Thermodynamics of the DNA binding of biogenic polyamines: Calorimetric and spectroscopic investigations

Kabir, Ayesha; Hossain, Maidul; Kumar, Gopinatha Suresh

doi:10.1016/j.jct.2012.09.025

Cited by 27 publications

(26 citation statements)

References 67 publications

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“…The present study suggests the importance of hydrophobic interactions in the binding mechanism along with strong contribution from electrostatic interactions. Thus, the salt dependent interaction of the polyamine analogue NASPM with DNA followed the same trend as observed with other biogenic polyamines [25].…”

Section: Salt Dependence Of the Interaction And Parsing Of The Standasupporting

confidence: 73%

“…This clear solution was used for all the binding experiments. Concentration of DNA was evaluated by the use of the spectrophotometer and expressed in terms of base pairs by using the molar absorption coefficient (e) value of 13,200 M À1 Á cm À1 at 260 nm [25,32]. The nativeness and duplex nature of the DNA sample was confirmed from optical melting and differential scanning calorimetry experiments where transitions with sharp melting temperatures were observed.…”

Section: Methodsmentioning

confidence: 99%

“…It has been reported that binding of polyamines to DNA is a entropy driven process [24,25,39]. Earlier reports on the interaction of biogenic polyamines with CT DNA have also suggested large entropic contribution [24,25]. The predominant positive entropy term in all the interactions is prerogative of the disruption and release of structured water molecules from the hydration layers of the helical double stranded nucleic acids, thereby facilitating the groove binding mode of the polyamines [40].…”

Section: Thermodynamics Of the Interaction By Isothermal Titration Camentioning

confidence: 97%

“…The entropy change (table 2) seemingly appears to be a major contribution to the standard molar Gibbs energy change than the enthalpy value. It has been reported that binding of polyamines to DNA is a entropy driven process [24,25,39]. Earlier reports on the interaction of biogenic polyamines with CT DNA have also suggested large entropic contribution [24,25].…”

Section: Thermodynamics Of the Interaction By Isothermal Titration Camentioning

confidence: 97%

“…A large volume of literature exists on the interaction of biogenic polyamines with DNA, RNA and tRNA [20][21][22][23][24][25]. However, a thorough understanding of the correct amalgamation of structural variations of polyamine analogues which will favour safety, efficacy and minimise toxicity is still awaited [8,9] that may legitimise the pursuit of analogues having the ability to interfere with polyamine metabolism and function.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Targeting of 1-Naphthyl acetyl spermine to DNA: A calorimetric and spectroscopic investigation

Kabir

Kumar

2016

The Journal of Chemical Thermodynamics

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Section: Salt Dependence Of the Interaction And Parsing Of The Standasupporting

confidence: 73%

Section: Methodsmentioning

confidence: 99%

Section: Thermodynamics Of the Interaction By Isothermal Titration Camentioning

confidence: 97%

Section: Thermodynamics Of the Interaction By Isothermal Titration Camentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Targeting of 1-Naphthyl acetyl spermine to DNA: A calorimetric and spectroscopic investigation

Kabir

Kumar

2016

The Journal of Chemical Thermodynamics

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Lysozyme binding with sulfa group of antibiotics: Comparative binding thermodynamics and computational study

2022

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Protein-drug binding study addresses a broad domain of biological problems associating molecular functions to physiological processes composing and modifying safe and coherent drug therapeutics. Comparison of the binding and thermodynamic aspect of sulfa drugs, sulfamethazine (SMZ) and sulfadiazine (SDZ) with the protein, lysozyme (Lyz) was carried out using spectroscopic, molecular docking, and dynamic simulation studies. The fluorescence quenching and apparent binding constant for the binding reaction were calculated to be in the order of 10 4 M À1 , slightly higher for SMZ as compared to that of SDZ and the binding stoichiometry values show 1:1 drug binding with each protein molecule. The binding was an enthalpy-driven spontaneous exothermic reaction favored by a negative enthalpy and a positive entropy contribution for both the complexes. The binding from the fluorescence quenching data suggests a static quenching mechanism dominated by non-polyelectrolytic components. Synchronous fluorescence denoted a conformational change in the tryptophan moiety of the protein. Molecular docking and dynamic simulation study provided a clearer view of the interaction pattern, where the drug resides on the binding pocket of the protein structure. Overall the protein, Lyz binding of SMZ was slightly more favored over SDZ.

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α-Hemolysin nanopore studies reveal strong interactions between biogenic polyamines and DNA hairpins

2015

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The α-hemolysin (α-HL) nanopore analyzes DNA as it is electrophoretically driven through the pore. The respective current vs. time (i-t) traces depends on the DNA sequence, its secondary structures, or on the physical conditions of the analysis. The current study describes analysis of a DNA hairpin with a 5'-extension with the α-HL nanopore in the presence of the polyamines spermine (Spm), spermidine (Spd), and putrescine (Put). These studies identified a new i-t trace characteristic of the DNA-polyamine complex. Voltage-dependent studies determined that the hairpin-Spm complex formed with excess Spm was not unzipped and translocated through the pore even when the voltage was increased to 180 mV. The DNA hairpin sample was titrated with Spm, Spd, or Put that showed a dose-dependent response in the characteristic event patterns for hairpins bound to Spm or Spd, but not for Put. Plots of the event types vs. count were used to calculate binding constants for the Spm or Spd hairpin interactions under these conditions. The titration also demonstrated that the event rate decreased ~10-fold when the Spm or Spd concentration was increased from 0 to 4 mM. These observations impose practical limitations on the ability to use Spm or Spd for DNA studies with the α-HL nanopore.

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Thermodynamics of the DNA binding of biogenic polyamines: Calorimetric and spectroscopic investigations

Cited by 27 publications

References 67 publications

Targeting of 1-Naphthyl acetyl spermine to DNA: A calorimetric and spectroscopic investigation

Targeting of 1-Naphthyl acetyl spermine to DNA: A calorimetric and spectroscopic investigation

Lysozyme binding with sulfa group of antibiotics: Comparative binding thermodynamics and computational study

α-Hemolysin nanopore studies reveal strong interactions between biogenic polyamines and DNA hairpins

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