2′,2′-Ligation demonstrates the thermal dependence of DNA-directed positional control

Yu Liu, Ruojie Sha, Risheng Wang, Liang Ding, James Canary, Nadrian Seeman

Research output: Contribution to journalArticle

Abstract

An oligodeoxynucleotide (ODN) containing a 2′-aminoalkylmercaptouridine was ligated chemically with another ODN containing a 2′-carboxyalkylmercaptouridine to produce a 2′,2′-amide linked conjugate. Templation by a DNA hairpin resulted in ligation yields of >95%. At room temperature, similar yields were obtained for amide ligations between pendent nucleotides located adjacent to each other or separated by three nucleotides. However, at 4 °C, ligation was vastly favored for the case where the pendent amine and carboxylate were attached to adjacent residues (i.e., at the 3′- and 5′-terminus of the two ODNs). No reaction was observed to occur either at 4 °C or at room temperature between pendent nucleotides separated by nine nucleotides. Denaturing gel electrophoresis, MALDI-TOF MS, and full nuclease digestion coupled with LC-MS were used to characterize the reaction products.

Original languageEnglish (US)
Pages (from-to)8417-8422
Number of pages6
JournalTetrahedron
Volume64
Issue number36
DOIs
StatePublished - Sep 1 2008

Fingerprint

Ligation
Nucleotides
Hot Temperature
Oligodeoxyribonucleotides
DNA
Amides
Temperature
Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
Electrophoresis
Reaction products
Amines
Digestion
Gels

Keywords

  • Nucleic acids
  • Positional synthesis
  • Reaction regioselectivity
  • Templated chemical ligation
  • Thermal control

ASJC Scopus subject areas

  • Biochemistry
  • Organic Chemistry
  • Drug Discovery

Cite this

2′,2′-Ligation demonstrates the thermal dependence of DNA-directed positional control. / Liu, Yu; Sha, Ruojie; Wang, Risheng; Ding, Liang; Canary, James; Seeman, Nadrian.

In: Tetrahedron, Vol. 64, No. 36, 01.09.2008, p. 8417-8422.

Research output: Contribution to journalArticle

Liu, Yu ; Sha, Ruojie ; Wang, Risheng ; Ding, Liang ; Canary, James ; Seeman, Nadrian. / 2′,2′-Ligation demonstrates the thermal dependence of DNA-directed positional control. In: Tetrahedron. 2008 ; Vol. 64, No. 36. pp. 8417-8422.
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