Select characteristics of representative DNA structures manifesting complex structural and multi-FRET process.
| DNA structure (estimated length) | # of ET steps | Fluorophores/D → A | r DA a | E ee | Notes | Ref. |
|---|---|---|---|---|---|---|
| 7 helix bundle | 2 | Py, Cy3, AF647 | <0.5 × R0 | 30–90% | Stepwise EFRET depended on ratio of dyes to each other at each step | 251 |
| Origami triangle (120 nm per side) | 2 | Fam, Cy3, Cy5 | 0.5 to 1 × R0 | 70% for 8 : 4 : 1 ratio | Concentric rings of D → relay → A highest AE ∼8 for 8 : 4 : 1 ratio | 150 |
| 7–10 oligo dual/split rail (∼10 nm for dye containing portion) | 3 | Cy3, Cy3.5, Cy5/A647, Cy5.5 | <0.5 × R0 | ∼50% | Replacing 2 Cy5 with a Cy5/A647 hybrid significantly improved Eee | 173 |
| Linear-8 arm; 2 : 1, 3 : 1, 4 : 1 DNA dendrimersb | 3,4 | A488, Cy3, Cy3.5, Cy5, Cy5.5 | 0.5, 1.0, 1.5 × R0 | 28% | Dendrimer yields > 500 increase in terminal A sensitization | 252 |
| 45 bp ds dimer (∼15 nm) | 4 | Tb-chelate, A546, A594, A647, Cy5.5 | 9 bp < 1 × R0 for each D–A pair | ∼8% | Decreased EFRET needed for Tb D to 1st A to meet time-gated requirements | 253 |
| DNA block (40 × 10 × 15 nm) | 4 | A488, Cy3, Cy3.5, A647, Cy5.5 | <0.5 × R0 | 22% | Improved 1/r4 ET distance dependency due to sheet regime effects | 103 |
| DNA dendrimer | 5 | Luc, A488, Cy3, Cy3.5, Cy5, Cy5.5 | 0.5 × R0 | 16–25% | 1st step Luc catalyzed BRET from Coel. Inward and outward directed cascades | 254 |
a
r DA D–A separation distance given as a function of R0 for the D–A pairs.
b
linear, bifurcated, Holliday junction, and 8 arm star. A in A546-Alexa Fluor and same for other A – designated dyes. AE – antenna effect; Coel – coelenterazine substrate; Luc – luciferase enzyme; Py – pyrene.