DNA-Catalyzed Amide Hydrolysis

Abstract

DNA catalysts (deoxyribozymes) for a variety of reactions have been identified by in vitro selection. However, for certain reactions this identification has not been achieved. One important example is DNA-catalyzed amide hydrolysis, for which a previous selection experiment instead led to DNA-catalyzed DNA phosphodiester hydrolysis. Subsequent efforts in which the selection strategy deliberately avoided phosphodiester hydrolysis led to DNA-catalyzed ester and aromatic amide hydrolysis, but aliphatic amide hydrolysis has been elusive. In the present study, we show that including modified nucleotides that bear protein-like functional groups (any one of primary amino, carboxyl, or primary hydroxyl) enables identification of amide-hydrolyzing deoxyribozymes. In one case, the same deoxyribozyme sequence without the modifications still retains substantial catalytic activity. Overall, these findings establish the utility of introducing protein-like functional groups into deoxyribozymes for identifying new catalytic function. The results also suggest the longer-term feasibility of deoxyribozymes as artificial proteases.

Surface-enhanced Raman scattering investigation of targeted delivery and controlled release of gemcitabine

“…Recent studies indicate that strength of amide bonds depends on the kind of groups on both sides of the bond, which may cause the so-called "bond-twisting", which decreases amide bond stability and makes it prone to acidolysis. 56,57 In addition to that, DNA 8,58 and enzymes that have the ability to promote cleaving the amide bonds will contribute to the drug release. The amide bond cleavage allows the GEM to diffuse away from the AuNPs unmasking the MBA Raman signal.…”

“…[1][2][3][4][5][6][7] Nanocarrier-based drug delivery systems afford key advantages to the conventional treatment modes: controlled release and targeted delivery. The ability to keep the drug inactive, while in transit, and release it in its active form, under the appropriate physiochemical conditions, [6][7][8][9][10] mitigates the collateral damage to healthy tissue, which in conventional approaches is an inherent consequence that goes largely unchecked. Additionally, through multifunctionalization, nanocarriers can contain not only anticancer payloads but also ligands that preferentially bind to surface receptor proteins of cancer cells and mediate endocytosis of the nanocarrier.…”

DNA Three Way Junction Core Decorated with Amino Acids-Like Residues-Synthesis and Characterization

“…The (5′S)-5′-C-propargylthymidine 9 (T) was cleanly incorporated in the middle of three different sequences alk S1 (5′-GCGACCTATTGCAAGTGG), alk S2 (5′-CCACTTGCATGTGTGTGCC) and alk S3 (5′-GGCACACT TAGGTCGC), that were purified by means of reverse phase HPLC and characterized by mass spectroscopy in MALDI-TOF mode ( alk S1 measured 5577.0 [calculated +38.0, found +38. 4 Figure S1-S3, Supplementary Materials). The sequences were chosen to be half complementary of each other in order to form a three way junction when mixed together with three non-pairing modified thymidines (T) at the core of the structure (Scheme 2 and Table 1).…”

“…10 eq.) was thereafter added under argon atmosphere and the mixture was diluted with freshly distilled THF (50 mL) and left stirring for 17 h. The silver nitrate salts were filtered off and the filtrate was washed with brine (~25 mL), dried on MgSO 4 and concentrated under reduced pressure. The crude product was thereafter without further purification re-dissolved in freshly distilled THF (20 mL) and a 1 M solution of TBAF in THF (3.15 mL, 3.15 mmol, 1.25 eq.)…”

“…Most of the efforts towards DNA-based artificial protease have been conducted by in vitro selection (SELEX methodology) but to date no unmodified nucleic acid sequences have been successfully selected for that purpose [3]. However, a very recent example from the Silverman's group showed that DNA featuring protein-like functional groups could be selected for the hydrolysis of an amide bond inserted within an oligonucleotide as substrate [4].…”