Skip to main content
. Author manuscript; available in PMC: 2021 Feb 2.
Published in final edited form as: Cell Host Microbe. 2011 Nov 17;10(5):451–63. doi: 10.1016/j.chom.2011.09.013

Figure 2. Identification of a Nuclear Protein-Binding Element in var Introns.

Figure 2

(A) EMSA screening strategy using biotin-labeled overlapping DNA fragments (bold sequences bound to nuclear proteins). The var intron (PF07_0048) containing a single repeat (RII-R1) was analyzed here. The sequences of the full-length intron and each probe are shown in Figure S1F and Table S4.

(B) A single intron region (iNPE25 or iNPE18) binds to nuclear proteins. The two iNPE-binding complexes (CP1 and CP2) were labeled with asterisks, respectively.

(C) Competition EMSA of biotin-labeled iNPE25 motif with various mutated nonlabeled iNPE18 sequences. Base pair exchanges in the mutated iNPE18 oligonucleotides are shown underlined. Competitor was used at a concentration of 100-fold excess of the labeled iNPE25 probe in each competition reaction. The decrease in intensity of CP1/CP2 bands was defined as strong (+++), medium (++), weak (+), and none (–), respectively, as shown in the table. Free probe, shifted bands CP1 and CP2, and running orientation of gel were labeled by arrows.

See also Figure S2 and Table S2.