A simple model for gene targeting
Journal article, 2001

Sequence-specific binding to genomic-size DNA sequences by artificial agents is of major interest for the development of gene-targeting strategies, gene-diagnostic applications, and biotechnical tools. The binding of one such agent, peptide nucleic acid (PNA), to a randomized human genome has been modeled with statistical mass action calculations. With the length of the PNA probe, the average per-base binding constant k(0), and the binding affinity loss of a mismatched base pair as main parameters, the specificity was gauged as a "therapeutic ratio" G = maximum safe [PNA](tot)/minimal efficient [PNA](tot). This general, though simple, model suggests that, above a certain threshold length of the PNA, the microscopic binding constant k(0) is the primary determinant for optimal discrimination, and that only a narrow range of rather low k(0) values gives a high therapeutic ratio G. For diagnostic purposes, the value of k(0) could readily be modulated by changing the temperature, due to the substantial DeltaH(o) associated with the binding equilibrium. Applied to gene therapy, our results stress the need for appropriate control of the binding constant and added amount of the gene-targeting agent, to meet the varying conditions (ionic strength, presence of competing DNA-binding molecules) found in the cell.


Tommi Ratilainen

Department of Physical Chemistry

Per Lincoln

Department of Physical Chemistry

Bengt Nordén

Department of Physical Chemistry

Biophysical Journal

0006-3495 (ISSN) 1542-0086 (eISSN)

Vol. 81 5 2876-2885

Areas of Advance

Nanoscience and Nanotechnology


Life Science Engineering (2010-2018)

Materials Science

Subject Categories

Physical Chemistry


Basic sciences



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