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Nucleic Acids Res. 2015 Jun 23;43(11):5275-83. doi: 10.1093/nar/gkv285. Epub 2015 Apr 30.

Intermolecular 'cross-torque': the N4-cytosine propargyl residue is rotated to the 'CH'-edge as a result of Watson-Crick interaction.

Author information

1
Department of Pharmaceutical Chemistry, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, 55128 Mainz, Rhineland-Palatinate, Germany.
2
Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Baden-Wuerttemberg, Germany.
3
Institute of Organic Chemistry, University of Innsbruck, 6020 Innsbruck, Tyrol, Austria.
4
Department of Pharmaceutical Chemistry, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, 55128 Mainz, Rhineland-Palatinate, Germany mhelm@uni-mainz.de.

Abstract

Propargyl groups are attractive functional groups for labeling purposes, as they allow CuAAC-mediated bioconjugation. Their size minimally exceeds that of a methyl group, the latter being frequent in natural nucleotide modifications. To understand under which circumstances propargyl-containing oligodeoxynucleotides preserve base pairing, we focused on the exocyclic amine of cytidine. Residues attached to the exocyclic N4 may orient away from or toward the Watson-Crick face, ensuing dramatic alteration of base pairing properties. ROESY-NMR experiments suggest a uniform orientation toward the Watson-Crick face of N(4)-propargyl residues in derivatives of both deoxycytidine and 5-methyl-deoxycytidine. In oligodeoxynucleotides, however, UV-melting indicated that N(4)-propargyl-deoxycytidine undergoes standard base pairing. This implies a rotation of the propargyl moiety toward the 'CH'-edge as a result of base pairing on the Watson-Crick face. In oligonucleotides containing the corresponding 5-methyl-deoxycytidine derivative, dramatically reduced melting temperatures indicate impaired Watson-Crick base pairing. This was attributed to a steric clash of the propargyl moiety with the 5-methyl group, which prevents back rotation to the 'CH'-edge, consequently preventing Watson-Crick geometry. Our results emphasize the tendency of an opposing nucleic acid strand to mechanically rotate single N(4)-substituents to make way for Watson-Crick base pairing, providing no steric hindrance is present on the 'CH'-edge.

PMID:
25934805
PMCID:
PMC4477647
DOI:
10.1093/nar/gkv285
[Indexed for MEDLINE]
Free PMC Article

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