Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices

Xi, Hongjuan; Kumar, Sunil; Došen‐Mićović, Ljiljana; Arya, Dev P.

doi:10.1016/j.biochi.2010.02.004

Cited by 34 publications

(39 citation statements)

References 125 publications

(124 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The slope from this log plot reveals the formation of one ion pair. This is in contrast to our findings for triple helical DNA (68) as well as previous work on binding of neomycin class antibiotics to the A-site rRNA construct where formation of three ion pairs was found (69). The formation of one ion pair thus suggests that binding occurs with lesser electrostatic interaction than what has been observed for the recognition of nucleic acid pockets in the aforementioned nucleic acids.…”

Section: Resultscontrasting

confidence: 99%

Aminoglycoside Binding toOxytricha novaTelomeric DNA

et al. 2010

Self Cite

View full text Add to dashboard Cite

Telomeric DNA sequences have been at the center stage of drug design for cancer treatment in recent years. The ability of these DNA structures to form four stranded nucleic acid structures, called G-quadruplexes, has been perceived as target for inhibiting telomerase activity vital for the longevity of cancer cells. Being highly diverse in structural forms, these G-quadruplexes are subjects of detailed studies of ligand–DNA interactions of different classes, which will pave the way for logical design of more potent ligands in future. The binding of aminoglycosides were investigated with Oxytricha Nova quadruplex forming DNA sequence (GGGGTTTTGGGG)2. Isothermal Titration calorimetry (ITC) determined ligand to quadruplex binding ratio shows 1:1 neomycin:quadruplex binding with association constants (Ka ) ~ 105M−1 while paromomycin was found to have a two-fold weaker affinity than neomycin. The CD titration experiments with neomycin resulted in minimal changes in the CD signal. FID assays, performed to determine the minimum concentration required to displace half of the fluorescent probe bound, showed neomycin as the best of the all aminoglycosides studied for quadruplex binding. Initial NMR footprint suggests that ligand-DNA interactions occur in the wide groove of the quadruplex. Computational docking studies also indicate that aminoglycosides bind in the wide groove of the quadruplex.

show abstract

Section: Resultscontrasting

confidence: 99%

Aminoglycoside Binding toOxytricha novaTelomeric DNA

et al. 2010

Self Cite

View full text Add to dashboard Cite

show abstract

“…Based on previous results of neomycin binding towards AT rich DNA duplex ( K a <10 5 M -1 ) and triplex, we estimate that 3 has at least a 1000 fold higher affinity than neomycin for the B* form AT rich DNA duplexes. 65 …”

Section: Resultsmentioning

confidence: 99%

Neomycin−Neomycin Dimer: An All-Carbohydrate Scaffold with High Affinity for AT-Rich DNA Duplexes

2011

Self Cite

View full text Add to dashboard Cite

A dimeric neomycin-neomycin conjugate 3 with a flexible linker, 2,2’-(Ethylenedioxy)bis(ethylamine), has been synthesized and characterized. Dimer 3 can selectively bind to AT rich DNA duplexes with high affinity. Biophysical studies have been performed between 3 and different nucleic acids with varying base composition and conformation by using ITC (Isothermal Calorimetry), CD (Circular Dichroism), FID (Fluorescent Intercalator Displacement), and UV (Ultra-Violet) thermal denaturation experiments. A few conclusions can be drawn from this study: (1) FID assay with 3 and polynucleotides demonstrates the preference of 3 towards AT rich sequences over GC-rich sequences. (2) FID assay and UV thermal denaturation experiments show that 3 has a higher affinity for the poly(dA).poly(dT) DNA duplex than the poly(dA).2poly(dT) DNA triplex. Contrary to neomycin, 3 destabilizes poly(dA).2poly(dT) triplex but stabilizes poly(dA).poly(dT) duplex, suggesting major groove as the binding site. (3) UV thermal denaturation studies and ITC experiments show that 3 stabilizes continuous AT-tract DNA better than DNA duplexes with alternating AT bases. (4) CD and FID titration studies show a DNA binding site size of 10~12 base pairs/drug, depending upon the structure/sequence of the duplex for AT rich DNA duplexes. (5) FID and ITC titration between 3 and an intramolecular DNA duplex [d(5’-A12-x -T12-3’), × = hexaethylene glycol linker] result in a binding stoichiometry of 1:1 with a binding constant ~ 108 M-1 at 100 mM KCl. (6) FID assay using 3 and 512 hairpin DNA sequences that vary in their AT base content and placement also show a higher binding selectivity of 3 toward continuous AT rich than towards DNA duplexes with alternate AT base pairs. (7) Salt dependent studies indicate the formation of 3 ion pairs during binding of the DNA duplex d[5’-A12-x -T12-3’] and 3. (8) ITC-derived binding constants between 3 and DNA duplexes follow the order, AT continuous, d[5’-G3A5T5C3-3’] > AT alternate, d[5’-G3(AT)5C3-3’] > GC rich d[5’-A3G5C5T3-3’]. (9) 3 binds to AT tract containing DNA duplex (B* DNA, d[5’-G3A5T5C3-3’]) with an order of magnitude higher affinity than to a DNA duplex with alternating AT base pairs (B DNA, d[5’-G3(AT)5C3-3’]) and with almost three orders of magnitude higher affinity than a GC rich DNA (A form, d[5’-A3G5C5T3-3’]).

show abstract

“…A full thermodynamic profile of aminoglycoside complexation with DNA triplexes detailing these studies has been recently published. 35 …”

Section: A Proposed Model For Neomycin Binding To the Dna Triplex mentioning

confidence: 99%

New Approaches Toward Recognition of Nucleic Acid Triple Helices

Arya¹

2010

Acc. Chem. Res.

Self Cite

152

116

View full text Add to dashboard Cite

We show that groove recognition of nucleic acid triple helices can be achieved with aminosugars. Among these aminosugars, neomycin is the most effective aminoglycoside (groove binder) for stabilizing a DNA triple helix. It stabilizes both the T·A·T triplex and mixed-base DNA triplexes better than known DNA minor groove binders (which usually destabilize the triplex) and polyamines. Neomycin selectively stabilizes the triplex (T·A·T and mixed base) without any effect on the DNA duplex. The selectivity of neomycin likely originates from its potential and shape complementarity to the triplex Watson–Hoogsteen groove, making it the first molecule that selectively recognizes a triplex groove over a duplex groove. The groove recognition of aminoglycosides is not limited to DNA triplexes, but also extends to RNA and hybrid triple helical structures. Intercalator–neomycin conjugates are shown to simultaneously probe the base stacking and groove surface in the DNA triplex. Calorimetric and spectrosocopic studies allow the quantification of the effect of surface area of the intercalating moiety on binding to the triplex. These studies outline a novel approach to the recognition of DNA triplexes that incorporates the use of non-competing binding sites. These principles of dual recognition should be applicable to the design of ligands that can bind any given nucleic acid target with nanomolar affinities and with high selectivity.

show abstract

Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices

Cited by 34 publications

References 125 publications

Aminoglycoside Binding toOxytricha novaTelomeric DNA

Aminoglycoside Binding toOxytricha novaTelomeric DNA

Neomycin−Neomycin Dimer: An All-Carbohydrate Scaffold with High Affinity for AT-Rich DNA Duplexes

New Approaches Toward Recognition of Nucleic Acid Triple Helices

Contact Info

Product

Resources

About