M13 phage vectors

bacteriophage M13 – filamentous bacteriophage

single-stranded circular DNA genome (6407 bp long)

– packaged inside rod-shaped protein capsid

M13 life cycle (Fig. 3.1)

phage particles bind to F pilus

– only infects F⁺, Hfr, F' cells

single-stranded DNA genome enters cell

designated as “+” strand

“+” strand repaired

– double-stranded replicative form (RF)

RF contains “+” and “–” strands

“–” strand is template – for mRNA synthesis

– for production of new “+” strands

– by rolling circle replication

“+” strands are packaged in phage coat protein

– exit cell as phage particle

Important points for cloning vectors

M13 occurs in both single and double stranded forms

RF can be digested with restriction endonucleases

inserts can be cloned in – like plasmid

“+” strands from phage particles

– convenient source of single-stranded DNA

– used for sequencing and site-directed mutagenesis

different sized DNA molecules packaged as phage particle

– (within reason)

– phage with inserts > 2 kb replicated slower

different sized DNA molecules

– produce different size phage particles

M13 does not kill host

– phage particles released without lysing cell membrane

– slows growth of host, produces turbid “plaques”

– really zones of slowed bacterial growth

single-stranded DNA

– collected by growing M13 infected cells in culture

– cultures centrifuged to pellet bacterial cells

– phage remains in supernatant

– until precipitated with Ficoll

DNA extracted from phage by phenol extraction

Production of single-stranded DNA requires:

M13 origin of replication – in DNA molecule

M13 gene products – in cell containing DNA molecule

Phage proteins can be provided in trans by helper phage

– allows “phagemid” vectors to be used

(plasmid + M13 origin of replication)

cloning vectors

first vectors used – M13mp18 & M13mp19 (Fig. 3.3)

M13 phage with lacZ ' containing multiple cloning site

same gene and cloning site as pUC18 & pUC19

advantages – blue/white screening system

– genes cloned in pUC18 or pUC19

– can be subcloned to same sites in M13mp equivalent

– different directions for multiple cloning sites

–both strands of cloned DNA

– converted to single-stranded form

– in different vectors

disadvantages – limits to size of cloned DNA (2 kb)

– low yield of DNA

– cannot amplify phage genome numbers much

– phage proteins toxic in high concentrations

phagemid vectors – plasmid + M13 origin of replication

e.g. pEMBL18 & pEMBL19

– pUC18 & pUC19 + M13 origin of replication

maintained in host cell like regular plasmid

– high copy number, lots of copies of cloned DNA

– if M13 helper phage infects cell containing pEMBL

– phage proteins package single-stranded plasmid

– in phage particles – collected like regular phage

Note – helper phage genomes packaged too

– but not as many present as plasmid

– get 100 fold excess of plasmid packaged

helper phage contamination not a problem for sequencing

– use “universal” primers

– homologous to plasmid sequences

– no cross-reaction with phage sequences

Improved phagemids

– e.g. Bluescript (Stratagene product) (Fig. 3.8)

contains: high copy number pMB1 ori

ampicillin resistance marker

lacZ ' containing multiple cloning site

– in 2 different orientations

– different construct than pUC

– allows different cloning strategies

M13 origin of replication

T7 & T3 phage promoter sequences

– flanking multiple cloning site

– used for in vitro RNA synthesis

T7 & T3 phage genomes

– code for unique RNA polymerase enzymes

– recognise different promoters than standard E. coli

Bluescript vector with cloned insert

– mixed with: phage RNA polymerase

radiolabelled NTPs

– get RNA version of cloned DNA

– used as hybridization probe

Note – do not confuse promoters with primers

promoters – needed for RNA synthesis

primers – needed for DNA synthesis

– e.g. sequencing