title: Shape readout of AT-rich DNA by carbohydrates.
abstract: Gene expression can be altered by small molecules that target DNA; sequence as well as shape selectivities are both extremely important for DNA recognition by intercalating and groove-binding ligands. We have characterized a carbohydrate scaffold (1) exhibiting DNA "shape readout" properties. Thermodynamic studies with 1 and model duplex DNAs demonstrate the molecule's high affinity and selectivity towards B* form (continuous AT-rich) DNA. Isothermal titration calorimetry (ITC), circular dichroism (CD) titration, ultraviolet (UV) thermal denaturation, and Differential Scanning Calorimetry were used to characterize the binding of 1 with a B* form AT-rich DNA duplex d[5'-G2 A6 T6 C2 -3']. The binding constant was determined using ITC at various temperatures, salt concentrations, and pH. ITC titrations were fit using a two-binding site model. The first binding event was shown to have a 1:1 binding stoichiometry and was predominantly entropy-driven with a binding constant of approximately 10(8) M(-1) . ITC-derived binding enthalpies were used to obtain the binding-induced change in heat capacity (ΔCp ) of -225 ± 19 cal/mol·K. The ionic strength dependence of the binding constant indicated a significant electrolytic contribution in ligand:DNA binding, with approximately four to five ion pairs involved in binding. Ligand 1 displayed a significantly higher affinity towards AT-tract DNA over sequences containing GC inserts, and binding experiments revealed the order of binding affinity for 1 with DNA duplexes: contiguous B* form AT-rich DNA (d[5'-G2 A6 T6 C2 -3']) >B form alternate AT-rich DNA (d[5'-G2 (AT)6 C2- 3']) > A form GC-rich DNA (d[5'-A2 G6 C6 T2 -3']), demonstrating the preference of ligand 1 for B* form DNA.
authors.affiliation: Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, 29634.
authors.forename: Sunil
authors.initials: S
authors.lastname: Kumar
authors.forename: Meredith
authors.initials: M
authors.lastname: Newby Spano
authors.forename: Dev P
authors.initials: DP
authors.lastname: Arya
mesh_terms: D020856:AT Rich Sequence; D000465:Algorithms; D001665:Binding Sites; D002152:Calorimetry, Differential Scanning; D002240:Carbohydrate Sequence; D002241:Carbohydrates / Q000737:chemistry*; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D020862:GC Rich Sequence; D007700:Kinetics; D008969:Molecular Sequence Data; D009355:Neomycin / Q000737:chemistry / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics
chemical_list: D002241:Carbohydrates; D009838:Oligodeoxyribonucleotides; D004247:DNA; D009355:Neomycin
keywords: DNA major groove; carbohydrate scaffold; shape recognition