and inositol monophosphatase (3.8 A) (35). The flexibility of the bridging carboxylates in 52 is manifested by the ca. 0.75-A range of Mg-Mg distances in these complexes, which can readily adjust the metal coordination environment. 

A search for other DNA polymerases led to the discovery of E. coli DNA polymerase II and DNA polymerase III in the early 1970s. DNA polymerase II... 

Most cells have several DNA polymerases. In E. coli, DNA polymerase III is the primary replication enzyme. DNA polymerase I is responsible for special functions during replication, recombination, and repair. 

FIGURE 25-20 Methylation and mismatch repair. Methylatlon of DNA strands can serve to distinguish parent (template) strands from newly synthesized strands in E. coli DNA, a function that is critical to mismatch repair (see Fig. 25-21). The methylation occurs at the /V6 of adenines in (5 )GATC sequences. This sequence is a palindrome (see Fig. 8-20), present in opposite orientations on the two strands. 

A sample of double-stranded DNA is denatured. One of the resulting single strands is used as a template to direct the synthesis of a complementary strand of radioactive DNA using a suitable DNA polymerase. The "Klenow fragment" of E. coli, DNA polymerase I, reverse transcriptase from a retrovirus, bacteriophage T7 DNA polymerase, Taq polymerase, and specially engineered enzymes produced from cloned genes have all been used. 

E. coli DNA polymerase I and Klenow fragment E. coli 5 —> 3 chain growth 3 —> 5 exonuclease 5 —> 3 exonuclease (lacking in Klenow fragment)... 

E. coli DNA ligase E. coli Ligation of DNA with cohesive ends uses NAD+ as energy source... 

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