Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments

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Monday, December 29, 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.



To verify that the walker walks on the origami using the intended mechanisms, we need a control where there are no tracks, except for the one that the walker is bound to, to see if the walker can simply dissociate off its track and bind to the walker goal, and another control where no walker trigger is released to see if the walker will start moving without the walker trigger. SEPX Results show that there is no decrease in fluorescence in the absence of tracks or walker trigger, but there is a decrease in fluorescence when both tracks and walker trigger are present.

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