148692-01-7Relevant academic research and scientific papers
CCR5 RNA Pseudoknots: Residue and Site-Specific Labeling correlate Internal Motions with microRNA Binding
Chen, Bin,Longhini, Andrew P.,Nu?baumer, Felix,Kreutz, Christoph,Dinman, Jonathan D.,Dayie, T. Kwaku
, p. 5462 - 5468 (2018)
Conformational dynamics of RNA molecules play a critical role in governing their biological functions. Measurements of RNA dynamic behavior sheds important light on sites that interact with their binding partners or cellular stimulators. However, such measurements using solution-state NMR are difficult for large RNA molecules (>70 nt; nt=nucleotides) owing to severe spectral overlap, homonuclear 13C scalar couplings, and line broadening. Herein, a strategic combination of solid-phase synthesis, site-specific isotopic labeled phosphoramidites, and enzymatic ligation is introduced. This approach allowed the position-specific insertion of isotopic probes into a 96 nt CCR5 RNA fragment. Accurate measurements of functional dynamics using the Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion (RD) experiments enabled extraction of the exchange rates and populations of this RNA. NMR chemical shift perturbation analysis of the RNA/microRNA-1224 complex indicated that A90-C1′ of the pseudoknot exhibits similar changes in chemical shift observed in the excited state. This work demonstrates the general applicability of a NMR-labeling strategy to probe functional RNA structural dynamics.
Synthesis and Conformational Properties of Oligonucleotides Incorporating 2′-O-Phosphorylated Ribonucleotides as Structural Motifs of Pre-tRNA Splicing Intermediates
Tsuruoka, Hiroyuki,Shohda, Koh-Ichiroh,Wada, Takeshi,Sekine, Mitsuo
, p. 7479 - 7494 (2007/10/03)
To synthesize oligonucleotides containing 2′-O-phosphate groups, four kinds of ribonucleoside 3′-phosphoramidite building blocks 6a-d having the bis(2-cyano-1,1-dimethylethoxy)thiophosphoryl (BCMETP) group were prepared according to our previous phosphorylation procedure. These phosphoramidite units 6a-d were not contaminated with 3′-regioisomers and were successfully applied to solid-phase synthesis to give oligodeoxyuridylates 15, 16 and oligouridylates 21, 22. Self-complementary Drew-Dickerson DNA 12mers 24-28 replaced by a 2′-O-phosphorylated ribonucleotide at various positions were similarly synthesized. In these syntheses, it turned out that KI3 was the most effective reagent for oxidative desulfurization of the initially generated thiophosphate group to the phosphate group on polymer supports. Without using this conversion step, a tridecadeoxyuridylate 17 incorporating a 2′-O-thiophosphorylated uridine derivative was also synthesized. To investigate the effect of the 2′-phosphate group on the thermal stability and 3D-structure of DNA(RNA) duplexes, Tm measurement of the self-complementary oligonucleotides obtained and MD simulation of heptamer duplexes 33-36 were carried out. According to these analyses, it was suggested that the nucleoside ribose moiety phosphorylated at the 2′-hydroxyl function predominantly preferred C2′-endo to C3′-endo conformation in DNA duplexes so that it did not significantly affect the stability of the DNA duplex. On the other hand, the 2′-modified ribose moiety was expelled to give a C3′-endo conformation in RNA duplexes so that the RNA duplexes were extremely destabilized.
Regioselective protection of the 2'-hydroxyl group of N-acyl-3',5'-O-di(t-butyl)silanediylnucleoside derivatives by use of t-BuMgCl and 2-(trimethylsilyl)ethoxymethyl chloride
Wada,Tobe,Nagayama,Furusawa,Sekine
, p. 1683 - 1684 (2007/10/02)
Regioselective 2'-O-protection of N-protected 3',5'-O-di(t-butyl)silanediylribonucleoside derivatives with the 2-(trimethylsilyl)ethoxymethyl (SEM) group has been achieved by use of t-BuMgCl and 2-(trimethylsilyl)ethoxymethyl chloride. The former was used
