Biophysical characterization of the strong stabilization of the RNA triplex poly(U)•poly(A)*poly(U) by 9-O-(ω-amino) alkyl ether berberine analogs.

Debipreeta Bhowmik,Suman Das,Lucy Haq,Maidul Hossain,Gopinatha Suresh Kumar,Haiwei Song

doi:10.1371/journal.pone.0037939

Debipreeta Bhowmik, Suman Das + Show 4 more

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https://doi.org/10.1371/journal.pone.0037939

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Abstract

BackgroundBinding of two 9-O-(ω-amino) alkyl ether berberine analogs BC1 and BC2 to the RNA triplex poly(U)•poly(A)*poly(U) was studied by various biophysical techniques.Methodology/Principal FindingsBerberine analogs bind to the RNA triplex non-cooperatively. The affinity of binding was remarkably high by about 5 and 15 times, respectively, for BC1 and BC2 compared to berberine. The site size for the binding was around 4.3 for all. Based on ferrocyanide quenching, fluorescence polarization, quantum yield values and viscosity results a strong intercalative binding of BC1 and BC2 to the RNA triplex has been demonstrated. BC1 and BC2 stabilized the Hoogsteen base paired third strand by about 18.1 and 20.5°C compared to a 17.5°C stabilization by berberine. The binding was entropy driven compared to the enthalpy driven binding of berbeine, most likely due to additional contacts within the grooves of the triplex and disruption of the water structure by the alkyl side chain.Conclusions/SignificanceRemarkably higher binding affinity and stabilization effect of the RNA triplex by the amino alkyl berberine analogs was achieved compared to berberine. The length of the alkyl side chain influence in the triplex stabilization phenomena.

Highlights

Triple helix formation has been proposed as a means for sequence-specific recognition and binding by a relatively short single stranded DNA or RNA to either a double-stranded DNA or RNA [1,2,3,4,5,6,7] originally discovered by Rich and coworkers as early as in 1957 [8]
Conclusions/Significance: Remarkably higher binding affinity and stabilization effect of the RNA triplex by the amino alkyl berberine analogs was achieved compared to berberine
The antiparallel arrangement of a purine strand flanked by two pyrimidine strands is termed as the ‘pyrimidine-purine*pyrimidine’ (YRY, Y is pyrimidine and R is purine) motif that yields C.G*C+, T.A*T (DNA triplexes) or the U.A*U triplex (RNA triplex)

Summary

Introduction

Triple helix formation has been proposed as a means for sequence-specific recognition and binding by a relatively short single stranded DNA or RNA to either a double-stranded DNA or RNA [1,2,3,4,5,6,7] originally discovered by Rich and coworkers as early as in 1957 [8]. Conclusions/Significance: Remarkably higher binding affinity and stabilization effect of the RNA triplex by the amino alkyl berberine analogs was achieved compared to berberine. In this manuscript we describe the triplex-binding affinities and the associated thermodynamic aspects of the interaction of two new 9-amino alkyl analogs (Figure 1) in comparison to berberine.

Results

Conclusion