title: Peptide nucleic acid-DNA duplexes containing the universal base 3-nitropyrrole.
abstract: A peptide nucleic acid (PNA) monomer containing the universal base 3-nitropyrrole was synthesized by coupling 1-carboxymethyl-3-nitropyrrole to ethyl N-[2-(tert-butoxycarbonylamino)ethyl]glycinate. The PNA sequence H-TGTACGTXACAACTA-NH2 (X = 3-nitropyrrole and C) and DNA sequence 5'-TGTACGTXACAACTA-3' were synthesized and thermal melting studies with the complementary DNA sequence 5'-TAGTTGTYACGTACA-3' (Y = A,C, G, T) compared. The T(m) data show that 3-nitropyrrole pairs indiscriminately with all four natural nucleobases as a constituent of either DNA or PNA. However, 3-nitropyrrole-containing PNA-DNA (average T(m) value = 51.1 degrees C) is significantly more thermally stable than 3-nitropyrrole-containing DNA-DNA (average T(m) value = 39.6 degrees C). From circular dichroism measurements, it is apparent that 3-nitropyrrole in the PNA strand causes a significant change in duplex structure.
authors.affiliation: Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, USA.
authors.forename: B P
authors.initials: BP
authors.lastname: Zhang
authors.forename: M
authors.initials: M
authors.lastname: Egholm
authors.forename: N
authors.initials: N
authors.lastname: Paul
authors.forename: M
authors.initials: M
authors.lastname: Pingle
authors.forename: D E
authors.initials: DE
authors.lastname: Bergstrom
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002855:Chromatography, Thin Layer; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D020135:Peptide Nucleic Acids / Q000737:chemistry* / Q000378:metabolism*; D017433:Protein Structure, Secondary; D011758:Pyrroles / Q000737:chemistry*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013696:Temperature; D014466:Ultraviolet Rays
chemical_list: D020135:Peptide Nucleic Acids; D011758:Pyrroles; C094911:3-nitropyrrole; D004247:DNA