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| 2. |
- Haaima, G., et al.
(författare)
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Peptide nucleic acids (PNA) derived from N-(N-methylaminoethyl)glycine. Synthesis, hybridization and structural properties
- 1999
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Ingår i: New Journal of Chemistry. - 1369-9261 .- 1144-0546. ; 23:8, s. 833-840
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Tidskriftsartikel (refereegranskat)abstract
- Backbone N-methylated peptide nucleic acids (PNAs) containing the four nucleobases adenine, cytosine, guanine and thymine were synthesized via solid phase peptide oligomerization. The oligomers bind to their complementary target with a thermal stability that is 1.5-4.5 degrees C lower per "N-methyl nucleobase unit" [dependent on the number and position(s) of the N-methyl] than that of unmodified PNA. However, even fully N-methyl modified PNAs bind as efficiently to DNA or RNA targets as DNA itself. Furthermore, the hybridization efficiency per N-methyl unit in a PNA decreased with increasing N-methyl content, and the effect was more pronounced when the N-methyl backbone units are present in the Hoogsteen versus the Watson-Crick strand in (PNA)(2)-DNA triplexes. Interestingly, CD spectral analyses indicate that 30% (3 out of ten) substitution with N-methyl nucleobases did not alter the structure of PNA-DNA (or RNA) duplexes or (PNA)(2)-DNA triplexes, and likewise CD spectroscopy and X-ray crystallography showed no major structural differences between N-methylated (30%) and unmodified PNA-PNA duplexes. However, PNA-DNA duplexes as well as triplexes adopted a different conformation when formed with all-Ai-methyl PNAs.
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| 3. |
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| 4. |
- Colmenarejo, G., et al.
(författare)
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Electronic Spectra and Transition Moments of 6-(2’-Pyridiniumyl)phenanthridinium Photoactive DNA Intercalators
- 1997
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Ingår i: Journal of Physical Chemistry B Materials. - : American Chemical Society (ACS). - 1089-5647 .- 1520-6106 .- 1520-5207. ; 101:26, s. 5196-5204
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Tidskriftsartikel (refereegranskat)abstract
- The electronic transitions giving rise to the UV-visible absorption spectra of two pyridinium-phenanthridinium viologens, 6,7-dihydropyridol[2',1':3,4]pyrazinol[1,2-f]phenanthridinediium dication (1) and 7,8-dihydro-6H-pyrido[2',1':3,4]diazepino[1,2-f]phenanthridinediium dication (2), have been investigated with respect to energies, intensities, and transition moment directions. A combination of methods has been applied: UV-visible absorption, circular dichroism, magnetic circular dichroism, fluorescence anisotropy, Linear dichroism In stretched poly(vinyl alcohol) films, and semiempirical molecular orbital calculations. For both drugs, the lowest energy absorption band, occurring around 400 nm, results from two separate transitions. The corresponding electric transition dipole moments lie in the phenanthridine plane and are polarized, respectively, in the direction of the pyridine moiety (the lower energy transition) and parallel to the phenanthridine long axis (the higher energy transition). Up to four additional different pi --> pi* transitions account for a second band that peaks at 250 nm; they show different polarizations within the phenanthridine plane. The lowest energy transition of the whole spectrum of both drugs corresponds to the promotion of an electron from the HOMO to the LUMO, which are molecular orbitals mainly localized in the phenanthridine and pyridine rings, respectively, thereby implying a charge transfer, upon excitation, from the phenanthridine toward the pyridine ring. The experimental and theoretical results are discussed in relation to the spectroscopic, redox, and photochemical properties of these drugs.
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| 5. |
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| 6. |
- Marincola, F.C., et al.
(författare)
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Recognition and characterization of binding modes of Δ- and Λ-[Ru(phen)3]2+ and Δ- and Λ-[Ru(phen)2DPPZ]2+ by the 23Na NMR Relaxation and Binding Free Energy Parameters
- 1998
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Ingår i: Chemical Physics. - 0301-0104. ; 236:1-3, s. 301-308
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Tidskriftsartikel (refereegranskat)abstract
- Na-23 NMR relaxation rates were measured in Na-DNA aqueous solutions in the presence of Delta- or Lambda-enantiomer of [Ru(phen)(3)](2+) and [Ru(phen)(2)DPPZ](2+). From the analysis of the spin-lattice and spin-spin relaxation rates evidence is given that a decrease of the quadrupolar coupling constant for the slow motions occurs, due to the structural and dynamical modifications of DNA induced by the binding of the ruthenium complexes. Furthermore a linear dependence between the changes of the broad component, R-2bB, and the relative polyelectrolyte contributions to the binding free energy, Delta G(pe)/Delta G, was found. In particular for the intercalators Delta- and Lambda-[Ru(phen)(2)DPPZ](2+), a direct dependence on Delta G(pe)/Delta G was observed, as already found for ethidium, propidium and dq2pyp; while [Ru(phen)(3)](2+) complexes and the pure electrostatic Mg2+ showed an inverse dependence. These results have been discussed in terms of the polyelectrolyte interactions responsible for the R-2bB changes.
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| 7. |
- Ratilainen, Tommi, 1970, et al.
(författare)
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Hybridization of peptide nucleic acid
- 1998
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 37:35, s. 12331-12342
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Tidskriftsartikel (refereegranskat)abstract
- The thermodynamics of hybridization and the conformations of decameric mixed purine-pyrimidine sequence PNA/PNA, PNA/DNA, and DNA/DNA duplexes have been studied using fluorescence energy transfer (FET), absorption hypochromicity (ABS), isothermal titration calorimetry (ITC), and circular dichroism (CD) techniques. The interchromophoric distances determined in the FET experiments on fluorescein- and rhodamine-labeled duplexes indicate that the solution structures of the duplexes are extended helices in agreement with available NMR (PNA/DNA) and crystal X-ray data (PNA/PNA). The melting thermodynamics of the duplexes was studied with both FET and ABS. The thermodynamic parameters obtained with ABS are in good agreement with the parameters from calorimetric measurements while FET detection of duplex melting gives in most cases more favorable free energies of hybridization. This discrepancy between FET and ABS detection is ascribed to the conjugated dyes which affect the stability of the duplexes substantially. Especially, the dianionic fluorescein attached via a flexible linker either to PNA or to DNA seems to be involved in an attractive interaction with the opposite dicationic lysine when hybridized to a PNA strand. This interaction leads to an increased thermal stability as manifested as a 3-4 degrees C increase of the melting temperature. For the PNA/DNA duplex where fluorescein is attached to the PNA strand, a large destabilization (Delta T-m = -12 degrees C) occurs relative to the unlabeled duplex, probably originating from electrostatic repulsion between the fluorescein and the negatively charged DNA backbone. In the case of the PNA/PNA duplex, the sense of helicity of the duplex is reversed upon conjugation of fluorescein via a flexible linker arm, but not when the fluorescein is attached without a linker to the PNA.
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| 8. |
- Son, G.S., et al.
(författare)
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Binding Mode of Norfloxacin to Calf Thymus DNA
- 1998
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 120:26, s. 6451-6457
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Tidskriftsartikel (refereegranskat)abstract
- Norfloxacin, a quinolone antibacterial reagent, has been studied with respect to its binding to calf thymus DNA using fluorescence and linear dichroism techniques and unwinding of supercoiled DNA. The fluorescence of norfloxacin is strongly quenched in the presence of DNA and using this decrease in a fluorescence titration the equilibrium constant of the complex formation was established to be 2.8 x 10(3) M-1. The electric transition moments of the norfloxacin chromophore have been analyzed using fluorescence anisotropy, magnetic circular dichroism, and linear dichroism in stretched poly(vinyl alcohol) film and INDO/S calculations. These data are then used to interpret flow linear dichroism results for the norfloxacin-DNA complex. The transition moments for the long-wavelength transitions are found to be oriented at about 65.0-85.0 degrees with respect to the DNA helix axis. A near perpendicular orientation of the norfloxacin chromophore plane makes it possible to exclude classical groove or surface binding modes. The possibility of a classical intercalation binding mode also can be ruled out from unwinding experiments. However, it is shown that the molecular plane of norfloxacin is near perpendicular relative to the DNA helix axis with a possibility of a bending of the DNA helix at the binding site.
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| 9. |
- Wittung, Pernilla, 1968, et al.
(författare)
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Phospholipid membrane permeability of peptide nucleic acid
- 1995
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Ingår i: FEBS Letters. - : Wiley. - 1873-3468 .- 0014-5793. ; 365:1, s. 27-29
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Tidskriftsartikel (refereegranskat)abstract
- Phospholipid vesicles (liposomes) as membrane models have been used to study the penetration properties of peptide nucleic acid (PNA), a new DNA analog in which the nucleobases are attached to a pseudo-peptide backbone, The liposomes were characterised by carboxyfluorescein efflux, light-scattering and cryogenic transmission electron microscopy. The liposome structure was found not to be affected by the incorporation of PNA or an oligonucleotide. Two 10-mer fluorescein-labelled PNAs were found to have low efflux rates (half-times of 5.5 and 11 days), comparable to a 10-mer oligonucleotide (half-time of 7 days). We conclude that passive diffusion of unmodified PNA is not an effective way of transport into biological cells.
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