DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes.
In this paper, we review recent DNA-binding agents that are expected to influence the field of DNA-targeting. We restrict ourselves to binders for which the three-dimensional structure in complex with DNA or RNA has been determined by X-ray crystallography or NMR. Furthermore, we primarily focus on unprecedented ways of targeting peculiar DNA structures, such as junctions, quadruplexes, and duplex DNAs different from the B-form. Classical binding modes of small molecular weight compounds to DNA, i.e. groove binding, intercalation and covalent addition are discussed in those cases where the structures represent a novelty. In addition, we review 3D structures of triple-stranded DNA, of the so-called Peptide Nucleic Acids (PNAs), which are oligonucleotide bases linked by a polypeptide backbone, and of aptamers, which are DNA or RNA receptors that are designed combinatorially. A discussion on perspectives in the field of DNA-targeting and on sequence recognition is also provided.
Boer
D Roeland
DR
Institute for Research in Biomedicine and Institut de Biologia Molecular de Barcelona (CSIC), Barcelona Science Park, Barcelona, Spain.
Canals
Albert
A
Coll
Miquel
M
D020650:Combinatorial Chemistry Techniques; D018360:Crystallography, X-Ray / Q000379:methods; D004247:DNA / Q000737:chemistry*; D045566:DNA, Cruciform / Q000737:chemistry; D015195:Drug Design; D007364:Intercalating Agents / Q000737:chemistry; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008956:Models, Chemical; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D020135:Peptide Nucleic Acids / Q000737:chemistry; D010710:Phosphates / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D013237:Stereoisomerism
D045566:DNA, Cruciform; D007364:Intercalating Agents; D008024:Ligands; D009841:Oligonucleotides; D020135:Peptide Nucleic Acids; D010710:Phosphates; D012313:RNA; D004247:DNA