P E Nielsen

Summary

Affiliation: University of Copenhagen
Country: Denmark

Publications

  1. pmc In vitro transcription of a torsionally constrained template
    Thomas Bentin
    Center for Biomolecular Recognition, IMBG, Laboratory B, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Nucleic Acids Res 30:803-9. 2002
  2. ncbi request reprint Substituted 1,8-naphthyridin-2(1H)-ones are superior to thymine in the recognition of adenine in duplex as well as triplex structures
    Anne B Eldrup
    Center for Biomolecular Recognition, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK 2100 Copenhagen Ø, Denmark
    J Am Chem Soc 124:3254-62. 2002
  3. ncbi request reprint PNA Technology
    Peter E Nielsen
    Center for Biomolecular Recognition, IMBG, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, Copenhagen DK 2200N, Denmark
    Mol Biotechnol 26:233-48. 2004
  4. ncbi request reprint Addressing the challenges of cellular delivery and bioavailability of peptide nucleic acids (PNA)
    Peter E Nielsen
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Q Rev Biophys 38:345-50. 2005
  5. pmc Structural diversity of target-specific homopyrimidine peptide nucleic acid-dsDNA complexes
    Thomas Bentin
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3 2200 Copenhagen N, Denmark
    Nucleic Acids Res 34:5790-9. 2006
  6. pmc Subnanomolar antisense activity of phosphonate-peptide nucleic acid (PNA) conjugates delivered by cationic lipids to HeLa cells
    Takehiko Shiraishi
    Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, The Panum Institute, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Nucleic Acids Res 36:4424-32. 2008
  7. pmc On the stability of peptide nucleic acid duplexes in the presence of organic solvents
    Anjana Sen
    Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, The Panum Institute, Blegdamsvej 3C, DK 2200 Copenhagen N, Denmark
    Nucleic Acids Res 35:3367-74. 2007
  8. ncbi request reprint Applications of peptide nucleic acids
    P E Nielsen
    Center for Biomolecular Recognition Department of Medical Biochemistry and Genetics Biochemical Laboratory B The Panum Institute Blegdamsvej 3c 2200 Copenhagen N Denmark
    Curr Opin Biotechnol 10:71-5. 1999
  9. ncbi request reprint Antisense peptide nucleic acids
    P E Nielsen
    Center for Biomolecular Recognition, Department for Biochemistry and Genetics, Laboratory B, The Panum Institute, Blegdamsvej 3C, DK 2200 N Copenhagen, Denmark
    Curr Opin Mol Ther 2:282-7. 2000
  10. ncbi request reprint Peptide nucleic acids: on the road to new gene therapeutic drugs
    P E Nielsen
    Center for Biomolecular Recognition, Department of Medical Biochemistry and Genetics, Panum Institute, Copenhagen N, Denmark
    Pharmacol Toxicol 86:3-7. 2000

Collaborators

  • Niels Erik Møllegaard
  • Anne Goldbech Olsen
  • Rikard Dryselius
  • V V Demidov
  • Takehiko Shiraishi
  • Thomas Bentin
  • Anne B Eldrup
  • Kagan Kerman
  • F Zoulim
  • Arzum Erdem
  • C Bailly
  • Steen Rasmussen
  • J S Kastrup
  • Frantisek Jelen
  • Michael M Seidman
  • Diane Krause
  • Yurii S Lazurkin
  • Andrea R Nawrocki
  • Uffe Koppelhus
  • Anjana Sen
  • Ki Hyun Kim
  • Satish Kumar Awasthi
  • Nadia Bendifallah
  • Stanislava Pankratova
  • Danfeng Yao
  • Peter M Glazer
  • Vladimir Zachar
  • Frank Winther Rasmussen
  • A Püschl
  • Mads E Hansen
  • Joanna Y Chin
  • Fatima Boutimah-Hamoudi
  • Tristan Rocheleau
  • Peter Ebbesen
  • Zhanna V Zhilina
  • Magdalena Robaczewska
  • Søren Lindemose
  • Britt Petersson
  • Fang Yu
  • Junyoung Kim
  • Eva Kathrin Sinner
  • Wolfgang Knoll
  • Natalia Nekhotiaeva
  • Olga V Krupnik
  • H Rasmussen
  • Andrew Dodd
  • Giulia Mearini
  • Liam Good
  • Ekaterina Protozanova
  • Ramin Hamzavi
  • Otto Dahl
  • Magdalena Eriksson
  • Caspar Christensen
  • Alexandre G Rebuffat
  • Dilsat Ozkan
  • C Behrens
  • G I Hansen
  • Birgit N Nielsen
  • Pallavi S Lonkar
  • Kenneth R Peterson
  • Jean Y Kuan
  • Ryszard Kole
  • Tula Ester Saison-Behmoaras
  • Erwan Leforestier
  • Xue Jun Fan
  • Catherine Senamaud-Beaufort
  • Hans Ziock
  • Carine Giovannangeli
  • Martin N Jacobi
  • Amy J Ziemba
  • Trine Fink
  • Scot W Ebbinghaus
  • Anna J Podhajska
  • Ramamurthy Narayan
  • Ingrid Kjøller Larsen
  • Hanne Rasmussen
  • Beatrice Seigneres
  • Olivier Schorr
  • Alexandre Thermet
  • Michael Gajhede
  • Christian Trepo
  • Bettina Bryde Nielsen
  • Lucyna Cova
  • B Petersson
  • T Liljefors
  • Judith Scholz
  • Donald R Love
  • Nina P Kvitko
  • Stephen P Chambers
  • Natalia V Fadeeva

Detail Information

Publications85

  1. pmc In vitro transcription of a torsionally constrained template
    Thomas Bentin
    Center for Biomolecular Recognition, IMBG, Laboratory B, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Nucleic Acids Res 30:803-9. 2002
    ..We conclude that transcription of a natural bacterial gene may proceed with high efficiency despite the fact that newly synthesized RNA is entangled around the template in the narrow confines of torsionally constrained supercoiled DNA...
  2. ncbi request reprint Substituted 1,8-naphthyridin-2(1H)-ones are superior to thymine in the recognition of adenine in duplex as well as triplex structures
    Anne B Eldrup
    Center for Biomolecular Recognition, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK 2100 Copenhagen Ø, Denmark
    J Am Chem Soc 124:3254-62. 2002
    ..Finally, and most surprisingly, we find no direct correlation between the end-stacking efficiency of this type of nucleobase and its helix stabilization when involved in Watson-Crick base pairing within a helix...
  3. ncbi request reprint PNA Technology
    Peter E Nielsen
    Center for Biomolecular Recognition, IMBG, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, Copenhagen DK 2200N, Denmark
    Mol Biotechnol 26:233-48. 2004
    ..Recent progress in studies of PNA properties and applications is reviewed...
  4. ncbi request reprint Addressing the challenges of cellular delivery and bioavailability of peptide nucleic acids (PNA)
    Peter E Nielsen
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Q Rev Biophys 38:345-50. 2005
    ..Recent results on the cellular delivery of antisense peptide nucleic acids (PNA) via peptide conjugation is briefly discussed, in particular in the context of endosomal entrapment and escape...
  5. pmc Structural diversity of target-specific homopyrimidine peptide nucleic acid-dsDNA complexes
    Thomas Bentin
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3 2200 Copenhagen N, Denmark
    Nucleic Acids Res 34:5790-9. 2006
    ..These result demonstrate a clear example of a 'triplex first' mechanism for PNA helix invasion...
  6. pmc Subnanomolar antisense activity of phosphonate-peptide nucleic acid (PNA) conjugates delivered by cationic lipids to HeLa cells
    Takehiko Shiraishi
    Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, The Panum Institute, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Nucleic Acids Res 36:4424-32. 2008
    ....
  7. pmc On the stability of peptide nucleic acid duplexes in the presence of organic solvents
    Anjana Sen
    Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, The Panum Institute, Blegdamsvej 3C, DK 2200 Copenhagen N, Denmark
    Nucleic Acids Res 35:3367-74. 2007
    ..These results support the possibility of having stable nucleobase paired double helices in organic solvents...
  8. ncbi request reprint Applications of peptide nucleic acids
    P E Nielsen
    Center for Biomolecular Recognition Department of Medical Biochemistry and Genetics Biochemical Laboratory B The Panum Institute Blegdamsvej 3c 2200 Copenhagen N Denmark
    Curr Opin Biotechnol 10:71-5. 1999
    ..PNA hybridization technology has developed rapidly within in situ hybridization, and exciting new methods based on MALDI-TOF detection have also been presented...
  9. ncbi request reprint Antisense peptide nucleic acids
    P E Nielsen
    Center for Biomolecular Recognition, Department for Biochemistry and Genetics, Laboratory B, The Panum Institute, Blegdamsvej 3C, DK 2200 N Copenhagen, Denmark
    Curr Opin Mol Ther 2:282-7. 2000
    ....
  10. ncbi request reprint Peptide nucleic acids: on the road to new gene therapeutic drugs
    P E Nielsen
    Center for Biomolecular Recognition, Department of Medical Biochemistry and Genetics, Panum Institute, Copenhagen N, Denmark
    Pharmacol Toxicol 86:3-7. 2000
    ..Recently, several studies reporting methods for cellular delivery of PNA as well as antisense effects of PNA in cells ex vivo and in rats have appeared. The potential of developing PNA derived gene therapeutic drugs is discussed...
  11. ncbi request reprint Strand displacement recognition of mixed adenine-cytosine sequences in double stranded DNA by thymine-guanine PNA (peptide nucleic acid)
    P E Nielsen
    Center for Biomolecular Recognition, Department for Biochemistry and Genetics, Biochemistry Laboratory B, The Panum Institute, Blegdamsvej 3C, DK 2200N Copenhagen, Denmark
    Bioorg Med Chem 9:2429-34. 2001
    ..These results for the first time demonstrate binding of an unmodified PNA oligomer to a mixed pyrimidine-purine target in double stranded DNA and illustrate a novel binding mode of PNA...
  12. ncbi request reprint Targeting double stranded DNA with peptide nucleic acid (PNA)
    P E Nielsen
    Center for Biomolecular Recognition, Department of Medical Biochemistry and Genetics, The Panum Institute, Blegdamsvej 3, Copenhagen N, DK 2200, Denmark
    Curr Med Chem 8:545-50. 2001
    ..The status of this field is discussed in terms of PNA binding modes and mechanism as well as applications...
  13. ncbi request reprint Peptide nucleic acids as antibacterial agents via the antisense principle
    P E Nielsen
    Center for Biomolecular Recognition, Department for Biochemistry and Genetics, Laboratory B, The Panum Institute, Blegdamsvej 3C, DK 2200 N, Copenhagen, Denmark
    Expert Opin Investig Drugs 10:331-41. 2001
    ..Most recently, these preliminary studies have been extended to demonstrate in vivo efficacy of antibacterial PNAs in an E. coli peritonitis/sepsis mouse model. Therefore, PNA drug development again is rapidly picking up pace...
  14. ncbi request reprint Peptide nucleic acids as therapeutic agents
    P E Nielsen
    Center for Biomolecular Recognition, Department of Medical Biochemistry and Genetics, The Panum Institute, Copenhagen, Denmark
    Curr Opin Struct Biol 9:353-7. 1999
    ..Finally, it has been shown that the bacterium Escherichia coli is susceptible to antisense gene regulation using PNA...
  15. ncbi request reprint Peptide nucleic acids and the origin of life
    Peter E Nielsen
    Department of Cellular and Molecular Medicine, University of Copenhagen, The Panum Institute, Blegdamsvej 3C, DK 2200 Copenhagen N
    Chem Biodivers 4:1996-2002. 2007
    ..In particular, the merits of an achiral prebiotic genetic material is discussed...
  16. ncbi request reprint Question 1: Peptide nucleic acids and the origin and homochirality of life
    Peter E Nielsen
    Department of Cellular and Molecular Medicine, University of Copenhagen, The Panum Institute, Blegdamsvej 3C, DK 2200, Copenhagen N, Denmark
    Orig Life Evol Biosph 37:323-8. 2007
    ....
  17. ncbi request reprint Extended target sequence specificity of PNA-minor-groove binder conjugates
    Peter E Nielsen
    Department of Medical Biochemistry and Genetics, University of Copenhagen, The Panum Institute, Blegdamsvej 3C, Copenhagen N 2200, Denmark
    Chembiochem 6:66-8. 2005
  18. ncbi request reprint Detection of intercalation-induced changes in DNA structure by reaction with diethyl pyrocarbonate or potassium permanganate. Evidence against the induction of Hoogsteen base pairing by echinomycin
    C Jeppesen
    Department of Biochemistry B, University of Copenhagen, Denmark
    FEBS Lett 231:172-6. 1988
    ..This thymine hyperreactivity is both sequence- and intercalator-dependent, thereby indicating the potential of KMnO4 as a useful probe for analyzing the structure of intercalator-DNA complexes in solution...
  19. pmc Peptide nucleic acid.DNA strand displacement loops as artificial transcription promoters
    N E Møllegaard
    Department of Biochemistry B, Panum Institute, Copenhagen, Denmark
    Proc Natl Acad Sci U S A 91:3892-5. 1994
    ..Our results have implications for the mechanism of action of RNA polymerase and suggest the use of PNA as specific gene activating reagents and drugs...
  20. ncbi request reprint Quinoxaline antibiotics enhance peptide nucleic acid binding to double-stranded DNA
    N E Møllegaard
    Department of Medical Biochemistry and Genetics, The Panum Institute, Copenhagen N, Denmark
    Biochemistry 39:9502-7. 2000
    ..This study establishes that the efficacy of DNA-targeted PNA antigene molecules could potentially be enhanced by judiciously adding certain DNA-interactive ligands...
  21. ncbi request reprint Psoralen photofootprinting of protein-binding sites on DNA
    W P Zhen
    Department of Biochemistry B, Panum Institute, University of Copenhagen, Denmark
    FEBS Lett 229:73-6. 1988
    ..coli or RNA polymerase are bound at their recognition DNA sequences (OR1 operator or deo1 promoter, respectively). These results show that psoralens can be used as photofootprinting reagents to study specific protein-DNA interactions...
  22. ncbi request reprint Photofootprinting of drug-binding sites on DNA using diazo- and azido-9-aminoacridine derivatives
    C Jeppesen
    Department of Biochemistry B, Panum Institute, University of Copenhagen, Denmark
    Eur J Biochem 182:437-44. 1989
    ..T)4 sequence, whereas protection by echinomycin was confined to a G + C-rich 8-base-pair region...
  23. ncbi request reprint Increased temperature and 2-methyl-2,4-pentanediol change the DNA structure of both curved and uncurved adenine/thymine-rich sequences
    Niels Erik Møllegaard
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Biochemistry 42:8587-93. 2003
    ..Thus, the rather subtle structural difference of AT regions and A-tracts in nonbent DNA versus A-tracts in bent DNA may be quantitative rather than qualitative; i.e., the structure is more persistent and/or rigid in bent DNA...
  24. ncbi request reprint Transcription arrest caused by long nascent RNA chains
    Thomas Bentin
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Biochim Biophys Acta 1727:97-105. 2005
    ..Based on available literature we discuss possible in vivo implications of the results...
  25. doi request reprint Hydrogen bonding versus stacking stabilization by modified nucleobases incorporated in PNA.DNA duplexes
    Anjana Sen
    Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Denmark
    Biophys Chem 141:29-33. 2009
    ....
  26. ncbi request reprint Synthesis and evaluation of a conformationally constrained pyridazinone PNA-monomer for recognition of thymine in triple-helix structures
    Anne Goldbech Olsen
    Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK 2100 Copenhagen Ø, Denmark
    Bioorg Med Chem Lett 14:1551-4. 2004
    ..Surprisingly, no significant difference was found in the thermodynamic parameters (DeltaH degrees, DeltaS degrees and DeltaG degrees ) for PNA-DNA triplex formation involving 2 or the unconstrained analogue 1...
  27. ncbi request reprint Enhanced delivery of cell-penetrating peptide-peptide nucleic acid conjugates by endosomal disruption
    Takehiko Shiraishi
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen, Denmark
    Nat Protoc 1:633-6. 2006
    ..The endosome-disruption treatment improves the nuclear antisense effects of CPP-PNA conjugates by up to two orders of magnitude using 24-hour delivery...
  28. ncbi request reprint Combined triplex/duplex invasion of double-stranded DNA by "tail-clamp" peptide nucleic acid
    Thomas Bentin
    Center for Biomolecular Recognition, IMBG, Department B, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Biochemistry 42:13987-95. 2003
    ..The results validate the tail-clamp PNA concept and expand the applications of the P-loop technology...
  29. ncbi request reprint Pyrrolidine PNA: a novel conformationally restricted PNA analogue
    A Püschl
    Center for Biomolecular Recognition, Department for Biochemistry and Genetics, Biochemistry Laboratory B, The Panum Institute, Blegdamsvej 3C, DK 2200, Copenhagen, Denmark
    Org Lett 2:4161-3. 2000
    ..A fully modified adenine decamer displayed improved binding affinity toward complementary DNA and RNA oligonucleotides as compared to that of the parent PNA adenine decamer...
  30. ncbi request reprint Structural isomers of bis-PNA bound to a target in duplex DNA
    G I Hansen
    Center for Biomolecular Recognition, IMBG, Department B, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    J Mol Biol 307:67-74. 2001
    ..The implications of these results are discussed in terms of DNA targeting by synthetic ligands...
  31. ncbi request reprint Synthesis of a Hoechst 32258 analogue amino acid building block for direct incorporation of a fluorescent, high-affinity DNA binding motif into peptides
    C Behrens
    Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen, Denmark
    Bioconjug Chem 12:1021-7. 2001
    ..10-fold), but similar sequence preference compared to Hoechst 33258 as analyzed by DNaseI footprinting. Finally, the fluorescence quantum yield of the new chromophore is found to increase 30% upon binding to double stranded DNA...
  32. pmc Unique properties of purine/pyrimidine asymmetric PNA.DNA duplexes: differential stabilization of PNA.DNA duplexes by purines in the PNA strand
    Anjana Sen
    Department of Medical Biochemistry and Genetics, Faculty of Health Sciences, University of Copenhagen, The Panum Institute, Copenhagen, Denmark
    Biophys J 90:1329-37. 2006
    ..DNA duplexes, the evidence does point to a significant structural component, which involves enthalpic contributions both within the duplex structure and also from bound water molecules...
  33. ncbi request reprint A novel PNA-monomer for recognition of thymine in triple-helix structures
    Anne Goldbech Olsen
    Department of Chemistry, University of Copenhagen, Copenhagen O, Denmark
    Nucleosides Nucleotides Nucleic Acids 22:1331-3. 2003
    ..A novel conformationally constrained PNA-monomer (II) capable of binding T in a triplex motif was designed and synthesized in 7 steps starting from commercially available dimethyl 2-oxoglutarate...
  34. ncbi request reprint Uranyl photoprobing of nonbent A/T- and bent A-tracts. A difference of flexibility?
    Niels Erik Møllegaard
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Biochemistry 44:7855-63. 2005
    ....
  35. ncbi request reprint Calcium ions effectively enhance the effect of antisense peptide nucleic acids conjugated to cationic tat and oligoarginine peptides
    Takehiko Shiraishi
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Chem Biol 12:923-9. 2005
    ..The present results show that Ca(2+) can be used as an effective enhancer for in vitro cellular delivery of cationic peptide-conjugated PNA oligomers, and also emphasize the significance of the endosomal escape route for such peptides...
  36. pmc Polyamines preferentially interact with bent adenine tracts in double-stranded DNA
    Søren Lindemose
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Nucleic Acids Res 33:1790-803. 2005
    ....
  37. ncbi request reprint Photochemically enhanced cellular delivery of cell penetrating peptide-PNA conjugates
    Takehiko Shiraishi
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    FEBS Lett 580:1451-6. 2006
    ....
  38. ncbi request reprint Sequence-selective targeting of duplex DNA by peptide nucleic acids
    Peter E Nielsen
    University of Copenhagen, The Panum Institute, Department of Cellular and Molecular Medicine, Blegdamsvej 3C, DK 2200, Copenhagen, Denmark
    Curr Opin Mol Ther 12:184-91. 2010
    ..Such modifications have also resulted in new approaches to targeted gene repair and sequence-selective double-strand cleavage of genomic DNA...
  39. pmc Kinetics and mechanism of the DNA double helix invasion by pseudocomplementary peptide nucleic acids
    Vadim V Demidov
    Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 99:5953-8. 2002
    ..A simplified kinetic model for pcPNAs helix invasion is proposed that interprets all unusual features of pcPNAs binding to dsDNA. Our findings have important implications for rational use of pcPNAs...
  40. ncbi request reprint Site-specific gene modification by PNAs conjugated to psoralen
    Ki Hyun Kim
    Department of Therapeutic Radiology, Yale University School of Medicine, Post Office Box 208040, New Haven, Connecticut 06520 8040, USA
    Biochemistry 45:314-23. 2006
    ..When the results are taken together, they demonstrate the ability of bis-PNAs conjugated with psoralen to mediate site-specific gene modification, and they further support the development of PNAs as tools for gene-targeting applications...
  41. pmc Pseudocomplementary PNAs as selective modifiers of protein activity on duplex DNA: the case of type IIs restriction enzymes
    Ekaterina Protozanova
    Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 31:3929-35. 2003
    ..Our results have general implications for effective pcPNA interference with the performance of DNA-processing proteins, thus being important for prospective applications of pcPNAs...
  42. ncbi request reprint Stability and transformations of bis-PNA/DNA triplex structural isomers
    Olga V Krupnik
    Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq 2, Moscow 123182, Russia
    J Biomol Struct Dyn 21:503-12. 2004
    ..The relationship between the yield of the isomer S1 formed on single-stranded DNA and the bis-PNA concentration was investigated and a kinetic model of the formation of S1 is presented...
  43. ncbi request reprint PNA-nitrogen mustard conjugates are effective suppressors of HER-2/neu and biological tools for recognition of PNA/DNA interactions
    Zhanna V Zhilina
    Arizona Cancer Center, University of Arizona, 1515 North Campbell, 85724, Tucson, Arizona, USA
    Bioconjug Chem 17:214-22. 2006
    ....
  44. ncbi request reprint The influence of a chiral amino acid on the helical handedness of PNA in solution and in crystals
    H Rasmussen
    Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK 2100, Copenhagen, Denmark
    J Biomol Struct Dyn 21:495-502. 2004
    ..The calculations indicate that the difference in the free energy of solvation between the left-handed and the right-handed helix is the determining factor for the preference of the left-handed helix in aqueous solution...
  45. ncbi request reprint Synthesis of pyrrolidinone PNA: a novel conformationally restricted PNA analogue
    A Püschl
    Center for Biomolecular Recognition, Department for Biochemistry and Genetics, Biochemistry Laboratory B, Panum Institute, Blegdamsvej 3C, DK 2200, Copenhagen, Denmark
    J Org Chem 66:707-12. 2001
    ..The (3S,5R) isomer was used to prepare a fully modified decamer which bound to rU10 with only a small decrease in Tm (delta Tm/mod = 1 degree C) relative to aminoethylglycine PNA...
  46. pmc High-affinity triplex targeting of double stranded DNA using chemically modified peptide nucleic acid oligomers
    Mads E Hansen
    Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200 N, Denmark
    Nucleic Acids Res 37:4498-507. 2009
    ..Together the data support the use of homopyrimidine PNAs as efficient and sequence selective tools in triplex targeting strategies under physiological relevant conditions...
  47. ncbi request reprint Targeted delivery of plasmid DNA into the nucleus of cells via nuclear localization signal peptide conjugated to DNA intercalating bis- and trisacridines
    Takehiko Shiraishi
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Bioconjug Chem 16:1112-6. 2005
    ..These conjugates have high reversible affinity for double stranded DNA by intercalation and the technique provides a simple means of associating NLS with DNA of any sequence and at any ratio...
  48. doi request reprint Improved cellular activity of antisense peptide nucleic acids by conjugation to a cationic peptide-lipid (CatLip) domain
    Uffe Koppelhus
    Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3C, DK 2200 Copenhagen N, Denmark
    Bioconjug Chem 19:1526-34. 2008
    ..These results provide a novel route for improving the (cellular) bioavailability of larger hydrophilic molecules...
  49. ncbi request reprint Efficient sequence-directed psoralen targeting using pseudocomplementary Peptide nucleic acids
    Ki Hyun Kim
    Department of Cellular and Molecular Medicine, University of Copenhagen, The Panum Institute, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Bioconjug Chem 18:567-72. 2007
    ..Thus, such psoralen-PNA conjugates could be very useful in a range of biology and drug discovery applications...
  50. ncbi request reprint Superior duplex DNA strand invasion by acridine conjugated peptide nucleic acids
    Thomas Bentin
    Center for Biomolecular Recognition, IMBG, Department B, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    J Am Chem Soc 125:6378-9. 2003
    ..Thus, simply conjugating the DNA intercalator 9-aminoacridine to PNA represents a major step toward the development of helix invading constructs for in vivo applications such as gene targeting...
  51. ncbi request reprint Evaluation of cell-penetrating peptides (CPPs) as vehicles for intracellular delivery of antisense peptide nucleic acid (PNA)
    Nadia Bendifallah
    Center for Biomolecular Recognition, Department of Medical Biochemistry and Genetics, Biochemistry Laboratory B, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, DK 2200 Copenhagen N, Denmark
    Bioconjug Chem 17:750-8. 2006
    ..However, no simple relationship between linker type and antisense activity of the conjugates could be deduced from the data...
  52. ncbi request reprint 1,8-Naphthyridin-2,7-(1,8H)-dione is an effective mimic of protonated cytosine in peptide nucleic acid triplex recognition systems
    Caspar Christensen
    Center for Biomolecular Recognition, Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3, DK 2200 N, Copenhagen, Denmark
    Bioorg Med Chem Lett 12:3121-4. 2002
    ..7 degrees C per unit) or pseudoisocytosine (1.5 degrees C per unit). Cooperative stabilization was observed when the K units were placed in adjacent positions ( approximately 3 degrees C per unit)...
  53. ncbi request reprint Cellular delivery of polyheteroaromate-peptide nucleic acid conjugates mediated by cationic lipids
    Takehiko Shiraishi
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Bioconjug Chem 17:189-94. 2006
    ..However, no clear structure/activity relations are apparent from the present results, except that both 9-aminoacridine and "Hoechst" are also nucleic acid binding ligands...
  54. ncbi request reprint In vitro transcription from peptide nucleic acid/DNA strand displacement loops
    Niels Erik Møllegaard
    Center for Biomolecular Recognition, IMBG, Panum Institute, University of Copenhagen, Copenhagen, Denmark
    Methods Mol Biol 208:249-56. 2002
  55. pmc Cellular antisense activity of peptide nucleic acid (PNAs) targeted to HIV-1 polypurine tract (PPT) containing RNA
    Fatima Boutimah-Hamoudi
    INSERM, U565, Acides nucléiques dynamique, ciblage et fonctions biologiques, 57 rue Cuvier, CP26, Paris Cedex 05, F 75231, France
    Nucleic Acids Res 35:3907-17. 2007
    ....
  56. pmc Surface density dependence of PCR amplicon hybridization on PNA/DNA probe layers
    Danfeng Yao
    Max Planck Institute for Polymer Research, 55128 Mainz, Germany
    Biophys J 88:2745-51. 2005
    ..As a consequence, a pseudo-first-order kinetic model was applicable to describe the hybridization kinetics, and affinity constants were derived for evaluating the influence of single nucleotide polymorphisms (SNPs)...
  57. ncbi request reprint Cell permeabilization and uptake of antisense peptide-peptide nucleic acid (PNA) into Escherichia coli
    Magdalena Eriksson
    Department of Physical Chemistry, Chalmers University of Technology, Gothenburg SE 41296, Sweden
    J Biol Chem 277:7144-7. 2002
    ..The enhanced cell-permeation properties of peptide-PNAs can explain their potent antisense activity, and the results indicate an unanticipated synergy between the peptide and PNA components...
  58. pmc Localization and dynamics of small circular DNA in live mammalian nuclei
    Giulia Mearini
    Department of Molecular Cell Biology, Heinrich Pette Institute, Martinistrasse 52, 20251 Hamburg, Germany
    Nucleic Acids Res 32:2642-51. 2004
    ..We show that the localization and the low mobility of plasmids is independent of the plasmid sequence, and does not require the presence of either a scaffold attachment region (SAR) DNA element or a functional promoter...
  59. pmc Down-regulation of MDM2 and activation of p53 in human cancer cells by antisense 9-aminoacridine-PNA (peptide nucleic acid) conjugates
    Takehiko Shiraishi
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    Nucleic Acids Res 32:4893-902. 2004
    ....
  60. ncbi request reprint PNA-mediated modulation and redirection of Her-2 pre-mRNA splicing: specific skipping of erbB-2 exon 19 coding for the ATP catalytic domain
    Stanislava Pankratova
    Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health Sciences, University of Copenhagen, DK 2200 Copenhagen N, Denmark
    Int J Oncol 36:29-38. 2010
    ..In the present study we identified PNA oligomers having such activity in SK-BR-3 and HeLa cancer cells in culture...
  61. ncbi request reprint Cellular delivery of peptide nucleic acid (PNA)
    Uffe Koppelhus
    Biochemistry Laboratory B, Center for Biomolecular Recognition, Department of Medical Biochemistry and Genetics, The Panum Institute, Blegdamsvej 3C, 2200 N Copenhagen, Denmark
    Adv Drug Deliv Rev 55:267-80. 2003
    ..This is followed by a comprehensive evaluation of the most interesting literature concerning cellular delivery and the intracellular effect of PNA. Also the current progress as regards using PNA as co-factor in DNA delivery is reviewed...
  62. doi request reprint Self-assembling, dynamic alphaPNAs
    Peter E Nielsen
    Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, Copenhagen DK 2200N, Denmark
    Chem Biol 16:689-90. 2009
    ..In the recent report published in Science, Ghadiri and coworkers describe dynamic tPNAs, alphaPNA derivatives with a nucleobase attached via a thioester bond that are a step forward toward self-repairing and replicating molecules...
  63. ncbi request reprint Measurement of PNA binding to double-stranded DNA
    Thomas Bentin
    Center for Biomolecular Recognition, IMBG, Panum Institute, University of Copenhagen, Copenhagen, Denmark
    Methods Mol Biol 208:91-109. 2002
  64. ncbi request reprint Synthesis and properties of ester-linked peptide nucleic acid prodrug conjugates
    Nadia Bendifallah
    Center for Biomolecular Recognition, Department of Medical Biochemistry and Genetics, University of Copenhagen, The Panum Institute, Blegdamsvej 3C, DK 2200 N Copenhagen, Denmark
    Bioconjug Chem 14:588-92. 2003
    ..Thus, a PNA prodrug approach may be useful for both ex vivo as well as in vivo applications...
  65. ncbi request reprint PNA technology
    Peter E Nielsen
    Center for Biomolecular Recognition, IMBG, Panum Institute, University of Copenhagen, Copenhagen N, Denmark
    Methods Mol Biol 208:3-26. 2002
  66. ncbi request reprint Evaluation of transfection protocols for unmodified and modified peptide nucleic acid (PNA) oligomers
    Frank Winther Rasmussen
    Pantheco A S, DK 2970 Hørsholm, Denmark
    Oligonucleotides 16:43-57. 2006
    ..An important lesson from the study was the finding that because of uncontrollable biologic variations, even optimal transfection conditions differed to a certain extend from experiment to experiment in an unpredictable way...
  67. ncbi request reprint Gene delivery by a steroid-peptide nucleic acid conjugate
    Alexandre G Rebuffat
    Division of Nephrology and Hypertension and Clinical Research, University of Berne, CH 3010 Berne Inselspital, Switzerland
    FASEB J 16:1426-8. 2002
    ..Thus, SMGD with PNA is a promising strategy for nonviral gene delivery into target tissues expressing specific steroid receptors...
  68. ncbi request reprint Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network
    Britt Petersson
    Biostructural Research, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK 2100 Copenhagen, Denmark
    J Am Chem Soc 127:1424-30. 2005
    ..The crystal structure further shows how PNA oligomers containing limited sequence complementarity may form complex hydrogen-bonding networks...
  69. ncbi request reprint Inhibition of Staphylococcus aureus gene expression and growth using antisense peptide nucleic acids
    Natalia Nekhotiaeva
    Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius vag 35, 171 77 Stockholm, Sweden
    Mol Ther 10:652-9. 2004
    ..Further development is needed to raise the antibacterial potential of PNAs, but the present results show that the approach can be used to study gene function and requirement in this important pathogen...
  70. ncbi request reprint DNA and PNA sensing on mercury and carbon electrodes by using methylene blue as an electrochemical label
    Dilsat Ozkan
    Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, 35100 Bornova, Izmir, Turkey
    Bioelectrochemistry 58:119-26. 2002
    ..These results demonstrated that MB could be used as an effective electroactive hybridization indicator for DNA biosensors. Performance characteristics of the sensor are described, along with future prospects...
  71. pmc Site-directed gene mutation at mixed sequence targets by psoralen-conjugated pseudo-complementary peptide nucleic acids
    Ki Hyun Kim
    Department of Therapeutic Radiology, Yale University School of Medicine, P O Box 208040, New Haven, CT 06520 8040, USA
    Nucleic Acids Res 35:7604-13. 2007
    ..These results identify pcPNAs as new tools for site-specific gene modification in mammalian cells without purine sequence restriction, thereby providing a general strategy for designing gene targeting molecules...
  72. ncbi request reprint Antibiotic-free bacterial strain selection using antisense peptide nucleic acid
    Rikard Dryselius
    Karolinska Institutet, Stockholm, Sweden
    Biotechniques 35:1060-4. 2003
    ..Also, the PNA-selected cells grow at a near normal rate. The results open possibilities to use antisense PNAs for strain selection and construction in research and industrial application...
  73. ncbi request reprint Parallel synthesis of PNA-peptide conjugate libraries
    Satish Kumar Awasthi
    Center for Biomolecular Recognition, IMBG, Panum Institute, University of Copenhagen, Copenhagen N, Denmark
    Methods Mol Biol 208:53-7. 2002
  74. ncbi request reprint Gene targeting using peptide nucleic acid
    Peter E Nielsen
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Denmark
    Methods Mol Biol 288:343-58. 2005
    ....
  75. ncbi request reprint Photoreactive bicyclic amino acids as substrates for mutant Escherichia coli phenylalanyl-tRNA synthetases
    Thomas Bentin
    Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
    J Biol Chem 279:19839-45. 2004
    ..The in vivo incorporation into a target protein of a bicyclic phenylalanine analogue, as described here, demonstrates the applicability of phenylalanine tRNA synthetase variants in expanding the scope of protein engineering...
  76. ncbi request reprint Modulation of the pharmacokinetic properties of PNA: preparation of galactosyl, mannosyl, fucosyl, N-acetylgalactosaminyl, and N-acetylglucosaminyl derivatives of aminoethylglycine peptide nucleic acid monomers and their incorporation into PNA oligomers
    Ramin Hamzavi
    Department of Medical Biochemistry and Genetics, University of Copenhagen, The Panum Institute, Blegdamsvej 3C, DK 2200 N Copenhagen, Denmark
    Bioconjug Chem 14:941-54. 2003
    ..These results could be of great significance for PNA drug development, as they should allow modulation and fine-tuning of the pharmacokinetic profile of a drug lead...
  77. ncbi request reprint PNA-mediated immobilization of supercoiled DNA
    Thomas Bentin
    Center for Biomolecular Recognition, IMBG, Panum Institute, University of Copenhagen, Copenhagen, Denmark
    Methods Mol Biol 208:111-8. 2002
  78. ncbi request reprint Parallel synthesis of PNA-peptide conjugate libraries
    Satish Kumar Awasthi
    Center for Biomolecular Recognition, IMBG, Biochemistry B, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, Copenhagen N, DK 2200, Denmark
    Comb Chem High Throughput Screen 5:253-9. 2002
    ..5 micromole scale the method typically yielded 2 mg product of 90% purity by HPLC/MALDI-TOF analysis. This approach is suitable for screening of a large number of PNA and/or peptide sequences for biochemical and biological studies...
  79. ncbi request reprint Synthesis of PNA-peptide conjugates
    Satish Kumar Awasthi
    Center for Biomolecular Recognition, IMBG, Panum Institute, University of Copenhagen, Copenhagen N, Denmark
    Methods Mol Biol 208:43-52. 2002
  80. pmc Surface plasmon field-enhanced fluorescence spectroscopy in PCR product analysis by peptide nucleic acid probes
    Danfeng Yao
    Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
    Nucleic Acids Res 32:e177. 2004
    ..Furthermore, SPFS was demonstrated to be capable of quantitatively discriminating the difference induced by single nucleotide substitution, even within one minute of contact time...
  81. ncbi request reprint Sequence-specific inhibition of duck hepatitis B virus reverse transcription by peptide nucleic acids (PNA)
    Magdalena Robaczewska
    INSERM U271, 151 Cours Albert Thomas, F 69424 Lyon Cedex 03, France
    J Hepatol 42:180-7. 2005
    ..Our aim was to study the ability of PNAs targeting the duck HBV (DHBV) encapsidation signal epsilon to inhibit reverse transcription (RT) and to compare their efficacy with phosphorothioate oligodeoxynucleotides (S-ODNs)...
  82. pmc Emergence of protocellular growth laws
    Tristan Rocheleau
    Self Organizing Systems, EES 6, Los Alamos National Laboratory, MS D462, Los Alamos, NM 87545, USA
    Philos Trans R Soc Lond B Biol Sci 362:1841-5. 2007
    ..Nature 409, 387-390; Pohorille & Deamer 2002 Trends Biotech. 20 123-128; Rasmussen et al. 2004 Science 303, 963-965; Szathma ry 2005 Nature 433, 469-470; Luisi et al. 2006 Naturwissenschaften 93, 1-13)...
  83. pmc Correction of a splice-site mutation in the beta-globin gene stimulated by triplex-forming peptide nucleic acids
    Joanna Y Chin
    Departments of Therapeutic Radiology and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 105:13514-9. 2008
    ..This work suggests that PNAs can be effective tools to induce heritable, site-specific modification of disease-related genes in human cells...
  84. ncbi request reprint Modeling human disease by gene targeting
    Andrew Dodd
    Molecular Genetics and Development Group, School of Biological Sciences, University of Auckland, Auckland 1001, New Zealand
    Methods Cell Biol 76:593-612. 2004
  85. ncbi request reprint The translation start codon region is sensitive to antisense PNA inhibition in Escherichia coli
    Rikard Dryselius
    Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
    Oligonucleotides 13:427-33. 2003
    ..Therefore, although other design parameters are also important, the start codon region in E. coli mRNA is the most reliable target site for antisense PNAs...