• Abstract
• Table of Contents
• Figures
• Literature Cited

Abstract

Reporter and conjugate groups can be added directly to the 5? terminus of oligonucleotides by appropriate modification. Conjugate groups can be used to increase the affinity of complementary strands, induce irreversible modification of target sequences, or enable sequences to recognize and permeate target cell membranes. This overview discusses the 5? modifications that can be used and strategies for the covalent attachment of ligands to the modified oligonucleotides. Step?by?step protocols for attachment of conjugate groups are given elsewhere in the series.

        GO TO THE FULL PROTOCOL: PDF or HTML at Wiley Online Library Table of Contents

• Synthesis
• Characterization
• Properties
• Conclusion
• Literature Cited
• Figures

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GO TO THE FULL PROTOCOL: PDF or HTML at Wiley Online Library Figures

• Figure 4.2.1 Functionalization of oligodeoxynucleotides via phosphite and phosphotriester derivatives. Abbreviations used in figures: B, nucleic base; B′, protected base; DMF, dimethylformamide; DMSO, dimethyl sulfoxide; DMTr, 4,4′‐dimethoxytrityl; Fmoc, 9‐fluorenylmethyl; L, linker; MMTr, monomethoxytrityl; Px,9‐phenylxanthen‐9‐yl(pixyl); R, oligodeoxynucleotide; R′, protected oligonucleotide; TCEP, tris‐(2‐carboxyethyl)phosphine; Tr, trityl; Z, functional group or ligand; Z′, protected functional group or ligand.

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• Figure 4.2.2 Incorporation of 5′‐phosphate and 5′‐phosphorothioate groups into oligodeoxynucleotides. Abbreviations: Thy, thymin‐l‐yl. See Figure for additional definitions of functional group abbreviations.

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• Figure 4.2.3 Incorporation of 5′‐thiol groups into oligodeoxynucleotides. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.4 Incorporation of 5′‐amino groups into oligodeoxynucleotides. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.5 Incorporation of 5′‐carboxyl groups into oligodeoxynucleotides. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.6 Some structures involved in the incorporation of 5′‐diol groups into oligodeoxynucleotides. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.7 Heterobifunctional reagents for the conversion of one oligodeoxynucleotide 5′‐functional group to another.

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• Figure 4.2.8 Modification of oligonucleotides via 5′‐terminal phosphate groups. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.9 Conjugation of ligands to oligonucleotides via 5′‐terminal phosphate groups. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.10 Attachment of ligands to oligonucleotides via 5′‐terminal phosphate groups. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.11 Conjugation of functional groups into oligonucleotides via 5′‐terminal phosphorothioate groups. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.12 Further structures involved in the modification of oligonucleotides via 5′‐terminal phosphorothioate groups. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.13 Conjugation of ligands to oligonucleotides via 5′‐thiol groups. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.14 Incorporation of conjugate groups into oligonucleotides via 5′‐thiol groups. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.15 Attachment of reporter and conjugate groups to oligonucleotides via 5′‐amino groups. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.16 Conjugation of functional groups to oligonucleotides via 5′‐amino groups. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.17 Introduction of functional groups to oligonucleotides via 5′‐amino groups. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.18 Conjugation of functional groups to oligonucleotides via 5′‐carboxyl groups. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.19 Attachment of functional groups to oligonucleotides via 5′‐terminal cis diols. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.20 Direct addition of ligands to the 5′ ends of oligonucleotides by the phosphotriester coupling method. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.21 Direct addition of ligands to the 5′ end of oligonucleotides by the phosphoramidite coupling method. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.22 Additional examples of direct addition of ligands to the 5′ ends of oligonucleotides by the phosphoramidite coupling method. See Figure for definitions of functional group abbreviations.

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• Figure 4.2.23 Direct addition of ligands to the 5′ terminus of oligonucleotides to permit sensitive fluorescence detection. Figure for definitions of functional group abbreviations.

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• Figure 4.2.24 An additional example of direct addition of ligands to the 5′ ends of oligonucleotides to provide fluorescence detection.

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• Figure 4.2.25 Conjugation of two third oligonucleotide strands for triple helical formation with double‐stranded DNA targets via alternate strand recognition. See Figure for definitions of functional group abbreviations.

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