Paulsson:Replication inhibitors

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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

Classes of drugs (generally defined by cellular target)

Gyrase inhibitors

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


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


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 [1]

Helicase (eg. DnaB, RepA of pRSF1010) inhibitors

Flavones [2]

DNA intercalators


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 [3], [4]

The bad: 1) in Bacillus HU has preferential effect on chromosomal DNA replication, very little effect on plasmid replication [5]
2) also preferential effect on chromosome replication found in Proteus mirabilis (Mol.Gen.Genet. 138:281, 75)

thermosensitive alleles


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



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