Xiangyu Cong, Jayeeta Banerjee, Ahmed M. Awad, Xiaoling Song, Long Qu and Marit Nilsen-Hamilton, Development of a Malachite Green RNA TRAP. In preparation.

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GRABIT PROJECT

Figure 1

PRINCIPLES OF THE TRAP DESIGN

Targeted Reversibly Attenuated Probe (TRAP)

The TRAP is a single stranded DNA or RNA sequence (Fig. 1). Every TRAP has three modules. At the one end of the TRAP there is a ligand-binding aptamer sequence. At the other end is the attenuator sequence that is the reverse complement of part of the aptamer sequence. In the middle of the TRAP, there is an antisense fragment, which is complementary to the target mRNA sequence.

The attenuator sequence of the TRAP is 5-10 nt. Because the TRAP has 5' end and 3' ends that are reverse complementary sequence like molecular beacons (6), it adopts a stem loop structure.

In the middle of the TRAP sequence is a 15-30 nt antisense sequence. The function of this intervening antisense sequence is to anneal with the complementary sequence on the target mRNA and to provide the energy to separate the stem of the TRAP

Limitations of Molecular Beacons

A: Fluorescence molecules need to be attached to the molecular beacons by in vitro
chemical reaction
B: Molecular Beacons need to be applied to the cell through micro-injection or transfection
C: Fluorescence is not strong enough to penetrate deep tissues or body.