DNA bacterial

However, the a helices are not packed against each other in the usual way as described in Chapter 3. Instead, a helices 2 and 3, residues 15-36, form a unique helix-turn-helix arrangement that in 1981 had only been observed once, in a different bacterial DNA-binding protein, the catabolite gene-activating protein CAR... 

Gyrase is another term for bacterial topoisomerase II. The enzyme consists of two A and two B subunits and is responsible for the negative supercoiling of the bacterial DNA. Negative supercoiling makes the bacterial DNA more compact and also more readily accessible to enzymes that cause duplication and transcription of the DNA to RNA. 

The chromosomes of Escherichia coli and other bacteria are single, double-stranded DNA molecules with a total length of more than 1,000 pm. Relaxed DNA exists as a helical molecule, with one full turn of the helix occurring approximately every 10.4 base pairs. This molecule must undergo several folding and compaction steps to fit into an E. coli cell which is only 1-3 pm long. Despite this enormous compaction, bacterial DNA must be accessible for the bacterial enzymes that catalize DNA replication and transcription... 

Bacterial as well as eukaryotic chromosomes contain too much DNA to fit easily into a cell. Therefore, the DNA must be condensed (compacted) to fit into the cell or nucleus. This is accomplished by supercoiling the DNA into a highly condensed form. When relaxed circular DNA is twisted in the direction that the helix turns, the DNA becomes positively supercoiled, if it is twisted in the opposite direction, it is called negatively supercoiled. Bacterial DNA is normally found in a negatively supercoiled state. Supercoiling reactions are catalyzed by topoisomerases. 

Sanjo H, Matsumoto M, Hoshino K, Wagner H. Takeda K, Akira S A Toll-like receptor recognizes bacterial DNA. Nature 2000 408 740-745. 

In mammahan cells, the polymerase is capable of polymerizing about 100 nucleotides per second, a rate at least tenfold slower than the rate of polymerization of deoxynucleotides by the bacterial DNA polymerase complex. This reduced rate may result from interference by nucleosomes. It is not known how the rephcation complex negotiates nucleosomes. 

Isolation and manipulation of DNA, including end-to-end joining of sequences from very different sources to make chimeric molecules (eg, molecules containing both human and bacterial DNA sequences in a sequence-independent fashion), is the essence of recombinant DNA research. This involves several unique techniques and reagents. 

Bacterial plasmids are small, circular, duplex DNA molecules whose natural function is to confer antibiotic resistance to the host cell. Plasmids have several properties that make them extremely useful as cloning vectors. They exist as single or multiple copies within the bacterium and replicate independently from the bacterial DNA. The complete DNA sequence of many plasmids is known hence, the precise location of restriction enzyme... 

Hurst, G. Doktycz, M. Vass, A. Buchanan, M. Detection of bacterial DNA polymerase chain reaction products by matrix assisted laser desorption/ionization mass spectrometry. Rapid. Commun. Mass Spectrom. 1996,10,377-382. 

Figure 2 Double-stranded oligonucleotide photoprobes that simulate modified DNA and intended to cross-link to DNA-binding proteins. (A) Probe modeling interstrand cross-linking by cisplatin Source From Ref. [63], with permission from the American Chemical Society via the Rightslink service (license number 2458870278307 granted June 30, 2010). The benzophenone probe prior to reaction with DNA is shown in the lower part of the panel. (B) Photoaffinity probe for bacterial DNA repair proteins. TT is a simulated thymine dimer intended to be recognized as a site of damage in DNA, and T (two instances) is the diazirine thymine derivative T Source From Ref. [64], with permission from Wiley.

To establish whether rifaximin, like the other members of the rifamycin family [36, 58], specifically inhibits bacterial RNA synthesis the effect of this antibiotic as well as that of rifampicin and chloramphenicol on RNA (via 3H-uridine incorporation), DNA (via 3H-thymidine incorporation) and protein (via 35S-methionine incorporation) synthesis was studied in growing cultures of Escherichia coli [59], While chloramphenicol reduced protein synthesis, both rifaximin and rifampicin inhibited RNA synthesis in a concentration-dependent fashion. In contrast, none of them affected 3H-thymidine incorporation into DNA. These data suggest that rifaximin, like rifampicin, inhibits RNA synthesis by binding the (3 subunit of the bacterial DNA-dependent RNA polymerase [60],... 

The answer is d. (Hardman, pp 1065—1067. Katzung, p 797.) Bacterial DNA gyrase is composed of four subunits, and levofloxacin binds to the strand-cutting subunits, inhibiting their activity... 

The mutagenic activity of A-acyloxy-A-alkoxyamides reflects their interaction with the primary target, which in this case is bacterial DNA. The predictive model (Equation 3) allows discovery of structural factors that either increase or diminish DNA damage. Such effects can operate either upon binding to DNA or reactivity with DNA. Both types of structural impacts have been observed. 

Such activity enhancement can be ascribed to planarity of the naphthalene nucleus and its disposition for n-n stacking between the DNA base pairs. There is no literature precedence for involvement of naphthalene in such processes unless it is % electron deficient.211,212 However, our results suggest that both alkylated and acylated naphthalenes are intercalators with bacterial DNA. 

They are direct-acting mutagens towards S. typhimurium TA100 with demonstrable ability to react with plasmid DNA at G-N7 or A-N3. The versatile synthetic protocol has enabled us to synthesise and test, reliably, many representatives and establish a working QSAR that has enabled us to understand intimate details of their interaction with bacterial DNA. Their biological activity can be sheeted home to binding to DNA followed, most likely, by an SN2 reaction with G-N7. Electronic and steric effects of substituents are in accord with this mechanism. 

---