Attachment of Reporter and Conjugate Groups to DNA

Beaucage, Serge L.

doi:10.1016/b978-0-08-091283-7.00061-8

Cited by 15 publications

(13 citation statements)

References 465 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The consequences of 2′‐hydroxy modifications of RNA are demonstrated in a variety of structural studies (Griffey et al, ; Silverman and Cech, ), as well as in antisense (Cook, ) and RNA interference–mediated gene silencing experiments (Rozners, ; Beaucage, ; Watts et al, ; UNIT here). Modification of the 2′‐hydroxy function of ribonucleosides with functional groups has traditionally been performed through the 2′‐ O ‐alkylation of 5′‐ O ‐protected or 5′‐ and 3′‐ O ‐protected ribonucleosides (Cook, ; Beaucage, ). However, this reaction is either lacking the regioselectivity needed for the production of conjugates free of isomeric impurities or requires laborious protection of both the 5′‐ and 3′‐hydroxy function of ribonucleosides.…”

Section: Commentarymentioning

confidence: 99%

“…The 2′‐hydroxyl function of ribonucleosides is an attractive target for conjugation reactions; numerous examples of ribonucleoside 2′‐conjugates have been described in various structural studies (Griffey et al, ; Silverman and Cech, ), as well as in therapeutic and diagnostic applications (Cook, ; Beaucage, ). Although the synthesis of ribonucleoside 2′‐conjugates has traditionally been carried out through alkylation of the 2′‐hydroxyl of ribonucleosides with functional groups (Cook, ; Beaucage, ), the regioselectivity of this method is poor and thus results in the production of conjugates that are not free of isomeric impurities. This unit provides an alternate strategy to the preparation of ribonucleosides 2′‐conjugates.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Convenient and Efficient Approach to the Permanent or Reversible Conjugation of RNA and DNA Sequences with Functional Groups

Cieślak

Ausín

Grajkowski

et al. 2012

CP Nucleic Acid Chemistry

Self Cite

View full text Add to dashboard Cite

The conversion of 3',5'-disilylated 2'-O-(methylthiomethyl)ribonucleosides to 2'-O-(phthalimidooxymethyl)ribonucleosides is achieved in yields of 66% to 94%. Desilylation and dephtalimidation of these ribonucleosides by treatment with NH(4)F in MeOH produce 2'-O-aminooxymethylated ribonucleosides, which are efficient in producing stable and yet reversible 2'-conjugates upon reaction with 1-pyrenecarboxaldehyde. Exposure of 2'-pyrenylated ribonucleosides to 0.5 M tetra-n-butylammonium fluoride (TBAF) in THF or DMSO results in the cleavage of their iminoether functions to give the native ribonucleosides along with an innocuous nitrile side product. Conversely, the reaction of 2'-O-(aminooxymethyl)uridine with 5-cholesten-3-one leads to a permanent uridine 2'-conjugate, which is left unreacted when treated with TBAF. The versatility and uniqueness of 2'-O-(aminooxymethyl)ribonucleosides is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2'-conjugate into an RNA sequence. Furthermore, the conjugation of 2'-O-(aminooxymethyl)ribonucleosides with various aldehydes, including those generated from their acetals, is also presented. The preparation of 5'-O-(aminooxymethyl)thymidine is also achieved, albeit in modest yields, from the conversion of 5'-O-methylthiomethyl-3'-O-(levulinyl)thymidine to 5'-O-phthalimidooxymethyl-3'-O-(levuliny)lthymidine followed by hydrazinolysis of both 5'-phthalimido and 3'-levulinyl groups. Pyrenylation of the 5'-O-(aminooxymethyl)deoxyribonucleoside also provides a reversible 5'-conjugate that is sensitive to TBAF, thereby further demonstrating the usefulness of 5'-O-(aminooxymethyl)deoxyribonucleosides for permanent or reversible modification of DNA sequences. Curr. Protoc. Nucleic Acid Chem. 50:4.52.1-4.52.36. © 2012 by John Wiley & Sons, Inc.

show abstract

Section: Commentarymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Convenient and Efficient Approach to the Permanent or Reversible Conjugation of RNA and DNA Sequences with Functional Groups

Cieślak

Ausín

Grajkowski

et al. 2012

CP Nucleic Acid Chemistry

Self Cite

View full text Add to dashboard Cite

show abstract

“…Since DNA synthesizers evolved to standard equipment, not only the production of relative large quantities of nonmodified DNA is feasible but also the generation of chemical modified DNA, Many variations of protecting groups and synthesis conditions allow the incorporation of a broad range of modifications. 16 The most straight-forward way is labelling after DNA synthesis at the 5' end and is most often used for attaching dyes for diagnostic applications, Some recent examples include phosphoramidite reagents for the attachment of fluorescein,23 tetramethyl rhodamine 24 and cyanine dyes,25 For the sensitive identification of oligonucleotides by mass spectrometry mass tags have been recently invented as 5' labels.2 6 But also modifiers for the 3' end as modified solid support have been developed and a range of fluorescent dyes, quenchers and affinity tags like biotin are commercially available. Widely used in real-time PCR and other diagnostic applications are both 5' and 3' labelled probes.…”

Section: Chemical Synthesis Of Functionalized Dnamentioning

confidence: 99%

Novel strategies for the site-specific covalent labelling of nucleic acids

2008

View full text Add to dashboard Cite

To broaden the scope of applications in DNA nano- and biotechnology, material science, diagnostics and molecular recognition the functionalization of DNA is of utmost importance. In the last decade many new methods have been developed to achieve this goal. Apart from the direct chemical synthesis of modified DNA by automated phosphoramidite chemistry incorporation of labelled triphosphates and the post-synthetic labelling approach evolved as valuable methods. New bioorthogonal reactions as Diels-Alder, click and Staudinger ligations pushed forward the post-synthetic approach as new insights into DNA polymerase substrate specificity allowed generation and amplification of labelled DNA strands. These novel developments are summarized herein.

show abstract

“…Actually, 2′-hydroxy modifications are known to impart high binding affinity to RNA sequences, increased lipophilicity, enhanced chemical stability and resistance to nucleases ( 1 , 2 , 5 ). The 2′-hydroxyl group of ribonucleosides is also an attractive function for conjugation reactions; there are numerous examples of ribonucleoside 2′-conjugates that have been reported in various structural studies ( 6 , 7 ) as well as in therapeutic and diagnostic applications ( 8 , 9 ). Although 2′- O -alkylation of ribonucleosides with functional groups has often been employed in the synthesis of ribonucleoside 2′-conjugates ( 8 , 9 ), this method is generally lacking the regioselectivity needed for the production of conjugates free of isomeric impurities.…”

Section: Introductionmentioning

confidence: 99%

Permanent or reversible conjugation of 2′-O- or 5′-O-aminooxymethylated nucleosides with functional groups as a convenient and efficient approach to the modification of RNA and DNA sequences

Cieślak

Grajkowski

Ausín

et al. 2011

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

2′-O-Aminooxymethyl ribonucleosides are prepared from their 3′,5′-disilylated 2′-O-phthalimidooxymethyl derivatives by treatment with NH4F in MeOH. The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2′-conjugates in yields of 69–82%. Indeed, exposure of these conjugates to 0.5 M tetra-n-butylammonium fluoride (TBAF) in THF results in the cleavage of their iminoether functions to give the native ribonucleosides along with the innocuous nitrile side product. Conversely, the reaction of 5-cholesten-3-one or dansyl chloride with 2′-O-aminooxymethyl uridine provides permanent uridine 2′-conjugates, which are left essentially intact upon treatment with TBAF. Alternatively, 5′-O-aminooxymethyl thymidine is prepared by hydrazinolysis of its 3′-O-levulinyl-5′-O-phthalimidooxymethyl precursor. Pyrenylation of 5′-O-aminooxymethyl thymidine and the sensitivity of the 5′-conjugate to TBAF further exemplify the usefulness of this nucleoside for modifying DNA sequences either permanently or reversibly. Although the versatility and uniqueness of 2′-O-aminooxymethyl ribonucleosides in the preparation of modified RNA sequences is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2′-conjugate into an RNA sequence, the conjugation of 2′-O-aminooxymethyl ribonucleosides with aldehydes, including those generated from their acetals, provides reversible 2′-O-protected ribonucleosides for potential applications in the solid-phase synthesis of native RNA sequences. The synthesis of a chimeric polyuridylic acid is presented as an exemplary model.

show abstract

Attachment of Reporter and Conjugate Groups to DNA

Cited by 15 publications

References 465 publications

Convenient and Efficient Approach to the Permanent or Reversible Conjugation of RNA and DNA Sequences with Functional Groups

Convenient and Efficient Approach to the Permanent or Reversible Conjugation of RNA and DNA Sequences with Functional Groups

Novel strategies for the site-specific covalent labelling of nucleic acids

Permanent or reversible conjugation of 2′-O- or 5′-O-aminooxymethylated nucleosides with functional groups as a convenient and efficient approach to the modification of RNA and DNA sequences

Contact Info

Product

Resources

About