Selective fluorescence-based detection of dihydrouridine with boronic acids

pH-controlled DNA- and RNA-templated assembly of short oligomers

“…[36][37][38][39] This reversible process has been studied extensively 40 and has allowed the remarkable development of boronic acid-based sensors for carbohydrates and anions. 36,[41][42][43][44] Hence in the presence of a 3 0 -ended ribonucleotide partner, the dynamic and reversible formation of a cyclic ve membered boronate internucleosidic linkage was found to provide reversible connectivity able to be activated by external stimuli (T, pH, anions) while maintaining the interstrand electrostatic repulsion (Fig. 1).…”

Identification of D Modification Sites Using a Random Forest Model Based on Nucleotide Chemical Properties

“…Some popular chemical modification databases have also been established to help provide a comprehensive understanding of the potential functions of different modifications, such as RMBase (version 2.0) [ 7 ] and MODOMICS [ 5 ], which also contain information on D modifications in various species. Although biochemical methods can produce reliable and accurate information about D modification, they have typically been time-consuming and laborious [ 24 , 25 , 26 , 27 ]. Thus, there is an urgent need to design a high-performance computational tool for the accurate identification of D modification sites.…”

Boron and nucleic acid chemistries: merging the best of both worlds

“…While fluorescent boronic acid sensors for saccharide recognition were extensively reported, 1,13,67,68 the detection of nucleosides or nucleotides by direct emission of fluorescence has not been the subject of many publications. [69][70][71] Fluorescence quenching induced by purine and pyrimidine nucleobases hampered the development of efficient fluorescent sensors. 72 Vasseur and Smietana et al used this phenomenon for the fluorescence sensing of dihydrouridine (10), a post-transcriptional modification in tRNA from bacteria and eukaryotes lacking the C5-C6 double bond present in uridine (11).…”

“…72 Vasseur and Smietana et al used this phenomenon for the fluorescence sensing of dihydrouridine (10), a post-transcriptional modification in tRNA from bacteria and eukaryotes lacking the C5-C6 double bond present in uridine (11). 69 Whereas uridine (11) always quenches fluorescence via p-p stacking interactions, boronic acid 12, among several boronic acid sensors, has been found to show substantial fluorescence enhancement upon binding with dihydrouridine (10) (Fig. 7).…”