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If much less fetal DNA binds to a probe than control DNA, the fetus is missing DNA at the corresponding location in the genome.
It is also possible that, once a target sequence binds to a probe with more than three cytosines, it is stably bound due to the large number of hydrogen bonds holding it in place.
When a target oligonucleotide binds to a probe in the upstream (Fig 1, top right), there is no elongation, because it provides no primer/template structure for the Taq polymerase.
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Electrophonetic mobility shift assay showed that OCT4B does not bind to a probe carrying the OCT4 consensus binding sequence due to the repressive effect of the OCT4B N-domain.
Interestingly, the Oct-4B isoform does not bind to a probe carrying the Oct-4 consensus-binding sequence, and two separate regions of its NTD are responsible for inhibiting DNA binding (Lee et al, 2006).
To a first approximation, the amount of mRNA produced by a gene should be the same no matter which part of the mRNA molecule is bound to a probe.
The fact that we observed a strong dependence on mismatch position suggests that the entropic contribution to the thermodynamic stability is important, and that careful consideration of the many different configurations in which a target strand can bind to a probe strand is required.
(A ) Electrophoretic mobility shift assay (EMSA) demonstrating that the recombinant KDM2B ZF-CxxC domain binds to a DNA probe containing non-methylated CpGs (left panel) in a concentration-dependent manner.
In contrast, a fragment lacking the first 181 N-terminal amino acids of FOXP3, here designated FOXP3-ΔN [25], bound to the A probe, although more weakly than that observed for Foxp1 (Figure 1B, lane 4).
Increasing the stringency to 4 and 5 out of 5 murine samples that must bind to a particular probe set before that probe is excluded from the analysis reduces the number of probe sets with the potential to cross-hybridize to murine RNA by 3-fold (to 2614).
Nuclear proteins were found to bind to a labeled probe with G at SNP-358 (-358G probe)(1st lane from the left), which was reduced by a cold competitor with G at SNP-358, but not by that with A at SNP-358 (2nd and 3rd lanes, respectively).
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