Carbohydrate-based DNA ligands: sugar-oligoamides as a tool to study carbohydrate-nucleic acid interactions.
Sugar-oligoamides have been designed and synthesized as structurally simple carbohydrate-based ligands to study carbohydrate-DNA interactions. The general design of the ligands 1-3 has been done as to favor the bound conformation of Distamycin-type gamma-linked covalent dimers which is a hairpin conformation. Indeed, NMR analysis of the sugar-oligoamides in the free state has indicated the presence of a percentage of a hairpin conformation in aqueous solution. The DNA binding activity of compounds 1-3 was confirmed by calf thymus DNA (ct-DNA) NMR titration. Interestingly, the binding of the different sugar-oligoamides seems to be modulated by the sugar configuration. Semiquantitative structural information about the DNA ligand complexes has been derived from NMR data. A competition experiment with Netropsin suggested that the sugar-oligoamide 3 bind to DNA in the minor groove. The NMR titrations of 1-3 with poly(dA-dT) and poly(dG-dC) suggested preferential binding to the ATAT sequence. TR-NOE NMR experiments for the sugar-oligoamide 3-ct-DNA complex both in D(2)O and H(2)O have confirmed the complex formation and given information on the conformation of the ligand in the bound state. The data confirmed that the sugar-oligoamide ligand is a hairpin in the bound state. Even more relevant to our goal, structural information on the conformation around the N-glycosidic linkage has been accessed. Thus, the sugar asymmetric centers pointing to the NH-amide and N-methyl rims of the molecule have been characterized.
Instituto de Química Orgánica, CSIC, c/ Juan de la Cierva 3, Madrid 28006, Spain.
Jason N
JN
Martin
Eva M
EM
Muñoz
Caroline
C
Schwergold
Florence
F
Souard
Juan Luis
JL
Asensio
Jesús
J
Jiménez-Barbero
Javier
J
Cañada
Cristina
C
Vicent
D000577:Amides / Q000737:chemistry; D000595:Amino Acid Sequence; D001665:Binding Sites; D050260:Carbohydrate Metabolism; D002241:Carbohydrates / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D017666:Deuterium Oxide / Q000737:chemistry; D019281:Dimerization; D004214:Distamycins / Q000737:chemistry* / Q000378:metabolism; D006027:Glycosides / Q000737:chemistry; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D011067:Poly dA-dT / Q000737:chemistry / Q000378:metabolism; D011089:Polydeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism; D014867:Water / Q000737:chemistry
D000577:Amides; D002241:Carbohydrates; D004214:Distamycins; D006027:Glycosides; D008024:Ligands; D011089:Polydeoxyribonucleotides; D014867:Water; D011067:Poly dA-dT; C019530:poly(dC-dG); D004247:DNA; C427203:calf thymus DNA; D017666:Deuterium Oxide