Schematic representation of the marker recombination system.

(A) Marker points were introduced by genetic changes that do not alter the amino acid sequence. (B) The distances between marker points within gag (C) Transfection-induced recombination was measured by direct sequencing of plasmid DNA extracted from co-transfected 293T cells (D) PCR-induced recombination was measured by separately infecting T-cells with homozygous virions derived from single transfections of WT and MK plasmid. Lysates were mixed before PCR. (E) Inter-virion recombination and PCR-induced recombination was measured by infecting T-cells with homozygous virions derived from single transfections of WT and MK plasmid. (F) The recombination rate in T-cells was measured by infection of T-cells with virus produced by co-transfection of 293T cells with WT and MK plasmid. (D,E,F) Recombination rates were measured by PCR of cellular lysates, cloning and sequencing.