Abstract
The synthesis of N-((N4-(benzoyl)cytosine-1-yl)acetyl)- N -(2-Boc-aminoethyl)glycine (CBz) and the incorporation of this monomer into PNA oligomers are described. A single CBzresidue within a 10mer homopyrimidine PNA is capable of switching the preferred binding mode from a parallel to an antiparallel orientation when targeting a deoxyribonucleotide sequence at neutral pH. The resulting complex has a thermal stability equal to that of the corresponding PNA-DNA duplex, indicative of a strong destabilization of Hoogsteen strand PNA binding due to steric interference by the benzoyl moieties. Accordingly, incorporation of the CBz residue into linked PNAs (bis-PNAs) results in greatly reduced thermal stability of the formed PNA:DNA complexes. Thus, incorporation of the CBz monomer could eliminate the stability bias of triplex-forming sequences in PNA used in hybridization arrays and combinatorial library formats. Furthermore, it is shown that the benzoyl moiety does not severely interfere with Watson-Crick hydrogen bonding, thereby presenting an interesting route for novel cytosine modifications.
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- Christensen L., Fitzpatrick R., Gildea B., Petersen K. H., Hansen H. F., Koch T., Egholm M., Buchardt O., Nielsen P. E., Coull J. Solid-phase synthesis of peptide nucleic acids. J Pept Sci. 1995 May-Jun;1(3):175–183. doi: 10.1002/psc.310010304. [DOI] [PubMed] [Google Scholar]
- Egholm M., Christensen L., Dueholm K. L., Buchardt O., Coull J., Nielsen P. E. Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA. Nucleic Acids Res. 1995 Jan 25;23(2):217–222. doi: 10.1093/nar/23.2.217. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Good L., Nielsen P. E. Progress in developing PNA as a gene-targeted drug. Antisense Nucleic Acid Drug Dev. 1997 Aug;7(4):431–437. doi: 10.1089/oli.1.1997.7.431. [DOI] [PubMed] [Google Scholar]
- Hanvey J. C., Peffer N. J., Bisi J. E., Thomson S. A., Cadilla R., Josey J. A., Ricca D. J., Hassman C. F., Bonham M. A., Au K. G. Antisense and antigene properties of peptide nucleic acids. Science. 1992 Nov 27;258(5087):1481–1485. doi: 10.1126/science.1279811. [DOI] [PubMed] [Google Scholar]
- Knudsen H., Nielsen P. E. Antisense properties of duplex- and triplex-forming PNAs. Nucleic Acids Res. 1996 Feb 1;24(3):494–500. doi: 10.1093/nar/24.3.494. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Koch T., Hansen H. F., Andersen P., Larsen T., Batz H. G., Otteson K., Orum H. Improvements in automated PNA synthesis using Boc/Z monomers. J Pept Res. 1997 Jan;49(1):80–88. doi: 10.1111/j.1399-3011.1997.tb01124.x. [DOI] [PubMed] [Google Scholar]
- Lesnik E. A., Risen L. M., Driver D. A., Griffith M. C., Sprankle K., Freier S. M. Evaluation of pyrimidine PNA binding to ssDNA targets from nonequilibrium melting experiments. Nucleic Acids Res. 1997 Feb 1;25(3):568–574. doi: 10.1093/nar/25.3.568. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nielsen P. E., Egholm M., Berg R. H., Buchardt O. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science. 1991 Dec 6;254(5037):1497–1500. doi: 10.1126/science.1962210. [DOI] [PubMed] [Google Scholar]
- Nielsen P. E., Egholm M., Buchardt O. Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement. J Mol Recognit. 1994 Sep;7(3):165–170. doi: 10.1002/jmr.300070303. [DOI] [PubMed] [Google Scholar]
- Weiler J., Gausepohl H., Hauser N., Jensen O. N., Hoheisel J. D. Hybridisation based DNA screening on peptide nucleic acid (PNA) oligomer arrays. Nucleic Acids Res. 1997 Jul 15;25(14):2792–2799. doi: 10.1093/nar/25.14.2792. [DOI] [PMC free article] [PubMed] [Google Scholar]