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Improved DNA Clamps by Stacking to Adjacent Nucleobases
Author(s) -
Fatthalla Maha I.,
Pedersen Erik B.
Publication year - 2012
Publication title -
helvetica chimica acta
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.74
H-Index - 82
eISSN - 1522-2675
pISSN - 0018-019X
DOI - 10.1002/hlca.201200130
Subject(s) - chemistry , stacking , nucleobase , linker , histone octamer , dna , nucleic acid , base pair , stereochemistry , combinatorial chemistry , organic chemistry , biochemistry , nucleosome , computer science , histone , operating system
Abstract Three or four aromatic rings interconnected by acetylene bridges form a stiff conjugated system with sufficient conformational freedom to make it useful to link together the two strands of a DNA clamp. Upon targeting a ssDNA, the conformational flexibility allows better stacking of the linker to the underlying non‐planar base triplet in the formed triplex. This type of triplexes has a substantially higher thermal melting temperature which can be further improved by inserting locked nucleic acids (LNAs) in the Hoogsteen part of the clamp. An extremely high sensitivity to mismatches is observed in an octamer triplex when placed in the middle of the sequence.