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.

Aminoglycoside–Nucleic Acid Interactions: The Case for Neomycin

“…Neomycin selectively stabilizes DNA triplex without affecting the duplex [113][114][115][116]. Increasing the molar ratios of neomycin from 0-25 µM, r db (ratio drug [neomycin]/base triplet)=1.67, increases the triplex melting point by nearly 25°C, whereas the duplex is virtually unaffected (Fig.…”

“…Previous studies of neomycin have shown that it has a marked preference for binding to the larger Watson-Hoogsteen (W-H) groove of the triplex [116]. Ring I/II amino groups and Ring IV amines were proposed to be involved in the recognition process.…”

Molecular recognition of single‐stranded RNA: Neomycin binding to poly(A)

“…There is extensive evidence describing the ability of aminoglycosides (e.g. neomycin) to bind both duplex and triplex forms of DNA, in addition to quadruplex structures, DNA:RNA hybrids, and to some extent, single-stranded nucleic acids [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20].…”

DNA Major Groove Binders: Triple Helix-Forming Oligonucleotides, Triple Helix-Specific DNA Ligands and Cleaving Agents

“…Some exceptions have been reported. The Crick-Hoogsteen groove is very narrow, but the Watson-Hoogsteen groove may accommodate the binding of some ligands, like neomycin [124]. It has also been reported that DAPI, which is usually a groove binder, may intercalate into some triple helices [125].…”

“…A rationale has been provided for the differential effects of 2,6-, 2,7-and 1,4-disubstituted anthraquinone derivatives on triplex stabilization [127,128]. Molecular modelling has also suggested that neomycin displays a good charge and shape complementarity with the Watson-Hoogsteen groove of triplexes [124,129].…”