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Peter E. Nielsen - One of the best experts on this subject based on the ideXlab platform.

  • potent antibacterial antisense Peptide Peptide Nucleic Acid conjugates against pseudomonas aeruginosa
    Nucleic Acid Therapeutics, 2012
    Co-Authors: Anubrata Ghosal, Peter E. Nielsen
    Abstract:

    Pseudomonas aeruginosa is an opportunistic pathogen causing severe infections in hospital settings, especially with immune compromised patients, and the increasing prevalence of multidrug resistant strains urges search for new drugs with novel mechanisms of action. In this study we introduce antisense Peptide–Peptide Nucleic Acid (PNA) conjugates as antibacterial agents against P. aeruginosa. We have designed and optimized antisense Peptide–PNA conjugates targeting the translation initiation region of the ftsZ gene (an essential bacterial gene involved in cell division) or the acpP gene (an essential bacterial gene involved in fatty Acid synthesis) of P. aeruginosa (PA01) and characterized these compounds according to their antimicrobial activity and mode of action. Four antisense PNA oligomers conjugated to the H-(R-Ahx-R)4-Ahx-βala or the H-(R-Ahx)6-βala Peptide exhibited complete growth inhibition of P. aeruginosa strains PA01, PA14, and LESB58 at 1–2 μM concentrations without any indication of bacteri...

  • Evaluation of Transfection Protocols for Unmodified and Modified Peptide Nucleic Acid (PNA) Oligomers
    Oligonucleotides, 2006
    Co-Authors: Frank Winther Rasmussen, Peter E. Nielsen, Nadia Bendifallah, Vladimir Zachar, Takehiko Shiraishi, Trine Fink, Peter Ebbesen, Uffe Koppelhus
    Abstract:

    We have compared the efficacy of different transfection protocols reported for Peptide Nucleic Acid (PNA) oligomers. A precise evaluation of uptake efficacy was achieved by using a positive readout assay based on the ability of a PNA oligomer to correct aberrant splicing of a recombinant luciferase gene. The study comprised transfection of PNA conjugated to acridine, adamantyl, decanoic Acid, and porphyrine (acr-PNA, ada-PNA, deca-PNA, and por-RNA, respectively) and unmodified PNA partially hybridized to a DNA oligomer (PNA/DNA cotransfection). Furthermore, the effect of conjugation to a nuclear localization signal (NLS) was evaluated as part of the PNA/DNA cotransfection protocol. Transfection of the tested PNAs was systematically optimized. PNA/DNA cotransfection was found to produce the highest luciferase activity, but only after careful selection of the DNA oligonucleotide. Both a cationic lipid, Lipofectamine, and a nonliposomal cationic polymer, polyethylenimine (PEI, ExGen 500), were efficient tran...

  • RNA Targeting Using Peptide Nucleic Acid
    Methods of Molecular Biology, 2006
    Co-Authors: Peter E. Nielsen
    Abstract:

    The efforts towards Peptide Nucleic Acid (PNA) drug discovery using cellular RNAs as molecular targets is briefly reviewed, with special emphasis on recent developments. Special attention is given to cellular delivery in vivo bioavailability and the possibilities of using PNA oligomers to (re)direct alternative splicing of pre-messenger (m)RNA.

  • Gene targeting using Peptide Nucleic Acid.
    Methods in molecular biology (Clifton N.J.), 2005
    Co-Authors: Peter E. Nielsen
    Abstract:

    A brief overview of the properties of the deoxyriboNucleic Acid mimic Peptide Nucleic Acid (PNA) is given, and the recent progress in cellular delivery of PNA and of using PNA oligomers for antisense and antigene gene targeting is presented.

  • Antisense properties of Peptide Nucleic Acid
    Methods in Enzymology, 2004
    Co-Authors: Peter E. Nielsen
    Abstract:

    The hybridization properties of Peptide Nucleic Acid (PNA) combined with its ease of synthesis and high chemical and biological stability rapidly made this molecule a very attractive lead compound for the development of antisense gene therapeutic drugs.

Robert H. E. Hudson - One of the best experts on this subject based on the ideXlab platform.

  • A Fmoc/Boc pseudoisocytosine monomer for Peptide Nucleic Acid synthesis
    Canadian Journal of Chemistry, 2008
    Co-Authors: Filip Wojciechowski, Robert H. E. Hudson
    Abstract:

    The synthesis of N-[2-(fluorenylmethoxycarbonyl)aminoethyl]-N-[(2-N-(tert-butoxycarbonyl)isocytosin-5-yl)acetyl]glycine Peptide Nucleic Acid monomer is described. The N-tert-butoxycarbonyl protected monomer is compatible with commercially available monomers designed for the Fmoc-oligomerization strategy and is deprotected under mild Acidolysis conditions.Key words: PNA, polyamide, pseudoisocytosine, J-base, triplex.

  • fluorescence and hybridization properties of Peptide Nucleic Acid containing a substituted phenylpyrrolocytosine designed to engage guanine with an additional h bond
    Journal of the American Chemical Society, 2008
    Co-Authors: Filip Wojciechowski, Robert H. E. Hudson
    Abstract:

    A new pyrrolocytosine derivative has been designed to selectively interact with guanine and has been evaluated in Peptide Nucleic Acid where it imparts increased selective binding affinity for complementary oligonucleotides. The modified nucleobase also possesses an exceptionally high fluorescence quantum yield that is responsive to hybridization.

  • hydrophilic modifications in Peptide Nucleic Acid synthesis and properties of pna possessing 5 hydroxymethyluracil and 5 hydroxymethylcytosine
    Canadian Journal of Chemistry, 2007
    Co-Authors: Robert H. E. Hudson, Filip Wojciechowski
    Abstract:

    We have investigated the chemistry for the incorporation of C5-hydroxymethyl-uracil and -cytosine in Peptide Nucleic Acid (PNA) and the subsequent effect of this modification on PNA hybridization behavior. Largely based on literature precedent, we prepared a Peptide Nucleic Acid monomer, possessing 5-hydroxymethyuracil, which was compatible with Fmoc-based oligoPeptide synthesis. An improved, large-scale synthesis of 5-hydroxymethylcytosine was developed, as a starting point for the synthesis of a monomer containing this nucleobase. In each case, the hydroxyl group was blocked as a t-butyldiphenylsilyl ether, and the exocyclic amino group of cytosine was additionally blocked with the benzoyl-group. The modified monomers were incorporated into isolated positions in the oligomer sequence using standard protocols. The modified oligomers showed that the 5-hydroxymethyl group is compatible with triplex and duplex formation.Key words: Peptide Nucleic Acid, hydroxymethyluracil, hydroxymethylcytosine, modified nu...

  • Hydrophilic modifications in Peptide Nucleic Acid — Synthesis and properties of PNA possessing 5-hydroxymethyluracil and 5-hydroxymethylcytosine
    Canadian Journal of Chemistry, 2007
    Co-Authors: Robert H. E. Hudson, Filip Wojciechowski
    Abstract:

    We have investigated the chemistry for the incorporation of C5-hydroxymethyl-uracil and -cytosine in Peptide Nucleic Acid (PNA) and the subsequent effect of this modification on PNA hybridization behavior. Largely based on literature precedent, we prepared a Peptide Nucleic Acid monomer, possessing 5-hydroxymethyuracil, which was compatible with Fmoc-based oligoPeptide synthesis. An improved, large-scale synthesis of 5-hydroxymethylcytosine was developed, as a starting point for the synthesis of a monomer containing this nucleobase. In each case, the hydroxyl group was blocked as a t-butyldiphenylsilyl ether, and the exocyclic amino group of cytosine was additionally blocked with the benzoyl-group. The modified monomers were incorporated into isolated positions in the oligomer sequence using standard protocols. The modified oligomers showed that the 5-hydroxymethyl group is compatible with triplex and duplex formation.Key words: Peptide Nucleic Acid, hydroxymethyluracil, hydroxymethylcytosine, modified nu...

  • The detrimental effect of orotic Acid substitution in the Peptide Nucleic Acid strand on the stability of PNA2:NA triple helices
    Canadian Journal of Chemistry, 2005
    Co-Authors: Robert H. E. Hudson, Filip Wojciechowski
    Abstract:

    We have investigated the incorporation of C6 derivatives of uracil into polypyrimidine Peptide Nucleic Acid oligomers. Starting with uracil-6-carboxylic Acid (orotic Acid), a Peptide Nucleic Acid monomer compatible with Fmoc-based synthesis was prepared. This monomer then served as a convertible nucleobase whereupon treatment of the resin-bound methyl orotate containing hexamers with hydroxide or amines cleanly converted the ester to an orotic Acid or orotamide-containing Peptide Nucleic Acid. Peptide Nucleic Acid hexamers containing the C6-modified nucleobase hybridized to both poly(riboadenylic Acid) and poly(deoxyriboadenylic Acid) via triplex formation. Complexes formed with poly(riboadenylic Acid) were more stable than those formed with poly(dexoyriboadenylic Acid), as measured by temperature-dependent UV spectroscopy. However, both of these complexes were destabilized relative to the complexes formed by an unmodified Peptide Nucleic Acid oligomers. Internal or doubly substituted hexamers are destabi...

Filip Wojciechowski - One of the best experts on this subject based on the ideXlab platform.

  • A Fmoc/Boc pseudoisocytosine monomer for Peptide Nucleic Acid synthesis
    Canadian Journal of Chemistry, 2008
    Co-Authors: Filip Wojciechowski, Robert H. E. Hudson
    Abstract:

    The synthesis of N-[2-(fluorenylmethoxycarbonyl)aminoethyl]-N-[(2-N-(tert-butoxycarbonyl)isocytosin-5-yl)acetyl]glycine Peptide Nucleic Acid monomer is described. The N-tert-butoxycarbonyl protected monomer is compatible with commercially available monomers designed for the Fmoc-oligomerization strategy and is deprotected under mild Acidolysis conditions.Key words: PNA, polyamide, pseudoisocytosine, J-base, triplex.

  • fluorescence and hybridization properties of Peptide Nucleic Acid containing a substituted phenylpyrrolocytosine designed to engage guanine with an additional h bond
    Journal of the American Chemical Society, 2008
    Co-Authors: Filip Wojciechowski, Robert H. E. Hudson
    Abstract:

    A new pyrrolocytosine derivative has been designed to selectively interact with guanine and has been evaluated in Peptide Nucleic Acid where it imparts increased selective binding affinity for complementary oligonucleotides. The modified nucleobase also possesses an exceptionally high fluorescence quantum yield that is responsive to hybridization.

  • hydrophilic modifications in Peptide Nucleic Acid synthesis and properties of pna possessing 5 hydroxymethyluracil and 5 hydroxymethylcytosine
    Canadian Journal of Chemistry, 2007
    Co-Authors: Robert H. E. Hudson, Filip Wojciechowski
    Abstract:

    We have investigated the chemistry for the incorporation of C5-hydroxymethyl-uracil and -cytosine in Peptide Nucleic Acid (PNA) and the subsequent effect of this modification on PNA hybridization behavior. Largely based on literature precedent, we prepared a Peptide Nucleic Acid monomer, possessing 5-hydroxymethyuracil, which was compatible with Fmoc-based oligoPeptide synthesis. An improved, large-scale synthesis of 5-hydroxymethylcytosine was developed, as a starting point for the synthesis of a monomer containing this nucleobase. In each case, the hydroxyl group was blocked as a t-butyldiphenylsilyl ether, and the exocyclic amino group of cytosine was additionally blocked with the benzoyl-group. The modified monomers were incorporated into isolated positions in the oligomer sequence using standard protocols. The modified oligomers showed that the 5-hydroxymethyl group is compatible with triplex and duplex formation.Key words: Peptide Nucleic Acid, hydroxymethyluracil, hydroxymethylcytosine, modified nu...

  • Hydrophilic modifications in Peptide Nucleic Acid — Synthesis and properties of PNA possessing 5-hydroxymethyluracil and 5-hydroxymethylcytosine
    Canadian Journal of Chemistry, 2007
    Co-Authors: Robert H. E. Hudson, Filip Wojciechowski
    Abstract:

    We have investigated the chemistry for the incorporation of C5-hydroxymethyl-uracil and -cytosine in Peptide Nucleic Acid (PNA) and the subsequent effect of this modification on PNA hybridization behavior. Largely based on literature precedent, we prepared a Peptide Nucleic Acid monomer, possessing 5-hydroxymethyuracil, which was compatible with Fmoc-based oligoPeptide synthesis. An improved, large-scale synthesis of 5-hydroxymethylcytosine was developed, as a starting point for the synthesis of a monomer containing this nucleobase. In each case, the hydroxyl group was blocked as a t-butyldiphenylsilyl ether, and the exocyclic amino group of cytosine was additionally blocked with the benzoyl-group. The modified monomers were incorporated into isolated positions in the oligomer sequence using standard protocols. The modified oligomers showed that the 5-hydroxymethyl group is compatible with triplex and duplex formation.Key words: Peptide Nucleic Acid, hydroxymethyluracil, hydroxymethylcytosine, modified nu...

  • The detrimental effect of orotic Acid substitution in the Peptide Nucleic Acid strand on the stability of PNA2:NA triple helices
    Canadian Journal of Chemistry, 2005
    Co-Authors: Robert H. E. Hudson, Filip Wojciechowski
    Abstract:

    We have investigated the incorporation of C6 derivatives of uracil into polypyrimidine Peptide Nucleic Acid oligomers. Starting with uracil-6-carboxylic Acid (orotic Acid), a Peptide Nucleic Acid monomer compatible with Fmoc-based synthesis was prepared. This monomer then served as a convertible nucleobase whereupon treatment of the resin-bound methyl orotate containing hexamers with hydroxide or amines cleanly converted the ester to an orotic Acid or orotamide-containing Peptide Nucleic Acid. Peptide Nucleic Acid hexamers containing the C6-modified nucleobase hybridized to both poly(riboadenylic Acid) and poly(deoxyriboadenylic Acid) via triplex formation. Complexes formed with poly(riboadenylic Acid) were more stable than those formed with poly(dexoyriboadenylic Acid), as measured by temperature-dependent UV spectroscopy. However, both of these complexes were destabilized relative to the complexes formed by an unmodified Peptide Nucleic Acid oligomers. Internal or doubly substituted hexamers are destabi...

Anton Y Peleg - One of the best experts on this subject based on the ideXlab platform.

Michael E Birnbaum - One of the best experts on this subject based on the ideXlab platform.

  • dna templated polymerization of side chain functionalized Peptide Nucleic Acid aldehydes
    Journal of the American Chemical Society, 2008
    Co-Authors: Ralph E Kleiner, Yevgeny Brudno, Michael E Birnbaum
    Abstract:

    The DNA-templated polymerization of synthetic building blocks provides a potential route to the laboratory evolution of sequence-defined polymers with structures and properties not necessarily limited to those of natural biopolymers. We previously reported the efficient and sequence-specific DNA-templated polymerization of Peptide Nucleic Acid (PNA) aldehydes. Here, we report the enzyme-free, DNA-templated polymerization of side-chain-functionalized PNA tetramer and pentamer aldehydes. We observed that polymerization of tetramer and pentamer PNA building blocks with a single lysine-based side chain at various positions in the building block could proceed efficiently and sequence specifically. In addition, DNA-templated polymerization also proceeded efficiently and in a sequence-specific manner with pentamer PNA aldehydes containing two or three lysine side chains in a single building block to generate more densely functionalized polymers. To further our understanding of side-chain compatibility and expand...