Aminoglycoside−Nucleic Acid Interactions:  Remarkable Stabilization of DNA and RNA Triple Helices by Neomycin

Abstract

The stabilization of poly(dA).2poly(dT) triplex, a 22-base DNA triplex, and poly(rA).2poly(rU) triple helix by neomycin is reported. The melting temperatures, the association and dissociation kinetic parameters, and activation energies (E(on) and E(off)) for the poly(dA).2poly(dT) triplex in the presence of aminoglycosides and other triplex binding ligands were determined by UV thermal analysis. Our results indicate that: (i) neomycin stabilizes DNA triple helices, and the double helical structures composed of poly(dA).poly(dT) are virtually unaffected. (ii) Neomycin is the most active and triplex-selective stabilization agent among all aminoglycosides, previously studied minor groove binders, and polycations. Its selectivity (DeltaT(m3-->2) vs DeltaT(m2)(-->)(1)) exceeds most intercalating drugs that bind to triple helices. (iii) Neomycin selectively stabilizes DeltaT(m3)(-->)(2) for a mixed 22-base DNA triplex containing C and T bases in the pyrimidine strand. (iv) The rate constants of formation of triplex (k(on)) are significantly enhanced upon increasing molar ratios of neomycin, making triplex association rates closer to duplex association rates. (v) E(on) values become more negative upon increasing concentration of aminoglycosides (paromomycin and neomycin). E(off) values do not show any change for most aminoglycosides except neomycin. (vi) Aminoglycosides can effectively stabilize RNA [poly(rA).2poly(rU)] triplex, with neomycin[being one of the most active ligands discovered to date (second only to ellipticine). (vii) The stabilization effect of aminoglycosides on triple helices is parallel to their toxic behavior, suggesting a possible role of intramolecular triple helix (H-DNA) stabilization by the aminoglycosides.

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

“…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].…”

Inhibition of pre-mRNA splicing by small molecules.

“…It has been demonstrated that several different types of small molecules act as inhibitors of various biological, RNA-catalyzed, key processes (Sucheck & Wong, 2000;Arya et al, 2001;Bryan et al, 2004;Bakkour et al, 2007), These inhibitors are useful for investigating the pre-mRNA splicing mechanism (Hertweck et. al, 2003;Kaida et.…”

“…The probable mode of action by methyl mercury would be through its positive ionic charge since it is an organometallic cation where it might displace any catalytic magnesium ions or it may even interact with the negatively charged backbone of the RNA, such as aminoglycosides (Sucheck & Wong, 2000;Arya et al, 2001;Bryan et al, 2004;Bakkour et al, 2007).…”

“…give any sort of leads, as it can build on biological knowledge gathered over years (Arya et al, 2001). …”