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Table 1 E. coli strains, plasmid DNAs, and synthetic oligonucleotides used in this study.

From: A single hydrophobic cleft in the Escherichia coli processivity clamp is sufficient to support cell viability and DNA damage-induced mutagenesis in vivo

E. coli strains:

Strain

Relevant genotype

Source

DH5α

endA1 hsdR17(rK- mK+) glnV44 thi-1 recA1 gyrA96 relA1 deoR nupG Δ(lacZYA-argF)U169 (φ80dlacZ ΔM15)

Invitrogen

MS101

thr-1 araD139 Δ(gpt-proA)62 lacY1 tsx-33 supE44 galK2 hisG4(Oc) rpsL31 xyl-5 mtl-1 argE3(Oc) thi-1 sulA211 dnaN159(Ts) tnaA300::Tn10

[26]

MS146

MS101 with Δ(araD-polB):: Ω

This work

MS125

MS101 with Δ(dinB-yafN)::kan

[28]

MS147

MS101 with ΔumuDC596::ermGT

This work

MS148

MS101 with Δ(dinB-yafN)::kan ΔmutL::cat

This work

Plasmid DNAs:

Plasmid

Relevant characteristics

Source

pWSK29

AmpR; pSC101 origin; low copy number general cloning vector

[39]

pJD100

AmpR; pWSK29 containing the dnaN++) gene under the control of its native promoters

[26]

pJD109

AmpR; pJD100 bearing dnaN159 (G66E and G174A substitutions; β159)

[27]

pMDS110

AmpR; pJD100 bearing dnaN lacking residues 362-366 (dnaNC; βC)

This work

pMDS111

AmpR; pJD100 bearing dnaN lacking residues 362-366 and containing a G66E substitution (dnaNC-G66E; βC-G66E)

This work

pMDS112

AmpR; pJD100 bearing dnaN lacking residues 362-366 and containing I272A and L273A substitutions (dnaNC-I272A-L273A; βC-I272A-L273A)

This work

pMDS113

AmpR; pJD100 bearing dnaN containing E93K and L98K substitutions (dnaNE93K-L98K; βE93K-L98K)

This work

pMDS114

AmpR; pJD100 bearing dnaN lacking residues 362-366 and containing E93K and L98K substitutions (dnaNC-E93K-L98K; βC-E93K-L98K)

This work

Oligonucleotides:

Name

Nucleotide sequence (5'→3')

Δ362-366-T

GGCTTATGTTGTCTAATGAATGAGACTG

Δ362-366-B

CAGTCTCATTCATTAGACAACATAAGCC

G66E-T

CAGCCACACGAGCCAGAAGCGACGACCGTTCCGG

G66E-B

CCGGAACGGTCGTCGCTTCTGGCTCGTGTGGCTG

I272A-L273A-T

GTTTGCTCGCGCGGCGGCTGCCTCTAACGAGAAATTCCG

I272A-L273A-B

CGGAATTTCTCGTTAGAGGCAGCCGCCGCGCGAGCAAAC

E93K-L98K-T

CGTGCAGCTGAAAGGTGAACGGATGAAAGTACGCTCCGG

E93K-L98K-B

CCGGAGCGTACTTTCATCCGTTCACCTTTCAGCTGCACG