Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments

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Monday, December 22, 2014

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SPEX Experiments

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Verification of Overall Mechanisms in Solution

Verification of Random Walking Mechanism on Origami

Fluorescent spectroscopy (SPEX) was used to verify random walk on the origami. We designed a strand named walker goal (WG) which can bind to walkers irreversibly due to its perfect complementarity with walkers. A ROX fluorophore was attached to the 5' end of the probe for the walker goal (PWG) and the corresponding quencher was attached to the 3' end of the walker (Figure 1). When the walker binds to the walker goal, its quencher is directly above the fluorophore of the walker goal, hence quenching it. Thus we can setup experiments where the fluorescent level slowly decreases as more and more walkers reach the walker goal.


Figure 1. The irreversible binding between walker (W) and walker goal (WG). A ROX fluorophore (red star) was attached to the 5' end of each probe for walker goal (PWG) and a quencher (black cross) was attached to the 3' end of each walker. TR1, track 1. PTR1, probe for track 1. Curved regions shown on the probes were inserted into the origami.
Figure 1. The irreversible binding between walker (W) and walker goal (WG). A ROX fluorophore (red star) was attached to the 5' end of each probe for walker goal (PWG) and a quencher (black cross) was attached to the 3' end of each walker. TR1, track 1. PTR1, probe for track 1. Curved regions shown on the probes were inserted into the origami.


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