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Sequence‐Dependent Duplex Stabilization upon Formation of a Metal‐Mediated Base Pair
Author(s) -
Scharf Philipp,
Jash Biswarup,
Kuriappan Jissy A.,
Waller Mark P.,
Müller Jens
Publication year - 2016
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.201503405
Subject(s) - base pair , duplex (building) , oligonucleotide , chemistry , dna , stereochemistry , nucleoside , context (archaeology) , sequence (biology) , crystallography , biology , biochemistry , paleontology
An artificial nucleoside surrogate with 1 H ‐imidazo[4,5‐ f ][1,10]phenanthroline ( P ) acting as an aglycone has been introduced into DNA oligonucleotide duplexes. This nucleoside surrogate can act as a bidentate ligand, and so is useful in the context of metal‐mediated base pairs. Several duplexes involving a hetero base pair with an imidazole nucleoside have been investigated. The stability of DNA duplexes incorporating the respective Ag I ‐mediated base pairs strongly depends on the sequence context. Quantum mechanical/molecular mechanical (QM/MM) calculations have been performed in order to gain insight into the factors determining this sequence dependence. The results indicated that, in addition to the stabilizing effect that results from the formation of coordinative bonds, destabilizing effects may occur when the artificial base pair does not fit optimally into the surrounding B‐DNA duplex.