After its entry into the plant cell the ssT-DNA complex crosses the nuclear membrane to enter the nucleus and subsequently integrates into the plant genome. VirD2 and VirE2 are the two most important proteins required for this process. VirF also plays a minor role in the same (Hooykaas, P.J.J. and Shilperoort, R.A. (1992). Agrobacterium and plant genetic engineering. Plant Molecular Biology 19: 15-38). The ss-T-DNA complex is coated by a single molecule of VirD2, attached covalently to the 5′ end of T-DNA; however, a large number of VirE2 molecules (approximately 600 per a 20 kb T-DNA) coat the ssT-DNA complex. The nuclear location signals (NLS) of VirD2 and VirE2 play an important role in nuclear targeting of the ss-T-DNA complex. The two NLS of each VirE2 are important for the continuos nuclear import of ss-T-DNA complex. They keep both sides of nuclear pores simultaneously open. The process of nuclear import is also probably mediated by certain NLS-binding proteins, which are present in plant cytoplasm.
The final step is the incorporation of T-DNA into the plant genome. The integration occurs by illegitimate recombination (Gheysen, G., Villarroel, R. and Van Montagu, M. (1989). Illegitimate recombination in plants: a model for T-DNA integration. Genes Development 5: 287-297), which requires pairing of a few bases, known as micro-homologies. “These homologies are very low and provide just a minimum specificity for the recombination process by positioning VirD2 for the ligation” (de la Riva et al., 1998. Agrobacterium tumefaciens: a natural tool for plant transformation. Elec. J. Biotech. Vol. 1). The 3´-end or adjacent sequences of T-DNA find some homologies with plant DNA and form a gap in 3′-5′ strand of plant DNA. The displaced plant DNA is cut at the 3′-end position of the gap by endonucleases. The first nucleotide of the 5′ attaches to VirD2, and pairs with a nucleotide in the top (5′-3′) plant DNA strand. The 3′ overhanging part of T-DNA and the displaced plant DNA are digested. “Then, the 5′ attached to VirD2 end and other 3′-end of T-strand (paired with plant DNA during since the first step of integration process) joins the nicks in the bottom plant DNA strand.” The repair mechanism of the plant cell is also activated during the process to make the complementary strand using T-DNA strand as a template. VirD2 plays an active role in the integration process (Jayaram, M. (1994). Phosphoryl transfer if FLP recombination: a template for strand transfer mechanisms. Trends Biotechnology. 19: 78-82).
Here is the figure detailing the complete T-DNA transfer process.