Making DNA more Protein-like for Artificial DNA-Enzyme Discovery: Where Chemistry Meets Molecular Biology

Enzyme mimicry can provide fundamental insight into catalyst design as well new catalysts for therapy, sensing, and fine chemical transformations. Nucleic acid catalysts hold great promise as enzyme mimics yet lack many of the chemical functionalities commonly seen at the active sites of protein enzymes.  Since 1999, co-workers and I have worked to extend the catalytic potential of DNAzymes by incorporating modified dNTPs that are appended with the side chains of key amino acids that are found at the active sites of protein enzymes.1-10

Our main interest in this approach has been the development of M2+-independent RNA cleaving DNAzymes. To mimic the M2+-independent protein endonuclease RNase A, we simultaneously used three chemically modified nucleotides 8-histaminyl-dATP (dAimTP), 5-aminoallyl-dCTP (dCaaTP), and 5-guanidinoallyl-dUTP (dUgaTP) adorned with respective side-chain functionalities of histidine, lysine, and arginine, in an in vitro combinatorial selection.  Our latest effort has given rise to several novel families of DNAzymes capable of catalyzing M2+-independent cleavage of an all-RNA substrate derived from HIV-LTR promoter in trans with multiple turnover. Work towards the development, synthesis and characterization of these RNA-cleavers will be discussed, along with other DNA-based catalysts discovered for heavy metal sensing 5 and Schiff base catalysis.11

References:

            (1)       Perrin, D. M.; Garestier, T.; Hélène, C. Expanding the catalytic repertoire of nucleic acid catalysts: Simultaneous incorporation of two modified deoxyribonucleoside triphosphates bearing ammonium and imidazolyl functionalities. Nucleosides Nucleotides 1999, 18, 377.

            (2)       Perrin, D. M.; Garestier, T.; Hélène, C. Bridging the gap between proteins and nucleic acids: A metal-independent RNAseA mimic with two protein-like functionalities Journal of the American Chemical Society 2001, 123, 1556.

            (3)       Lermer, L.; Hobbs, J.; Perrin, D. M. Incorporation of 8-histaminyldeoxyadenosine [8-(2-(4-imidazolyl)ethylamino)-2 '-deoxyriboadenosine] into oligodeoxyribonucleotides by solid phase phosphoramidite coupling Nucleosides Nucleotides & Nucleic Acids 2002, 21, 651.

            (4)       Lermer, L.; Roupioz, Y.; Ting, R.; Perrin, D. M. Toward an RNaseA mimic: A DNAzyme with imidazoles and cationic amines Journal of the American Chemical Society 2002, 124, 9960.

            (5)       Hollenstein, M.; Hipolito, C.; Lam, C.; Dietrich, D.; Perrin, D. M. A highly selective DNAzyme sensor for mercuric ions Angewandte Chemie International Edition 2008, 47, 4346.

            (6)       Lam, C.; Hipolito, C.; Perrin, D. M. Synthesis and Enzymatic Incorporation of Modified Deoxyadenosine Triphosphates European Journal of Organic Chemistry 2008, 4915.

            (7)       Hollenstein, M.; Hipolito, C.; Lam, C.; Perrin, D. M. A self-cleaving DNA enzyme modified with amines, guanidines and imidazoles operates independently of divalent metal cations (M2+) Nucleic Acids Research 2009, 37, 1638.

            (8)       Hollenstein, M.; Hipolito, C. J.; Lam, C. H.; Perrin, D. M. A DNAzyme with Three Protein-Like Functional Groups: Enhancing Catalytic Efficiency of M2+-Independent RNA Cleavage ChemBioChem 2009, 10, 1988.

            (9)       Thomas, J. M.; Yoon, J. K.; Perrin, D. M. Investigation of the Catalytic Mechanism of a Synthetic DNAzyme with Protein-like Functionality: An RNaseA Mimic? Journal of the American Chemical Society 2009, 131, 5648.

            (10)     Hollenstein, M.; Hipolito, C. J.; Lam, C. H.; Perrin, D. M. Toward the Combinatorial Selection of Chemically Modified DNAzyme RNase A Mimics Active Against all-RNA Substrates Acs Combinatorial Science 2013, 15, 174.

            (11)     May, J. P.; Ting, R.; Lermer, L.; Thomas, J. M.; Roupioz, Y.; Perrin, D. M. Covalent Schiff base catalysis and turnover by a DNAzyme: a M2+ -independent AP-endonuclease mimic Journal of the American Chemical Society 2004, 126, 4145.