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Chapter 4 Table 4-1. PNA sequences and melting temperatures of the PNA:DNA antiparallel fullmatch/mismatch duplexes in phospate buffer (pH=7) at a 5µm concentration for each strand PNA Sequence [a] Tm (°C) PNA/DNA Fullmatch [b] Tm (°C) PNA/DNA Mismatch [b] ΔTm (°C) 1 2 3 4 H(AEEA) 2 GCCGCA (2D,5LArg) CACGT-NH 2 78 (with 1’) 61 (with 3’) 17 H-(AEEA) 2 CAGGCA (2D,5L-Arg) CTTCT-NH 2 69 (with 2’) 50 (with 4’) 19 H(AEEA) 2 GCCGCG (2D,5LArg) CACGT- NH 2 85 (with 3’) 69 (with 1’) 16 H-(AEEA) 2 CAGGCG (2D,5L-Arg) CTTCT-NH 2 75 (with 4’) 60 (with 2’) 15 [a] The chiral monomer corresponding to the SNP position is underlined in bold [b] Oligonucleotide sequences (SNP base is underlined in bold): 1’: 5’-ACGTGTGCGGC-3’, 2’: 5’- AGAAGTGCCTG-3’,3’: 5’-ACGTGCGCGGC-3’, 4’: 5’-AGAAGCGCCTG-3’ PNAs were synthesized by using common SPPS protocol based on the Boc strategy for the standard monomers, combined to the Boc submonomeric strategy for the chiral monomer only, since better suited to preserve the optical purity at the 2 position 28 and also because one single submonomer can be used for the synthesis of PNAs bearing different nucleobases on the chiral residue. The submonomer was prepared, as reported in Chapter 3, starting from the commercial D- and L-Boc-Arginine(Tos)-OH. Boc-L-Arg(Tos)-OH was transformed in the corresponding Weinreb amide and then reduced to the aldehyde. Boc-D-Arg(Tos)-OH was transformed in the methyl ester and Boc deprotected. The PNA backbone was then synthesized by reductive amination of D-Arg(Tos)-OMe with the Boc-L-Arg(Tos) aldehyde. The methyl ester was hydrolyzed and the secondary amine was protected by the introduction of a Fmoc group. According to previously reported procedures 15 , the chiral submonomers units were inserted by manual coupling with the HATU/DIEA protocol and, after Fmoc deprotection, the nucleobase residues were introduced by a double coupling with DIC/DhBTOH. All the PNA oligomers were purified by RP-HPLC and characterized by ESI-mass spectrometry (Figure 4-2). 78
Arg-PNA Microarrays Figure 4-2: HPLC profiles and mass spectra of PNAs 1-4 79
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2.4.4 Fluorescence measurements ...
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Chapter 6 The double nature of Pept
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Preface In Chapter 2 a particular t
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Chapter 1 PNAs: From birth to adult
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PNAs: from birth to adulthood one,
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PNAs: from birth to adulthood betwe
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PNAs: from birth to adulthood explo
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PNAs: from birth to adulthood well,
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PNAs: from birth to adulthood + Res
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PNAs: from birth to adulthood repet
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PNAs: from birth to adulthood 1.6 M
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PNAs: from birth to adulthood amino
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PNAs: from birth to adulthood Cycli
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PNAs: from birth to adulthood DNA a
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Chapter 6 12 B. P. Gangamani, V. A.
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Contributions Publications includin
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