Folic acid binds DNA and RNA at different locations

Spectroscopic, biochemical and computational studies of bioactive DNA minor groove binders targeting 5'-WGWWCW-3' motif

Spectroscopic, biochemical, and computational modelling studies have been used to assess the binding capability of a set of minor groove binding (MGB) ligands against the self-complementary DNA sequences 5'-d(CGCACTAGTGCG)-3' and 5'-d(CGCAGTACTGCG)-3'. The ligands were carefully designed to target the DNA response element, 5'-WGWWCW-3', the binding site for several nuclear receptors. Basic 1D 1H NMR spectra of the DNA samples prepared with three MGB ligands show subtle variations suggestive of how each ligand associates with the double helical structure of both DNA sequences. The variations among the investigated ligands were reflected in the line shape and intensity of 1D 1H and 31P-{1H} NMR spectra. Rapid visual inspection of these 1D NMR spectra proves to be beneficial in providing valuable insights on MGB binding molecules. The NMR results were consistent with the findings from both UV DNA denaturation and molecular modelling studies. Both the NMR spectroscopic and computational analyses indicate that the investigated ligands bind to the minor grooves as antiparallel side-by-side dimers in a head-to-tail fashion. Moreover, comparisons with results from biochemical studies offered valuable insights into the mechanism of action, and antitumor activity of MGBs in relation to their structures, essential pre-requisites for future optimization of MGBs as therapeutic agents.

Responsive Carbonized Polymer Dots for Optical Super-resolution and Fluorescence Lifetime Imaging of Nucleic Acids in Living Cells

The rapid development of advanced optical imaging methods including stimulated emission depletion (STED) and fluorescence lifetime imaging microscopy (FLIM) has provided powerful tools for real-time observation of submicrometer biotargets to achieve unprecedented spatial and temporal resolutions. However, the practical imaging qualities are often limited by the performance of fluorescent probes, leading to unsatisfactory results. In particular, long-term imaging of nucleic acids in living cells with STED and FLIM remained desirable yet challenging due to the lack of competent probes combining targeting specificity, biocompatibility, low power requirement, and photostability. In this work, we rationally designed and synthesized a nanosized carbonized polymer dot (CPD) material, CPDs-3, with highly efficient and photostable emission for the super-resolution and fluorescence lifetime imaging of nucleic acids in living cells. The as-fabricated nanoprobe showed responsive emission properties upon binding with nucleic acids, providing an excellent signal-to-noise ratio in both spatial and temporal dimensions. Moreover, the characteristic saturation intensity value of CPDs-3 was as low as 0.68 mW (0.23 MW/cm²), allowing the direct observation of chromatin structures with subdiffraction resolution (90 nm) at very low excitation (<1 μW) and depletion power (<5 mW). Owing to its low toxicity, high photonic efficiency, and outstanding photostability, CPDs-3 was capable of performing long-term imaging both with STED and FLIM setups, demonstrating great potential for the dynamic study of nucleic acid functionalities in the long run.

Molecular complexes of calf thymus DNA with various bioactive compounds: Formation and characterization

The interaction between biomacromolecules and ligands has attracted great interest because of their biological properties. Calf thymus DNA (ctDNA) can interact with bioactive compounds to form complexes. Here, ctDNA-ligand complexes were studied using fluorescence, absorption, and infrared spectroscopy, circular dichroism, ABTS assay and competitive displacement. The binding constants of bioactive compounds at the intercalative site of ctDNA ranked in order kaempferol > apigenin > quercetin > curcumin > riboflavin, while the binding constants at minor groove sites ranked quercetin > kaempferol > naringenin ~ apigenin > hesperetin > curcumin ~ resveratrol ~ riboflavin > caffeic acid. CtDNA maintained stable B-form with an enhancement of base stacking and a decrease of right-handed helicity in the presence of these bioactive compounds, except for hesperetin and caffeic acid. Bioactive compounds preferentially bound to guanine bases and tended to transfer into a more hydrophobic environment upon complexation with ctDNA. The DNA complexation did not affect the ABTS·⁺ scavenging capacity of quercetin, kaempferol, resveratrol and apigenin but increased the ones of naringenin, caffeic acid, curcumin, hesperetin and riboflavin. The data gathered here should be useful to understand the binding modes of DNA with ligands for their potential application in pharmaceutical and food industries.

Locating the binding sites of two aminobenzoic acid derivatives on tRNA: drug binding efficacy and RNA structure

The binding of tRNA to aminobenzoic acid derivatives DAB-0 (N'-[4-(2,5-dioxo-pyrrolidin-1-yl)-benzoyl]-hydrazine carboxylic acid tert-butyl ester) and DAB-1 (N'-[4-(2,5-dioxo-2,5-dihydro-pyrrol-1-yl)-benzoyl]-hydrazine carboxylic acid tert-butyl ester) was investigated in aqueous solution at physiological pH. Thermodynamic parameters ΔH⁰ -4.8 to -4.30 (kJ mol^-1), ΔS⁰ 24.20 to 22 (J mol^-1K^-1) and ΔG⁰ -12 to -11.40 (kJ mol^-1) showed that DAB-0 and DAB-1 readily bind tRNA via ionic interactions with DAB-1 forming stronger tRNA adducts. Similar binding sites to A-T and G-C bases were located with DAB-0 and DAB-1. The binding efficacy ranged from 40% to 50%. No alteration of tRNA conformation was detected upon drug complexation. Communicated by Ramaswamy H. Sarma.

Binding efficacy of aminobenzoic acid derivatives with DNA duplex: drug binding sites and DNA structure and dynamics

Communicated by Ramaswamy H. Sarma.

Demonstration of the lack of cytotoxicity of unmodified and folic acid modified graphene oxide quantum dots, and their application to fluorescence lifetime imaging of HaCaT cells

The authors describe the synthesis of water-soluble and fluorescent graphene oxide quantum dots via acid exfoliation of graphite nanoparticles. The resultant graphene oxide quantum dots (GoQDs) were then modified with folic acid. Folic acid receptors are overexpressed in cancer cells and hence can bind to functionalized graphene oxide quantum dots. On excitation at 305 nm, the GoQDs display green fluorescence with a peak wavelength at ~520 nm. The modified GoQDs are non-toxic to macrophage cells even after prolonged exposure and high concentrations. Fluorescence lifetime imaging and multiphoton microscopy was used (in combination) to image HeCaT cells exposed to GoQDs, resulting in a superior method for bioimaging. Graphical abstract Schematic representation of graphene oxide quantum dots, folic acid modified graphene oxide quantum dots (red), and the use of fluorescence lifetime to discriminate against green auto-fluorescence of HeCaT cells.

tRNA conjugation with folic acid-chitosan conjugates

The conjugation of tRNA with folic acid-chitosan conjugates was studied, using multiple spectroscopic methods and transmission electron microscopy (TEM). Thermodynamic analysis ΔH -14 to -10 (KJMol^-1) and ΔS 14 to -1 (JMol^-1, K^-1) showed tRNA-folic acid-chitosan bindings occur via H-bonding, hydrophobic and van der Waals contacts. The loading efficacy and the stability of tRNA conjugates were enhanced as folic acid-chitosan size increased. TEM analysis showed major tRNA morphological changes, upon folic acid-chitosan conjugation. No alteration of tRNA conformation was observed on conjugate formation. Folic acid-chitosan conjugates can deliver tRNA in vitro.