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Specific Purine‐Purine Base Pairing in Linear Alanyl‐Peptide Nucleic Acids
Author(s) -
Hoffmann Markus F. H.,
Brückner Arndt M.,
Hupp Thomas,
Engels Bernd,
Diederichsen Ulf
Publication year - 2000
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 - 10.1002/1522-2675(20000906)83:9<2580::aid-hlca2580>3.0.co;2-6
Subject(s) - chemistry , nucleobase , pairing , tautomer , xanthine , base pair , stereochemistry , guanine , nucleic acid , purine , stacking , peptide nucleic acid , nucleotide , dna , biochemistry , quantum mechanics , organic chemistry , physics , superconductivity , gene , enzyme
Purine‐purine base pairing with guanine, isoguanine, 2,6‐diaminopurine, and xanthine is investigated within the topology of alanyl‐PNA. Alanyl‐PNA is based on a regular peptide backbone with alternating configuration of the amino acids. The nucleobases are covalently linked as side chains. Their distance in peptides with β ‐sheet conformation is similar to the favored base‐pair stacking distance. Therefore, alanyl‐PNA provides self‐pairing linear double‐strands. The linear double‐strand topology does not restrict base‐pair size and geometry. The favored base pairs are formed mostly dependent on recognition by H‐bonding. The synthesis of the nucleo‐amino acids with unnatural nucleobases and their oligomerization is described. Hexamers and a tetramer based on 2,6‐diaminopurine‐xanthine and guanine‐isoguanine base pairs were observed with very high stabilities. For xanthine‐xanthine self‐pairing, an unusual tridentate reverse Watson‐Crick pairing mode is indicated, that is only possible with xanthines pairing in different tautomeric forms. To investigate the nature of xanthine‐xanthine base pairs in more detail, quantum‐chemical calculations were performed. They establish the easier tautomerization of xanthine compared to uracil and indicate that, in the AO basis‐set limit, the tridentate pairing mode with mixed tautomers is favored.