The selection of a hydrophobic 7-phenylbutyl-7-deazaadenine-modified DNA aptamer with high binding affinity for the Heat Shock Protein 70

Abstract

Hydrophobic 7-phenylbutyl-7-deaadenine-modified DNA aptamers were selected against the Heat Shock Protein 70 via PEX and magnetic bead-based SELEX. After 9 rounds of selection, the pool was sequenced and a number of candidates were identified. Following initial screening, two modified aptamers were chemically synthesised in-house and their binding affinity analysed by two methods, bio-layer interferometry and fluorescent-plate-based binding assay. The binding affinities of the modified aptam,ers were compared with that of their natural counterparts. The resulting modified aptamers bound with higher affinity (low nanomolar range) to the Hsp70 than their natural sequence (> 5 µM) and hence have potential for applications and further development towards Hsp70 diagnostics or even therapeutics.

Controlled enzymatic synthesis of oligonucleotides

“…For instance, oligonucleotides are important building blocks in DNA-encoded libraries (DELs) for drug discovery campaigns 1,2 , storage of digital information 3,4 , and computing 5 . In addition, DNA and RNA can serve as potent catalysts [6][7][8][9][10] , binders [11][12][13][14][15][16][17] , and therapeutic agents 18,19 . The increasing popularity of nucleic acids is accompanied by an important surge in the demand of synthetic oligonucleotides, particularly of sequences containing chemical modifications.…”

Increasing the functional density of threose nucleic acid

“…[19][20][21][22] Functionally enhanced libraries prepared using nucleoside triphosphates that are modified to include additional functionality at the C-5 position of pyrimidines and N-7 or C-8 positions of purines offer a different path for improving aptamer activity. 14,[23][24][25][26][27] Slow off-rate modified aptamers (SOMAmers), for example, utilize a highly versatile palladium-catalyzed carboxyamidation reaction to install diversity enhancing functional groups at the C-5 position of pyrimidines. 28 This approach revolutionized the field of aptamer-based diagnostics by increasing the success rate of aptamer selections from B30% for standard base libraries to 84% for functionally enhanced libraries.…”