The proteins involved in the shelterin complex include TRF (telomeric repeat-binding factor) 1 and TRF2, which bind to the double-stranded segment of telomeric DNA [ 9, 10].
As expected in this competition experiment, Phen-DC3 did not bind to the double-stranded DNA competitor since the T1/2 was not affected by increasing concentrations of this duplex (Fig. 2D,F).
In methanol-fixed cells, the PI molecules translocate into the nucleus and bind to the double-stranded DNA.
TRF1 and TRF2 bind to the double-stranded portion of telomeres and dictate the state of the telomere end in either an open (telomerase accessible) or closed (telomerase inaccessible) state [ 19].
Additionally, it has been reported that NS1 could bind to the double-stranded viral RNA-sensing protein kinase (PKR) and thereby inhibit the PKR-eIF2 α signaling pathway[ 49].
Moreover, the loop connecting domains D and E contains the double-stranded DNA binding (DsDB) domain, which in this structural model would be positioned such that it could bind to the double-stranded region of DNA adjacent to a lesion site in genomic DNA.
Once amplification has occurred, the dye binds to the double stranded DNA and generates a fluorescent signal without the need for a third dye-labeled oligonucleotide probe.
A recent study using a quantitative fluorescence titration technique showed that Pol X binds gapped DNA in two distinct modes: one utilizing the total DNA binding site of Pol X and the other utilizing only the auxiliary DNA binding site where the enzyme binds to the double-stranded region of the DNA (28).
Here we show that in two mutant cell lines (XR-V15B and XR-V9B) from group 5, the genetic defects are in the gene encoding the 86-kDa subunit of the Ku autoantigen, a nuclear protein that binds to the double-stranded DNA ends.
For instance, TRF1 binds to the double-stranded TTAGGG/CCCTAA repeats, TRF2 binds to the junction of the double-stranded and single-stranded telomeric region, and POT1 binds to single-stranded telomeric repeats (G-tails).
