Paulsson:Replication inhibitors

What I want: fast (cell permeant) plasmid DNA replication inhibitor that doesn't interfere with transcription or protein synthesis

Possibilities: drugs, operator arrays, trx through ori, ts-alleles, combinations

Gyrase inhibitors
Good review in Biochemistry 27(7):2253, Karl Drlica and Robert Franco, 1988.

gyrA
quinolones (naladixic acid, oxolinic acid, ciprofloxacin) MOA: create gyrase-DNA adduct that can be processed into strand breaks by protein denaturation.

gyrB
coumarins (novobiocin, coumermycin A1)

The good: fast and full inhibition

The bad: also interferes with RNA polymerase, affects transcription of different genes to varying degree

Polymerase inhibitors
nucleotide analogs - generally not permeant cells can be made permeable with toluene and other treatments 

Helicase (eg. DnaB, RepA of pRSF1010) inhibitors
Flavones

DNA intercalators
ethidium acridine

Nucleotide reductase inhibitors
Hydroxyurea (HU)(use at 50mM, make fresh 1M stock in water or media; some store at -20deg as 1M stock)

The good: 1)fast inhibition; 2) limited effect on RNA synthesis, protein synthesis, cell viability; 3) reversible(?); 4) better than ts-allele of nrdA , 

The bad: 1) in Bacillus HU has preferential effect on chromosomal DNA replication, very little effect on plasmid replication 2) also preferential effect on chromosome replication found in Proteus mirabilis (Mol.Gen.Genet. 138:281, 75)

dnaA
large collection of well characterized alleles, but R1 replication is DnaA independent! and different ori's have different DnaA dependencies

nrdA101
interesting allele, but not good for my purposes (see HU ref, 2007)