Global InformationDeoxyribozyme information
Deoxyribozymes, also called DNA enzymes, DNAzymes, or catalytic DNA, are DNA oligonucleotides that are capable of performing a specific chemical reaction, often but not always catalytic. This is similar to the action of other biological enzymes, such as proteins or ribozymes (enzymes composed of RNA).[1] However, in contrast to the abundance of protein enzymes in biological systems and the discovery of biological ribozymes in the 1980s,[2][3] there is only little evidence for naturally occurring deoxyribozymes.[4][5] Deoxyribozymes should not be confused with DNA aptamers which are oligonucleotides that selectively bind a target ligand, but do not catalyze a subsequent chemical reaction.
With the exception of ribozymes, nucleic acid molecules within cells primarily serve as storage of genetic information due to its ability to form complementary base pairs, which allows for high-fidelity copying and transfer of genetic information. In contrast, nucleic acid molecules are more limited in their catalytic ability, in comparison to protein enzymes, to just three types of interactions: hydrogen bonding, pi stacking, and metal-ion coordination. This is due to the limited number of functional groups of the nucleic acid monomers: while proteins are built from up to twenty different amino acids with various functional groups, nucleic acids are built from just four chemically similar nucleobases. In addition, DNA lacks the 2'-hydroxyl group found in RNA which limits the catalytic competency of deoxyribozymes even in comparison to ribozymes.[6]
In addition to the inherent inferiority of DNA catalytic activity, the apparent lack of naturally occurring deoxyribozymes may also be due to the primarily double-stranded conformation of DNA in biological systems which would limit its physical flexibility and ability to form tertiary structures, and so would drastically limit the ability of double-stranded DNA to act as a catalyst;[6] though there are a few known instances of biological single-stranded DNA such as multicopy single-stranded DNA (msDNA), certain viral genomes, and the replication fork formed during DNA replication. Further structural differences between DNA and RNA may also play a role in the lack of biological deoxyribozymes, such as the additional methyl group of the DNA base thymidine compared to the RNA base uracil or the tendency of DNA to adopt the B-form helix while RNA tends to adopt the A-form helix.[1] However, it has also been shown that DNA can form structures that RNA cannot, which suggests that, though there are differences in structures that each can form, neither is inherently more or less catalytic due to their possible structural motifs.[1]
In 2021, the DNAmoreDB database for cataloguing known deoxyribozymes was released.[7]
- ^ a b c Breaker RR (May 1997). "DNA enzymes". Nature Biotechnology. 15 (5): 427–431. doi:10.1038/nbt0597-427. PMID 9131619. S2CID 1918660.
- ^ Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR (November 1982). "Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena". Cell. 31 (1): 147–157. doi:10.1016/0092-8674(82)90414-7. PMID 6297745. S2CID 14787080.
- ^ Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S (December 1983). "The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme". Cell. 35 (3 Pt 2): 849–857. doi:10.1016/0092-8674(83)90117-4. PMID 6197186. S2CID 39111511.
- ^ Köhler T, Patsis PA, Hahn D, Ruland A, Naas C, Müller M, Thiele J (April 2020). "DNAzymes as Catalysts for l-Tyrosine and Amyloid β Oxidation". ACS Omega. 5 (13): 7059–7064. doi:10.1021/acsomega.9b02645. PMC 7143405. PMID 32280846.
- ^ Breaker RR, Joyce GF (September 2014). "The expanding view of RNA and DNA function". Chemistry & Biology. 21 (9): 1059–1065. doi:10.1016/j.chembiol.2014.07.008. PMC 4171699. PMID 25237854.
- ^ a b Silverman SK (October 2004). "Deoxyribozymes: DNA catalysts for bioorganic chemistry". Organic & Biomolecular Chemistry. 2 (19): 2701–2706. CiteSeerX 10.1.1.626.8241. doi:10.1039/B411910J. PMID 15455136.
- ^ Ponce-Salvatierra A, Boccaletto P, Bujnicki JM (January 2021). "DNAmoreDB, a database of DNAzymes". Nucleic Acids Research. 49 (D1): D76–D81. doi:10.1093/nar/gkaa867. PMC 7778931. PMID 33053178.