Structure-Guided Designing Pre-Organization in Bivalent Aptamers

Abstract

Multivalent interaction is often used in molecular design and leads to engineered multivalent ligands with increased binding avidities toward target molecules. The resulting binding avidity relies critically on the rigid scaffold that joins multiple ligands as the scaffold controls the relative spatial positions and orientations toward target molecules. Currently, no general design rules exist to construct a simple and rigid DNA scaffold for properly joining multiple ligands. Herein, we report a crystal structure-guided strategy for the rational design of a rigid bivalent aptamer with precise control over spatial separation and orientation. Such a pre-organization allows the two aptamer moieties simultaneously to bind to the target protein at their native conformations. The bivalent aptamer binding has been extensively characterized, and an enhanced binding has been clearly observed. This strategy, we believe, could potentially be generally applicable to design multivalent aptamers.

G-Quadruplex-Proximized Aptamers (G4PA) Efficiently Targeting Cell-Surface Transferrin Receptors for Targeted Cargo Delivery

“…The designed aptamer nanodevice serves as a dimerization-enhanced TfR ligand that fully draws on the structural features of natural Tf. Instead of only superimposing aptamer numbers, , the enhancement binding effect originates from the structurally stable and conformationally homogeneous bi-G4 mediated TfR aptamer dimerization. It also results in dimerization-enhanced uptake and ability to target cancer cells.…”

Thermodynamic and Kinetic Modulation of Microfluidic Interfaces by DNA Nanoassembly Mediated Merit-Complementary Heteromultivalency

“…Such aspects are often not implemented for microfluidic affinity interface engineering. This could potentially become a general strategy for improving the performance of affinity microfluidics for a wide variety of targets, because many aptamers or antibodies have been reported with multiple recognition sites against the same target. , They all provide chances for a merit-complementary-heteromultivalency strategy. One current main limitation is that the accurate interaction information on the individual aptamer–target binding is required.…”

“…When the linker length of binding partners is insufficient, two affinity moieties usually cannot bind to two target proteins simultaneously due to the steric hindrance. In other cases, the linker is too long or flexible, leading to a significant loss in entropy upon multivalent binding to the target. , …”

“…In other cases, the linker is too long or flexible, leading to a significant loss in entropy upon multivalent binding to the target. 20,21 The other key to improve the P value is to minimize the activation energy barrier, so that the increased speed of interaction ensures that the target can still be efficiently identified by the microfluidic affinity interface under shear stress. However, previous efforts at multivalent constructs have not indicated that a significant increase in binding rate is accompanied by higher affinity.…”

DNA Tetrahedron Framework Guided Conjugation and Assembly of Gold Nanoparticles

“…DNA nanotechnology relies on the high-fidelity principles of base pairing to fabricate DNA functional materials as well as regulates the assembly of DNA-templated hybrid materials [16][17][18] in multiple dimensions with the defined size and shape, [19][20][21] biocompatibility and near-atomic precision. [22] Recently, the concept of framework nucleic acids (FNAs) is established that describes the synthetic DNA/RNA nanostructures that has wellcontrolled geometry. [8] DNA tetrahedron is among the simplest DNA frameworks, which can be prepared readily with as less as four single strands.…”