Uridine 2′‐Carbamates: Facile Tools for Oligonucleotide 2′‐Functionalization
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Abstract
A facile method for preparation of uridine 2??carbamate derivatives based on reaction of 3?,5??disilyl?protected uridine with 1,1??carbonyldiimidazole followed by treatment with an aliphatic amine is presented. A phosphoramidite monomer suitable for automated oligonucleotide synthesis is obtained in a few steps. The compounds are useful for the introduction of various labels and modifications into an oligonucleotide chain. Although 2??carbamate modification is somewhat destabilizing for DNA?DNA and DNA?RNA duplexes, it is suitable for the direction of ligands into the minor groove of duplexes or at non?base?paired sites (e.g., loops and bulges) of oligonucleotides. Pyrene?modified oligonucleotide 2??carbamates show a considerable increase in fluorescence intensity upon hybridization to a complementary RNA (but not DNA).
Keywords: nucleoside; uridine carbamate; oligonucleotide modification; duplex stability; pyrene; fluorescence
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- Basic Protocol 1: Preparation of Uridine 2′‐Carbamate Phosphoramidites from Primary and Secondary Amines
- Alternate Protocol 1: Preparation of Uridine 2′‐Carbamate Phosphoramidites from Primary Amines that Require Additional Side‐Chain Protection
- Basic Protocol 2: Synthesis, Isolation, and Characterization of Oligonucleotides Containing Uridine 2′‐Carbamates
- Commentary
- Literature Cited
- Figures
- Tables
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Basic Protocol 1: Preparation of Uridine 2′‐Carbamate Phosphoramidites from Primary and Secondary Amines
Materials
Alternate Protocol 1: Preparation of Uridine 2′‐Carbamate Phosphoramidites from Primary Amines that Require Additional Side‐Chain Protection
Basic Protocol 2: Synthesis, Isolation, and Characterization of Oligonucleotides Containing Uridine 2′‐Carbamates
Materials
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Figure 4.21.1 General scheme for conversion of uridine into 2′‐carbamate 3′‐phosphoramidites (see ). For R and R1 groups, see Figure . View Image -
Figure 4.21.2 Side‐chain substituents of uridine 2′‐carbamates. R2 stands for the rest of the molecule; see Figures and . View Image -
Figure 4.21.3 Preparation of side‐chain‐protected 3′,5′‐ O ‐silylated uridine 2′‐carbamates (see ). View Image -
Figure 4.21.4 MALDI‐TOF mass spectra of 2′‐carbamate oligodeoxyribonucleotides containing two modified uridines CundefinedCCCAGGCundefinedCAAAT, where undefined is from phosphoramidites S.7d (A) , S.7e (B ), and S.7h (C ) (see Figures and and Table ). View Image -
Figure 4.21.5 Fluorescence spectra of 2′‐pyrene carbamate oligodeoxyribonucleotide CTCCCAGGCundefinedCAAAT (1) and its duplex with complementary DNA (2) and RNA (3) (see Table ). View Image
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Literature Cited
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