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Affinity and selectivity of C2‐ and C5‐substituted “chiral‐box” PNA in solution and on microarrays
Author(s) -
Manicardi Alex,
Calabretta Alessandro,
Bencivenni Mariangela,
Tedeschi Tullia,
Sforza Stefano,
Corradini Roberto,
Marchelli Rosangela
Publication year - 2010
Publication title -
chirality
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.43
H-Index - 77
eISSN - 1520-636X
pISSN - 0899-0042
DOI - 10.1002/chir.20865
Subject(s) - chemistry , peptide nucleic acid , monomer , selectivity , oligonucleotide , combinatorial chemistry , dna , nucleic acid , circular dichroism , epimer , stereochemistry , crystallography , organic chemistry , biochemistry , polymer , catalysis
Two peptide nucleic acids (PNAs) containing three adjacent modified chiral monomers (chiral box) were synthesized. The chiral monomers contained either a C2‐ or a C5‐modified backbone, synthesized starting from D ‐ and L ‐arginine, respectively (2D‐ and 5L‐PNA). The C2‐modified chiral PNA was synthesized using a submonomeric strategy to avoid epimerization during solid‐phase synthesis, whereas for the C5‐derivative, the monomers were first obtained and then used in solid‐phase synthesis. The melting temperature of these PNA duplexes formed with the full‐match or with single‐mismatch DNA were measured both by UV and by CD spectroscopy and compared with the unmodified PNA. The 5L‐chiral‐box‐PNA showed the highest T m with full‐match DNA, whereas the 2D‐chiral‐box‐PNA showed the highest sequence selectivity. The PNA were spotted on microarray slides and then hybridized with Cy5‐labeled full match and mismatched oligonucleotides. The results obtained showed a signal intensity in the order achiral >2D‐chiral box >5L‐chiral box, whereas the full‐match/mismatch selectivity was higher for the 2D chiral box PNA. Chirality, 2010. © 2010 Wiley‐Liss, Inc.