Abstract
The conformation of complementary determining region (CDR) is crucial in dictating its specificity and affinity for binding with an antigen, making it a focal point in artificial antibody engineering. Although desirable, programmable scaffolds that can regulate the conformation of individual CDRs with nanometer precision are still lacking. Here, we devise a strategy to program the CDR conformation by anchoring both ends of a free CDR loop to specific sites of a DNA framework structure. This method allows us to define the span of a single CDR loop with an ∼2 nm resolution. Using this approach, we create a series of DNA framework based artificial antibodies (DNFbodies) with varied CDR loop spans, leading to different antibody-antigen binding affinities. We find that an optimized single CDR loop (∼2.3 nm span) exhibits ∼3-fold improved affinity relative to natural antibodies, confirming the critical role of the CDR conformation. This study may inspire the rational design of artificial antibodies.