Nucleic acids ligand interactions modeling

Relationships in Modeling Nucleic Acid Ligand Interactions. 

STRUCTURE-ACTIVITY RELATIONSHIPS IN MODELING NUCLEIC ACID LIGAND INTERACTIONS... 

DNA Bases and Base Pairs Ab Initio Calculations Nucleic Acid Conformation and Flexibility Modeling Using Molecular Mechanics Nucleic Acid Force Fields Structure-Activity Relationships in Modeling Nucleic Acid Ligand Interactions. 

We see that DFT is increasingly used to model a wide range of weak interactions in protein-ligand and nucleic acid-ligand systems. Often, DFT is the only method that can incorporate all electron correlated calculations and that can be applied in... 

Shafer, RH (1998) Stability and structure of model DNA triplexes and quadruplexes and their interactions with small ligands. Prog. Nucleic Acid Bes. Mol. Biol. 59, 55-94. 

Computational biochemistry and computer-assisted molecular modeling have rapidly become a vital component of biochemical research. Mechanisms of ligand-receptor and enzyme-substrate interactions, protein folding, protein-protein and protein-nucleic acid recognition, and de novo protein engineering are but a few examples of problems that may be addressed and facilitated by this technology. 

We can now identify the major factors which play a role in the DNA-platination and chelation steps i) The nature and charge of the actual platinum species, ii) the bases to be platinated and their neighboring sequences, and iii) the nature of the nonleaving platinum ligands and their eventual interaction with the nucleic acid. To get a deeper insight into these parameters, in order to achieve selective DNA-platination, the study of oligonucleotide models is an appropriate approach. 

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