Part:BBa_K4983000

Profile Name: dAPT (deltamethrin aptamer)

Base pairs : 54

Properties : deltamethrin binding

Introduction

The basic part that our team is listing is a component of a cell-free biosensor that is intended to detect whether or not a liquid sample contains a significant and measurable deltamethrin concentration. Since this part is the element that identifies and binds deltamethrin and initiates a hybridization cascade with the ultimate goal of qualitative pesticide detection by a chromatic shift in the solution, the aptamer is essential to the detection process.

Detailed description

In more detail, the detection process starts with a double-stranded DNA chain consisting of dAPT and cdAPT. dAPT is composed of the selective to deltamethrin sequence and the S segment. The selective sequence plays a major role in the stability of the double-stranded DNA chain due to 8 bases of the sequence (GGACAGCG) mediating the hybridisation with the complementary region of cdAPT (CCTGTCGC). The hybridization of the remaining part of cdAPT (TGTGATAT) is accomplished by region a (ACACTATA) of the S segment of dAPT. Due to interactions between deltamethrin and dAPT, cdAPT will be subsequently released from the dAPT-cdAPT duplex in the presence of the pesticide. As a result, domain a in the S strand is liberated and can bind to domain a* in L1. At this point it's important to underline that L1 and L2 are two DNA molecules that play an important role in the detection system mainly due to several physicochemical and stereochemical properties of theirs such as their ability to auto-hybridize and create loops (hairpins) in the absence of deltamethrin. This toehold binding catalyzes the branch migration (domains b–b* and c–c* hybridization) to open L1 (toehold-mediated strand displacement reaction) and form the S-L1 duplex . In order to open L2 and produce the S-L1-L2 hybrid, domain c* in L2 is hybridized with the exposed domain c in L1, once more triggering a branch migration (domain d-d* hybridization). The b and c domains in L2 antagonize the b and c domains in S to hybridize with the b* and c* domains in L1 forming the S-L1-L2 hybrid. The stable L1-L2 complex may then develop as the S strand of this hybrid separates on its own. As a result, the S strand can be recycled along with the aptamer-deltamethrin complex and to start a new cycle of detection. The details about the remaining steps of the detection system are documented on our engineering page.

Picture 1. Detection system mechanism after deltamethrin binding