DNA Crosslinking and Ligation

Crosslinking is used to stabilize the interaction of two weakly bound biomolecules using covalent bonds. Examples of the use of crosslinking include affinity labeling of DNA- and RNA-binding proteins, inter-strand crosslinks between DNA and/or RNA, and capturing any molecule’s approach to DNA or RNA. Crosslinking may be initiated by a variety of chemical reactions, for example, disulfide formation, but the predominant procedure is photo-induced crosslinking.

Ligation may be considered to be a subset of crosslinking.  In non-enzymatic ligation of oligonucleotides, the 5'-terminus of the oligonucleotide to be ligated is modified as a 5'-iodo group. The 3'-terminus to be ligated is modified as a 3'-thiophosphate, prepared by sulfurizing in the first cycle using 3'-phosphate CPG.  Chemical ligation occurs spontaneously by reaction of the thiophosphate to displace the iodo group using a short "splint" oligonucleotide complementary to the ends to bring them together.  

A possible alternative approach to the chemical synthesis of large DNA strands is to join together synthetic oligonucleotides by chemical methods. Recently click ligation by the copper-catalyzed azide-alkyne cycloaddition (CuAAC) has been shown to facilitate this process, and a biocompatible triazole linkage has been developed that mimics a normal phosphodiester group.  This requires an oligonucleotide with a 5’-azide and another with a 3’-propargyl group. The two oligonucleotides can be joined together by splint mediated ligation to produce a triazole linkage at the ligation site.

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  • Psoralen C2 Phosphoramidite
    Psoralen C2 Phosphoramidite (10-1982)
    Catalog #: 10-1982  |  CAS #: 126221-83-8
    Formal Name: 2-[4'-(hydroxymethyl)-4,5',8-trimethylpsoralen]-ethyl-1-O-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite
  • Psoralen C6 Phosphoramidite
    Psoralen C6 Phosphoramidite (10-1983)
    Catalog #: 10-1983  |  CAS #: 518046-08-7
    Formal Name: 6-[4'-(Hydroxymethyl)-4,5',8-trimethylpsoralen]-hexyl-1-O-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite
  • 3-Cyanovinylcarbazole Phosphoramidite (CNVK)
    3-Cyanovinylcarbazole Phosphoramidite (CNVK) (10-4960)
    Catalog #: 10-4960
    Formal Name:

    5'-O-(4,4'-Dimethoxytrityl)-1'-(3-cyanovinylcarbazol-9-yl)-2'-deoxy-β-D-ribofuranosyl- 3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite

  • 8-Br-dA-CE Phosphoramidite
    8-Br-dA-CE Phosphoramidite (10-1007)
    Catalog #: 10-1007  |  CAS #: 207906-54-5
    Formal Name: 5'-Dimethoxytrityl-N6-dimethylaminomethylidene-8-bromo-2'-deoxyAdenosine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
  • 8-Br-dG-CE Phosphoramidite
    8-Br-dG-CE Phosphoramidite (10-1027)
    Catalog #: 10-1027  |  CAS #: 198080-37-4
    Formal Name: 5'-Dimethoxytrityl-N2-dimethylaminomethylidene-8-bromo-2'-deoxyGuanosine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
  • 4-Thio-dT-CE Phosphoramidite
    4-Thio-dT-CE Phosphoramidite (10-1034)
    Catalog #: 10-1034  |  CAS #: 1290537-73-3
    Formal Name: 5'-Dimethoxytrityl-2'-deoxy-4-(2-cyanoethylthio)-Thymidine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
  • 2-Thio-dT-CE Phosphoramidite
    2-Thio-dT-CE Phosphoramidite (10-1036)
    Catalog #: 10-1036  |  CAS #: 156783-23-2
    Formal Name: 5'-Dimethoxytrityl-(N3/O4-toluoyl)-2'-deoxy-2-thioThymidine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
  • 6-thio-dG-CE Phosphoramidite
    6-thio-dG-CE Phosphoramidite (10-1072)
    Catalog #: 10-1072  |  CAS #: 146691-59-0
    Formal Name: 5'-Dimethoxytrityl-N2-trifluoroacetyl-2'-deoxy-6-(2-cyanoethyl)thio-Guanosine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
  • 5-Br-dC-CE Phosphoramidite
    5-Br-dC-CE Phosphoramidite (10-1080)
    Catalog #: 10-1080  |  CAS #: 178925-43-4
    Formal Name: 5'-Dimethoxytrityl-N-benzoyl-5-bromo-2'-deoxyCytidine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
  • 5-I-dC-CE Phosphoramidite
    5-I-dC-CE Phosphoramidite (10-1081)
    Catalog #: 10-1081  |  CAS #: 178925-44-5
    Formal Name: 5'-Dimethoxytrityl-N-benzoyl-5-iodo-2'-deoxyCytidine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
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15 Product Results