Hybridization of peptide nucleic acid
Journal article, 1998

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.

Author

Tommi Ratilainen

Department of Physical Chemistry

Anders Holmén

Department of Physical Chemistry

Eimer Tuite

Department of Physical Chemistry

G. Haaima

L. Christensen

P.E. Nielsen

Bengt Nordén

Department of Physical Chemistry

Biochemistry

0006-2960 (ISSN) 1520-4995 (eISSN)

Vol. 37 35 12331-12342

Areas of Advance

Nanoscience and Nanotechnology (2010-2017)

Energy

Life Science Engineering (2010-2018)

Materials Science

Subject Categories

Physical Chemistry

Roots

Basic sciences

DOI

10.1021/bi9808722

More information

Created

10/7/2017