Stacking Interactions: The Key Mechanism for Binding of Proteins to Single-Stranded Regions of Native and Damaged Nucleic Acids?

  • Jean-Jacques Toulmé
Part of the NATO ASI Series book series (NSSA, volume 101)


The enzymatic removal of chemical damage in DNA, the regulation of gene expression by a repressor molecule, and the binding of RNA polymerase to a promoter are some examples of processes which involve specific interactions between proteins and nucleic acids. Actually, most of the steps of replication, transcription, and translation of the genetic information, as well as DNA repair, RNA maturation, or building of nucleosomes or ribosomes require the specific recognition of a nucleic acid structure or base sequence by proteins. Besides gross structural complementarity between the two interacting macromolecules, interactions between individual amino acids and nucleotides can provide the required specificity. We may consider the active center of a nucleic acid-binding protein as a three dimensional distribution of functional groups able to form ionic bonds, hydrogen bonds, and hydrophobic bonds (including stacking). Specificity will be attained when this distribution corresponds to a complementary one on a polynucleotide chain. This might also involve conformational changes of the macromolecule(s).


Aromatic Amino Acid Indole Ring Nucleic Acid Basis Nucleic Acid Structure Polynucleotide Chain 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Plenum Press, New York 1985

Authors and Affiliations

  • Jean-Jacques Toulmé
    • 1
  1. 1.Laboratoire de Biophysique, INSERM U.201Muséum National d’Histoire NaturelleParisFrance

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