Issue February 2003

category image Volume 20
No. 4 (p 487-614)
February 2003
ISSN 0739-1102

Melting of Cross-Linked DNA V. Cross-Linking Effect Caused by Local Stabilization of the Double Helix (p. 533-546)

DNA interstrand cross-links are usually formed due to bidentate covalent or coordination binding of a cross-linking agent to nucleotides of different strands. However interstrand linkages can be also caused by any type of chemical modification that gives rise to a strong local stabilization of the double helix. These stabilized sites conserve their helical structure and prevent local and total strand separation at temperatures above the melting of ordinary AT and GC base pairs. This local stabilization makes DNA melting fully reversible and independent of strand concentration like ordinary covalent interstrand cross-links. The stabilization can be caused by all the types of chemical modifications (interstrand cross-links, intrastrand cross-links or monofunctional adducts) if they give rise to a strong enough local stabilization of the double helix. Our calculation demonstrates that an increase in stability by 25 to 30 kcal in the free energy of a single base pair of the double helix is sufficient for this ?cross-linking effect? (i.e. conserving the helicity of this base pair and preventing strand separation after melting of ordinary base pairs). For the situation where there is more then one stabilized site in a DNA duplex (e.g., 1 stabilized site per 1000 bp), a lower stabilization per site is sufficient for the ?cross-linking effect? (18 - 20 kcal). A substantial increase in DNA stability was found in various experimental studies for some metal-based anti-tumor compounds. These compounds may give rise to the effect described above. If ligand induced stabilization is distributed among several neighboring base pairs, a much lower minimum increase per stabilized base pair is sufficient to produce the cross-linking effect (1 bp- 24.4 kcal; 5 bp- 5.3 kcal; 10 bp- 2.9 kcal, 25 bp- 1.4 kcal; 50 bp- 1.0 kcal). The relatively weak non-covalent binding of histones or protamines that cover long regions of DNA (20- 40 bp) can also cause this effect if the salt concentration of the solution is sufficiently low to cause strong local stabilization of the double helix. Stretches of GC pairs more than 25 bp in length inserted into poly(AT) DNA also exhibit properties of stabilizing interstrand cross-links.

Alexander S. Fridman1
Viktor Brabec2
Samvel G. Haroutiunian3
Roger M. Wartell4
Dmitri Y. Lando1,*

1Institute of Bioorganic Chemistry
Belarus National Academy of Sciences
Kuprevich St. 5/2
220141 Minsk, Belarus
2Institute of Biophysics
Academy of Sciences of the Czech Republic
Královopolská 135
CZ-61265 Brno, Czech Republic
3Chair of Molecular Physics
Department of Physics
Yerevan State University
375049 Yerevan, Armenia
4School of Biology
Georgia Institute of Technology
Atlanta, Georgia 30332-0230, USA
*Lando@iboch.bas-net.by

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