Enzymatic Recognition of 2′‐Modified Ribonucleoside 5′‐Triphosphates: Towards the Evolution of Versatile Aptamers

Abstract

The quest for effective, selective and nontoxic nucleic-acid-based drugs has led to designing modifications of naturally occurring nucleosides. A number of modified nucleic acids have been made in the past decades in the hope that they would prove useful in target-validation studies and therapeutic applications involving antisense, RNAi, aptamer, and ribozyme-based technologies. Since their invention in the early 1990s, aptamers have emerged as a very promising class of therapeutics, with one drug entering the market for the treatment of age-related macular degeneration. To combat the limitations of aptamers containing naturally occurring nucleotides, chemically modified nucleotides have to be used. In order to apply modified nucleotides in aptamer drug development, their enzyme-recognition capabilities must be understood. For this purpose, several modified nucleoside 5'-triphosphates were synthesized and investigated as substrates for various enzymes. Herein, we review studies on the enzyme-recognition of various 2'-sugar-modified NTPs that were carried out with a view to their effective utilization in SELEX processes to generate versatile aptamers.

Smart functional nucleic acid chimeras: Enabling tissue specific RNA targeting therapy

“…[122][123][124][125] Very recently, Lauridsen et al reported a review article describing the enzymatic recognition capabilities of various 2 0 -modified nucleotides. 126 Stemming from their initial enzymatic recognition studies, 2 0 -amino pyrimidines, 2 0 -fluoro pyrimidines and 2 0 -O-Methyl nucleotides have been successfully applied in aptamer development by conventional SELEX-based methodologies. [127][128][129][130][131][132][133][134] LNA is one of the successful nucleotide analogs extensively utilized in various fields because of their remarkable properties.…”

In vitro selection of BNA (LNA) aptamers

“…[48][49][50][51][52][53][54][55][56][57][58][59][60][61][62][63][64][65] Veedu et al first tested B/L nucleotide incorporation using Phusion High Fidelity DNA polymerase, 9°Nm DNA polymerase, and Pfu DNA polymerase, and observed that the first and second of these three polymerases to exhibit superior stability in human plasma and target binding affinity (t 1/2 = 53 h, EC 50 = 2.0 nM) compared with TTA1 (t 1/2 = 42 h, EC 50 = 5.8 nM). In contrast, replacement with 2'-OMe nucleotides at the same positions, which yielded TTA1.1, resulted in a more than 2-fold decrease in binding affinity, although stability was substantially improved (t 1/2 = 49 h, EC 50 = 13.7 nM).…”

Nucleic Acid Aptamers as Potential Therapeutic and Diagnostic Agents for Lymphoma

“…Recently, two classes of modified nucleotides, Locked Nucleic Acids and spiegelmers (mirror image of aptamers) have been adapted into the PCR amplification and T7 transcription [27,28]. Thus, aptamers can be tailored to achieve certain functions through site-specific chemical modifications that are especially important for in vivo uses [29]. …”