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Table 1 Distribution of 5' recombination junctions in vector mutants isolated in vitro and in vivo with respect to flanking nucleotide sequence homology and EMCV IRES secondary structure

From: Influence of vector design and host cell on the mechanism of recombination and emergence of mutant subpopulations of replicating retroviral vectors

  in vitroa in vivob TOTAL
  NIH-3T3 HEK293 U87-MG TOTAL   
within IRES 2 3 1 6 10 16
pairedc 1 0 0 1 7 8
unpairedd 1 3 1 5 3 8
≥ 4 nt repeate 0 0 0 0 0 0
outside IRES 3 5 2 10 5 15
≥ 4 nt repeat 2 4 1 7 3 10
TOTAL 5 8 3 16 15 31
  1. aDistribution of 5' recombination junctions in vector mutants isolated from in vitro infected NIH-3T3, HEK293, and U87-MG cells at the end of each cycle
  2. bDistribution of 5' recombination junctions in vector mutants isolated from pre-formed subcutaneous U87-MG tumours growing in nude mice and infected in vivo
  3. c5' recombination junctions which fall within paired regions of the EMCV IRES RNA secondary structure [44, 67]
  4. d5' recombination junctions which fall within unpaired regions of the EMCV IRES RNA secondary structure [44, 67]
  5. e5' recombination junctions which are flanked by nucleotide sequence homology (direct or inverted repeats) of = 4 nt in length