Evolution of Sequence-Defined Highly Functionalized Nucleic Acid Polymers

Template-directed synthesis of modified DNA sequences can provide a rich source of material for generating new therapies featuring modified nucleic acid polymers. The Liu lab has previously developed pioneering methods to generate nucleic acid based polymers with modified side chains (J. Am. Chem. Soc. 135, 98–101 (2013)). Further improvements have been made in both the codon design and side chain design thus enabling a larger and more diverse library to be interrogated for desired chemical outcomes. Despite this diversity, key features important for iterative evolution/selection processes (such as Polymerase Chain Reaction and Watson-Crick base pairing) are retained. The process can further be simplified if prior knowledge exists regarding the need for specific scaffolds as the starting library can be based on this knowledge. Screening/selection of libraries made from such highly functionalized nucleic acid polymers (HFNAPs) led to the identification of highly evolved HFNAPs that can bind therapeutically relevant human proteins as discussed below.


PCSK9 binds the Low Density Lipoprotein Receptor (LDLR) and promotes degradation of the latter. Blocking PCSK9-LDLR interactions can lead to a decrease in systemic levels of low density lipoprotein particles (due to higher availability of LDLR) and dramatically improve cardiovascular outcomes. Through the use of HFNAP technology, highly potent polymers that block PCSK9-LDL receptor interactions were discovered with Kd’s in the low nM range. Results from the selection process as well as those from structure-activity studies identified the importance of specific modifications and their polymeric positions in mediating PCSK9 binding. Interleukin-6 (IL6) binding HFNAPs were also identified using a similar approach and collectively, these results demonstrates the general applicability of HFNAP as a platform technology to target disease-associated proteins. These results have been published (Nature Chemistry|Vol10|April 2018|420-427).