7-Substituted 8-aza-7-deazaadenosines for modification of the siRNA major groove

Abstract

Here we describe the synthesis of new 7-substituted 8-aza-7-deazaadenosine ribonucleoside phosphoramidites and their use in generating major groove-modified duplex RNAs. A 7-ethynyl analog leads to further structural diversification of the RNA via post-automated RNA synthesis azide/alkyne cycloaddition reactions. In addition, we report preliminary studies on the effects of eight different purine 7-position modifications on RNA duplex stability and pairing specificity. Finally, the effect on RNAi activty of this type of modification at eight different positions in an siRNA guide strand has been explored. Analogs were identified with large 7-position substituents that maintain adenosine pairing specificity and are well-tolerated at specific positions in an siRNA guide strand.

Click Modification of RNA at Adenosine: Structure and Reactivity of 7-Ethynyl- and 7-Triazolyl-8-aza-7-deazaadenosine in RNA

“…4,16 A fraction of the 7-EAA-containing RNA was then subjected to a CuAAC reaction with N -ethylpiperidine azide to give a 16 nt RNA bearing the N -ethylpiperidine 7-EAA triazole (Figure 3A). After purification by polyacrylamide gel electrophoresis, 16 nt RNAs bearing 7-EAA, 7-EAA triazole, and adenosine (for comparison) were crystallized.…”

Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics

“…363 The modification is accomplished at the 7-position of purine, since this site is not directly involved in Watson Crick base-pairing. 364 The click reactions in cells occur in very limited area so that the location of biomaterials in cells can be analyzed with nanometer resolution by use of electron microscopy. Tsien et al devised elegant systems in which DNA, RNA and lipids in cultured cells and neurons can be labelled and clearly distinguished on electron microscopy from the other molecules in cells (Figure 21).…”

Structural and Energetic Impact of Non-Natural 7-Deaza-8-Azaadenine and Its 7-Substituted Derivatives on H-Bonding Potential with Uracil in RNA Molecules

“…19,[24][25][26][27][28][29] In particular, 7-deazapurines, as well as 7-deaza-8-azapurine analogues have been reported to be suitable for modification by copper-catalyzed azide/alkyne cycloaddition (CuAAC or click) chemistry, and used to modify siRNA molecules and to probe RNA editing by adenosine deaminases. 18,19,30,31 This explains why several efforts have been aimed at the synthesis of different purine analogues including 7-deaza-8-azapurine and its 7-substituted derivatives. In particular, Beal's group focused on exploring modifications of nucleic acid residues that project different substituents either in the minor groove (the sugar edge) or in the major groove (the Hoogsteen edge) of a siRNA duplex.…”

“…In particular, Beal's group focused on exploring modifications of nucleic acid residues that project different substituents either in the minor groove (the sugar edge) or in the major groove (the Hoogsteen edge) of a siRNA duplex. 19,30,31 Indeed, the synthesis of nucleobase analogues that retains the 'Watson-Crick' like pairing and that place the substituent in the major-groove is of particular interest, since they preserve the duplex stability and do not alter recognition by the nuclease of the RNA interference (RNAi) pathway. 31 In this context, a very recent study 31 reported the impact on RNA duplexes of two modifications located on the major groove (the "Hoogsteen edge") of the adenine moiety, namely 7-ethynyl-7-deaza-8-aza adenine (here-on 7-E-7-DAA) and 7-triazole-7-deaza-8-azaadenine (7-T-7-DAA),…”

“…16,17 Recently, non natural (synthetic) modifications have been introduced to complement the natural ones. Synthetically modified nucleosides are being used in numerous applications, such as expanding the genetic code, probing biological interactions and functions, 18 imparting favorable properties on small interfering RNAs (siRNAs), 19,20 and even creating a semi-synthetic organism with increased potential for information storage and retrieval. 21,22 Thus, ribonucleoside non-natural modifications further extend the structural repertoire and, in turn, the functional properties of RNA molecules.…”