RNA-Synthesis Using the H-Phosphonate Approach and an Improved Protecting Group Strategy

Westman, Eric; Sigurdsson, Susannah; Almer, Helena; Thelin, Mats; Stawiński, Jacek; Rozners, Eriks; Strömberg, Roger

doi:10.1080/15257779508012495

Cited by 6 publications

(4 citation statements)

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“…Dimers 5 were then treated with 1.1 equiv of o ‐chlorobenzoyl chloride (ClBz‐Cl) at −78 °C and successively phosphonylated (by treatment with the phosphorous chloride/imidazole/triethylamine reagent28, 29) in the same reaction mixture to give the dimeric building blocks 6 . Automated solid‐phase H‐phosphonate RNA synthesis30, 31 with regular monomers and dimers 6 gave the modified oligonucleotides Mod 16 , Mod 15 and Mod 13 10…”

Section: Resultsmentioning

confidence: 99%

Oligoribonucleotide Analogues Containing a Mixed Backbone of Phosphodiester and Formacetal Internucleoside Linkages, Together with Vicinal 2′‐O‐Methyl Groups

2007

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Oligoribonucleotides containing formacetal internucleoside linkages have been prepared and studied by UV melting experiments. In RNA duplexes, the formacetal substitution is stabilizing (Deltat(m)=0 to +0.9 degrees C per modification) at physiological salt concentrations (0.1 M) but destabilizing (Deltat(m)=-0.4 to -0.8 degrees C per modification) at high salt concentrations (1 M); this suggests that reduction of electrostatic repulsion contributes substantially to the stabilization. The presence of 2'-O-Me substituents increases the stabilities of the duplexes (Deltat(m)=+0.5 to +1.1 degrees C per modification). The positive effects of formacetals and 2'-O-Me groups were independent and additive. (1)H NMR studies on monomeric model compounds containing 3'-(ethyl phosphate) or 3'-O-ethoxymethyl groups showed that the formacetal and 2'-O-Me substitutions shift the conformational equilibria of the ribose residues towards the North conformers by 5 to 12 %. Although the preference for the North conformers qualitatively correlates with increased duplex stabilities, changes in thermodynamic parameters (DeltaH degrees and TDeltaS degrees ) for formation of oligonucleotide duplexes and differences in dependence on concentrations of sodium acetate, sodium chloride and sodium perchlorate suggest that solvation effects are also important for the duplex stabilities. Overall the formacetal linkages fit well in A-type RNA duplexes, making them potentially interesting modifications for RNA-based gene-control strategies (e.g., antisense and RNA interference).

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Section: Resultsmentioning

confidence: 99%

Oligoribonucleotide Analogues Containing a Mixed Backbone of Phosphodiester and Formacetal Internucleoside Linkages, Together with Vicinal 2′‐O‐Methyl Groups

2007

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“…Three Model Oligoribonucleotides (Figure ) having two (Mod 16 ), three ( Mod 15 ) and six ( Mod 13 ) internucleoside amide linkages ( x ) were prepared using dimers 17 or 20 and standard H-phosphonate oligoribonucleotide synthesis procedure . Reference oligoribonucleotides (unmodified and having 2‘-O-Me groups vicinal to the phosphodiester linkages x ) and the complementary oligoribonucleotides were also synthesized via the H-phosphonate route 44 and the stabilities of the corresponding duplexes (Figure ) were characterized by UV melting experiments .…”

Section: Resultsmentioning

confidence: 99%

Synthesis and Properties of RNA Analogues Having Amides as Interuridine Linkages at Selected Positions

et al. 2003

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Oligoribonucleotide analogues having amide internucleoside linkages (AM1: 3'-CH(2)CONH-5' and AM2: 3'-CH(2)NHCO-5') at selected positions have been synthesized and the thermal stability of duplexes formed by these analogues with complementary RNA fragments has been evaluated by UV melting experiments. Two series of oligomers with either 2'-OH or 2'-OMe vicinal to the amide linkages were studied. Monomeric synthons (3' and 5'-C amines and carboxylic acids) were synthesized as follows: For synthesis of the AM1 analogue, the known sequence of radical allylation followed by the cleavage of the double bond was adopted. For synthesis of the AM2 analogue, novel routes via addition of nitromethane followed by conversion of the nitro function to either amino or carboxyl groups were developed. Coupling of monomeric amines and carboxylic acids followed by protecting group manipulation and phosphonylation gave dimeric 3'-hydrogenphosphonate building blocks for oligonucleotide synthesis. Monomeric model compounds having 3'-amide and 2'-OH or 2'-OMe groups were also prepared and their conformational equilibrium was determined by (1)H NMR. The AM1 and AM2 models showed equal preferences for the North conformers (at 40 degrees C, 88-89% with 2'-OH, and 92-93% with 2'-OMe). At physiological salt concentration (0.1 M NaCl) the duplexes between AM1 modified oligonucleotides and RNA had stability similar to unmodified RNA-RNA duplexes (Delta t(m)= -0.2 to +0.7 degrees C per modification). However, the AM2 modification resulted in substantial stabilization of duplexes: Delta t(m)= +1 to +2.4 degrees C per modification compared to all RNA. A 2'-O-methyl vicinal to the AM2 linkage further increased the duplex stability. Our results suggest that RNA analogues having amide internucleoside bonds are very promising candidates for medicinal applications.

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“…Solutions such as 1% TFA or 2Ϫ3% dichloroacetic acid (advisable with DNA) in a chlorinated solvent are normally employed, and complete detritylation occurs within 2 min. [27,28] However, in order to provide a large safety margin and to stretch the limits of applicability to other groups that may require stronger acid for removal, we decided to use 3% TFA solution. It should be mentioned that concentrations of TFA much higher than this would be precluded due to rapid degradation of the oligonucleotide component of the conjugate.…”

Section: Resultsmentioning

confidence: 99%

Stability Studies of N-Acylimidazoles

Zaramella¹,

Strömberg²,

Yeheskiely³

2002

Eur. J. Org. Chem.

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RNA-Synthesis Using the H-Phosphonate Approach and an Improved Protecting Group Strategy

Cited by 6 publications

References 1 publication

Oligoribonucleotide Analogues Containing a Mixed Backbone of Phosphodiester and Formacetal Internucleoside Linkages, Together with Vicinal 2′‐O‐Methyl Groups

Oligoribonucleotide Analogues Containing a Mixed Backbone of Phosphodiester and Formacetal Internucleoside Linkages, Together with Vicinal 2′‐O‐Methyl Groups

Synthesis and Properties of RNA Analogues Having Amides as Interuridine Linkages at Selected Positions

Stability Studies of N-Acylimidazoles

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