Understanding of the interactions of ctDNA with an antioxidant flavone analog: Exploring the utility of the small molecule as fluorescent probe for biomacromolecule

Karmakar, Abhijit; Mallick, Tamanna; Alam, Niharul; Das, Shantanu; Batuta, Shaikh; Chandra, Swapan K.; Mandal, Debabrata; Begum, Naznin Ara

doi:10.1016/j.molstruc.2018.03.113

Cited by 17 publications

(5 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As shown in Fig. (A), the relative viscosity of ctDNA showed a slight change with the addition of 5‐HMF, which was similar to the effect of H33258, a classic groove binder . The result was consistent with a previous report of the interaction of sorafenib with ctDNA, indicating the binding mode of 5‐HMF with ctDNA may be groove or electrostatic binding.…”

Section: Resultsmentioning

confidence: 93%

Exploring the binding interaction of Maillard reaction by‐product 5‐hydroxymethyl‐2‐furaldehyde with calf thymus DNA

Zhou

Zhang

et al. 2019

J Sci Food Agric

View full text Add to dashboard Cite

BACKGROUND 5‐Hydroxymethyl‐2‐furaldehyde (5‐HMF), a by‐product of the Maillard reaction, usually present in fried and baked food, may cause potential harm to the human body. Here, the interaction between 5‐HMF and calf thymus DNA (ctDNA) under physiological buffer (pH 7.4) was studied using multi‐spectroscopic methods combined with multivariate curve resolution–alternating least squares (MCR‐ALS) chemometrics and molecular simulation techniques. RESULTS The concentration profiles and pure spectra of the three components (5‐HMF, ctDNA and 5‐HMF–ctDNA complex) were extracted from highly overlapping spectra using MCR‐ALS analysis, which verified the formation of 5‐HMF–ctDNA complex. The binding constant being of the order of 103 L mol−1 at four temperatures (292, 298, 304 and 310 K) indicated a weak affinity in the binding of 5‐HMF to ctDNA. The binding interaction was mainly driven by hydrogen bonds and van der Waals forces. Viscosity analysis, melting assay, ionic strength effect and competitive fluorescence studies ascertained that 5‐HMF bound to ctDNA through groove binding, and it tended to bind to guanine–cytosine rich region of ctDNA which was characterized using Fourier transform infrared spectra and molecular docking. Circular dichroism spectral analysis and DNA cleavage assays indicated that the ctDNA conformation was altered from B to A form and 5‐HMF caused DNA damage at higher concentration. CONCLUSIONS The results suggested that 5‐HMF bound to ctDNA through groove binding and caused DNA damage. This research may contribute to understand the binding mechanism of 5‐HMF to ctDNA and to the assessment of the toxicological effect of 5‐HMF in biological processes. © 2018 Society of Chemical Industry

show abstract

Section: Resultsmentioning

confidence: 93%

Exploring the binding interaction of Maillard reaction by‐product 5‐hydroxymethyl‐2‐furaldehyde with calf thymus DNA

Zhou

Zhang

et al. 2019

J Sci Food Agric

View full text Add to dashboard Cite

show abstract

“…The λ em(max) at 480 nm of DMAHF corresponds to its enol or normal (E* or N*) form, and its keto tautomeric (T*) form (Figure 1) is related to the λ em(max) at 550 nm. 26 On gradual addition of IAA solution, the fluorescence intensity of both of these two bands of DMAHF was found to be enhanced significantly with a concomitant gradual red shift (∼20 nm). Moreover, these bands became sharper.…”

Section: ■ Results and Discussionmentioning

confidence: 95%

“…As shown in Figure a, upon excitation of DMAHF at λ ex 420 nm, an ESIPT-based dual-emission curve consisting of emission maxima (λ em(max) ) at 480 and 550 nm was observed in Tris-HCl buffer (50 mM, pH = 7.4). The λ em(max) at 480 nm of DMAHF corresponds to its enol or normal (E* or N*) form, and its keto tautomeric (T*) form (Figure ) is related to the λ em(max) at 550 nm . On gradual addition of IAA solution, the fluorescence intensity of both of these two bands of DMAHF was found to be enhanced significantly with a concomitant gradual red shift (∼20 nm).…”

Section: Resultsmentioning

confidence: 98%

“…This change of microenvironment of DMAHF showed a substantial influence on its ESIPT-based dual-emission fluorescence behavior. 21,26 From a structural point of view, DMAHF is a potential candidate to interact with IAA or any amyloidogenic protein via various noncovalent interactions, that is, hydrogen bonding, hydrophobic, and π−π stacking interactions. Such interactions of DMAHF with IAA instigated a change in its immediate environment, which is responsible for its drastic change of fluorescence spectral pattern.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Unfolding the Role of a Flavone-Based Fluorescent Antioxidant towards the Misfolding of Amyloid Proteins: An Endeavour to Probe Amyloid Aggregation

et al. 2020

Self Cite

View full text Add to dashboard Cite

4′-N,N-Dimethylamino-3-hydroxyflavone (DMAHF), a synthetic fluorescent flavone analogue with potent antioxidant activity, was explored as a molecular rotor-like fluoroprobe for amyloid aggregations, a causative factor in Alzheimer's disease, Parkinson's disease, type-2 diabetes, etc. During its interactions with (human) insulin amyloid aggregation (IAA), its microenvironment was changed. This instigated a drastic change in its excited-state intramolecular proton transfer-based dual emission behavior, which was tracked to monitor its amyloid probing activity. Thus, the amyloid probing potential of DMAHF was originated from its interactions with IAA, which were studied by various spectroscopic techniques and molecular docking and quantum-mechanical calculations. Morphological changes of the IAA in the presence of DMAHF were studied by scanning electron microscopy. DMAHF also probed efficiently the islet amyloid polypeptide deposition in the pancreatic β-cells of diabetic mice. DMAHF showed significant sensitivity and specificity towards amyloid aggregation without having any complexity in its photophysical behavior. This indicates its potential as an ideal bio-friendly and cost-effective fluoroprobe for amyloid proteins.

show abstract

“…60 The interaction of 4′-N,N-dimethylamino-3-hydroxyflavone (Figure 12-5b) as a minor groove intercalator with the B-form of calf thymus DNA leads to enhancement of fluorescence emission, showing its promising behavior as a biomimetic fluorescence probe. 61 Yang et al showed that the isorhamnetin (Figure 12-5c) as a flavonoid extracted from Ginkgo Biloba leaves could be used for fluorescent sensing of Cu(II) in river and lake water samples and fruit and vegetable samples with satisfactory results. The complex formation Cu(II)-isorhamnetin and resulting fluorescence quenching of isorhamnetin was considered as the proposed mechanism for fluorescence detection of Cu(II) in the developed sensor.…”

mentioning

confidence: 99%

Phytochemicals toward Green (Bio)sensing

et al. 2020

View full text Add to dashboard Cite

Because of numerous inherent and unique characteristics of phytochemicals as bioactive compounds derived from plants, they have been widely used as one of the most interesting nature-based compounds in a myriad of fields. Moreover, a wide variety of phytochemicals offer a plethora of fascinating optical and electrochemical features that pave the way toward their development as optical and electrochemical (bio)sensors for clinical/ health diagnostics, environmental monitoring, food quality control, and bioimaging. In the current review, we highlight how phytochemicals have been tailored and used for a wide variety of optical and electrochemical (bio)sensing and bioimaging applications, after classifying and introducing them according to their chemical structures. Finally, the current challenges and future directions/perspective on the optical and electrochemical (bio)sensing applications of phytochemicals are discussed with the goal of further expanding their potential applications in (bio)sensing technology. Regarding the advantageous features of phytochemicals as highly promising and potential biomaterials, we envisage that many of the existing chemical-based (bio)sensors will be replaced by phytochemical-based ones in the near future.

show abstract

Understanding of the interactions of ctDNA with an antioxidant flavone analog: Exploring the utility of the small molecule as fluorescent probe for biomacromolecule

Cited by 17 publications

References 37 publications

Exploring the binding interaction of Maillard reaction by‐product 5‐hydroxymethyl‐2‐furaldehyde with calf thymus DNA

Exploring the binding interaction of Maillard reaction by‐product 5‐hydroxymethyl‐2‐furaldehyde with calf thymus DNA

Unfolding the Role of a Flavone-Based Fluorescent Antioxidant towards the Misfolding of Amyloid Proteins: An Endeavour to Probe Amyloid Aggregation

Phytochemicals toward Green (Bio)sensing

Contact Info

Product

Resources

About