title: Neomycin binding to Watson-Hoogsteen (W-H) DNA triplex groove: a model.
abstract: Neomycin is the most effective aminoglycoside (groove binder) in stabilizing a DNA triple helix. It stabilizes TAT, as well as mixed base DNA triplexes, better than known DNA minor groove binders (which usually destabilize the triplex) and polyamines. Neomycin selectively stabilizes the triplex (in the presence of salt), without any effect on the DNA duplex. (1) Triplex stabilization by neomycin is salt dependent (increased KCl and MgCl(2) concentrations decrease neomycin's effectiveness, at a fixed drug concentration). (2) Triplex stabilization by neomycin is pH dependent (increased pH decreases neomycin's effectiveness, at a fixed drug concentration). (3) CD binding studies indicate approximately 5-7 base triplets/drug apparent binding site, depending upon the structure/sequence of the triplex. (4) Neomycin shows nonintercalative groove binding to the DNA triplex, as evident from viscometric studies. (5) Neomycin shows a preference for stabilization of TAT triplets but can also accommodate CGC(+) triplets. (6) Isothermal titration calorimetry (ITC) studies reveal an association constant of approximately 2 x 10(5) M(-)(1) between neomycin and an intramolecular triplex and a higher K(a) for polydA.2polydT. (7) Binding/modeling studies show a marked preference for neomycin binding to the larger W-H groove. Ring I/II amino groups and ring IV amines are proposed to be involved in the recognition process. (8) The novel selectivity of neomycin is suggested to be a function of its charge and shape complementarity to the triplex W-H groove, making neomycin the first molecule that selectively recognizes a triplex groove over a duplex groove.
authors.affiliation: Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, South Carolina 29634, USA. dparya@clemson.edu
authors.forename: Dev P
authors.initials: DP
authors.lastname: Arya
authors.forename: Ljiljana
authors.initials: L
authors.lastname: Micovic
authors.forename: I
authors.initials: I
authors.lastname: Charles
authors.forename: R Lane
authors.initials: RL
authors.lastname: Coffee
authors.forename: Bert
authors.initials: B
authors.lastname: Willis
authors.forename: Liang
authors.initials: L
authors.lastname: Xue
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D002151:Calorimetry; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D015636:Magnesium Chloride / Q000737:chemistry; D008958:Models, Molecular; D009355:Neomycin / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D009690:Nucleic Acid Conformation; D011067:Poly dA-dT / Q000737:chemistry; D011189:Potassium Chloride / Q000737:chemistry; D013056:Spectrophotometry, Ultraviolet; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D013816:Thermodynamics; D014783:Viscosity
chemical_list: D000900:Anti-Bacterial Agents; C051802:triplex DNA; D015636:Magnesium Chloride; D011067:Poly dA-dT; D011189:Potassium Chloride; D004247:DNA; D009355:Neomycin