DNA Base Pairs Research Articles

Phenylboronic acid-modified polymaleic anhydride-F127 micelles for pH-activated targeting delivery of doxorubicin

Phenylboronic acid (PBA) is a tumor-targeting molecule which selectively recognizes sialic acid (SA) overexpressed in tumors. In the study, PBA, F127 and ethanolamine were conjugated with poly(maleic anhydride) by one-step reaction to form amphiphilic polymer for doxorubicin encapsulation. Two drug-carrying micelles with different mass ratio of polymer to drug were prepared by dialysis method to study effect of PBA on doxorubicin release, tumor-targeting and antitumor activity. The study results showed that doxorubicin release from the formulations was acid-sensitive and affected by the polymer dosage, and its acid-induced release behavior improved its insertion into DNA base pairs. Formulation with high polymer dosage showed better tumor targeting and antitumor activity, and activity of inhibiting HepG2 with higher content of SA-containing glycosphingolipids was higher than that of anti-B16. In vivo studies on the activity of B16-bearing mice showed that the doxorubicin-loaded micelles could inhibit the tumor growth and were safer than free doxorubicin. Thus, the PBA-modified nano-polymer micelles have potential biomedical applications due to their nanostructure and tumor-targeting ability.

Nanomaterial-Embedded DNA Films on 2D Frames.

Recently, 3D printing has provided opportunities for designing complex structures with ease. These printed structures can serve as molds for complex materials such as DNA and cetyltrimethylammonium chloride (CTMA)-modified DNA that have easily tunable functionalities via the embedding of various nanomaterials such as ions, nanoparticles, fluorophores, and proteins. Herein, we develop a simple and efficient method for constructing DNA flat and curved films containing water-soluble/thermochromatic dyes and di/trivalent ions and CTMA-modified DNA films embedded with organic light-emitting molecules (OLEM) with the aid of 2D/3D frames made by a 3D printer. We study the Raman spectra, current, and resistance of Cu2+-doped and Tb3+-doped DNA films and the photoluminescence of OLEM-embedded CTMA-modified DNA films to better understand the optoelectric characteristics of the samples. Compared to pristine DNA, ion-doped DNA films show noticeable variation of Raman peak intensities, which might be due to the interaction between the ion and phosphate backbone of DNA and the intercalation of ions in DNA base pairs. As expected, ion-doped DNA films show an increase of current with an increase in bias voltage. Because of the presence of metallic ions, DNA films with embedded ions showed relatively larger current than pristine DNA. The photoluminescent emission peaks of CTMA-modified DNA films with OLEMRed, OLEMGreen, and OLEMBlue were obtained at the wavelengths of 610, 515, and 469 nm, respectively. Finally, CIE color coordinates produced from CTMA-modified DNA films with different OLEM color types were plotted in color space. It may be feasible to produce multilayered DNA films as well. If so, multilayered DNA films embedded with different color dyes, ions, fluorescent materials, nanoparticles, proteins, and drug molecules could be used to realize multifunctional physical devices such as energy harvesting and chemo-bio sensors in the near future.

Concerted Double Hydrogen-Bond Breaking by Intermolecular Coulombic Decay in the Formic Acid Dimer.

Hydrogen bonds are ubiquitous in nature and of fundamental importance to the chemical and physical properties of molecular systems in the condensed phase. Nevertheless, our understanding of the structural and dynamical properties of hydrogen-bonded complexes in particular in electronic excited states remains very incomplete. Here, by using formic acid (FA) dimer as a prototype of DNA base pair, we investigate the ultrafast decay process initiated by removal of an electron from the inner-valence shell of the molecule upon electron-beam irradiation. Through fragment-ion and electron coincident momentum measurements and ab initio calculations, we find that de-excitation of an outer-valence electron at the same site can initiate ultrafast energy transfer to the neighboring molecule, which is in turn ionized through the emission of low-energy electrons. Our study reveals a concerted breaking of double hydrogen-bond in the dimer initiated by the ultrafast molecular rotations of two FA+ cations following this nonlocal decay mechanism.

Co(III)-tetra(4-sulfonatophenyl)porphyrin complexes with bidentate ligands in aqueous buffer media

The processes of hydrophilic Co(III)-tetra(4-sulfonatophenyl)porphyrin supramolecular assembly with 4,4-bipyridyl in aqueous buffer media have been studied by UV-vis, 1D and 2D 1H NMR-spectroscopy. In the case of 1,4-diazabicyclo[2.2.2]octane, pyrazine and piperazine in aqueous solutions, no assembly was observed. Interactions of the hydrophilic Co(III)-tetraarylporphyrin with ionic micelles (cationic surfactants with different alkyl tail lengths) in buffer media were investigated. These studies were performed by the UV-vis, 1D NOESY-spectroscopy and dynamic lightscattering (DLS) methods. The metalloporphyrins were incorporated into the hydrophobic part of micelles, which led to Co(III) reduction to Co(II) in the Co-porphyrinate composition. The rate of Co(III) reduction accompanied by detachment of additional ligands coordinated on Co(III)-porphyrins or disruption of supramolecular dimers and depends on the surfactant concentration and nature. The results obtained indicate the possibility of creating supramolecular porphyrin-based assemblies with the preprogrammed lifetime (from several hours to several days) and could be used in the creation of host-guest systems for recognition, selective binding and the prolonged release of bioactive substrates as the means in the designing of biomimetic systems with effective binding affinities to heterocycles, DNA base pairs and RNA.

Some assembly required: structural and mechanistic studies of histone chaperones, nucleosome assembly factors and ATP dependent chromatin remodelers

All eukaryotes organize their DNA into nucleosomes, consisting of an octamer of the four core histone proteins H2A, H2B, H3, and H4, around which 147 base pairs of DNA are wrapped in two tight superhelical turns. Nucleosomes pack into higher order structures and require histone chaperones and ATP‐dependent remodelers to make the DNA accessible. I will discuss our recent progress in understanding the higher order structure of chromatin at the centromere, and the role of centromere‐binding proteins in locally folding the chromatin fiber. I will also discuss mechanisms by which nucleosomes are remodeled and assembled in an ATP dependent and ATP‐independent manner. The histone chaperone FACT binds and stabilizes partially disassembled nucleosomes by employing an acidic C‐terminal domain as a DNA mimic to clamp down a histone dimer. The chromatin remodeler SMARCAD1 requires ATP hydrolysis to remove histones from a nucleosome, which it then can deposit onto a new DNA segment in an ATP‐independent mechanism, and I will present biochemical and structural evidence for this mode of action.

Canonical, and Multistranded, Alternative and Transitional Helical (C‐MATH) Nucleic Acid Microarrays: Next Generation Double‐, and Four‐Stranded DNA and RNA Microarrays

Many different types of nucleic acids, with unique structures, play important roles in prokaryotic and eukaryotic regulation of an organisms genome, e.g., canonical double‐stranded (ds‐) right‐handed B‐DNA, alternative left‐handed ds‐Z‐DNA, triplex DNA, G4‐quadruplex DNA, i‐motif DNA, slipped‐strand DNA and cruciform DNA. These canonical and exotic (e.g., Z‐DNA, and four‐stranded G4‐quadruplex DNA) nucleic acid structures also regulate many different pathological conditions. The application of exotic nucleic acids, based on its structure, has not been applied to commercial, conventional DNA microarrays. Conventional DNA microarrays are powerful tools that allow for gene expression studies, however, they have severe limitations. The basic principle behind conventional DNA microarrays is that complementary sequences of DNA molecules will bind to each other. Commercial DNA microarrays measure the relative abundance of mRNA sequences isolated from cells by taking advantage of complementary DNA base pairing. Researchers employ DNA microarrays to quantify the different levels of gene expression involving very large numbers of genes simultaneously, or to genotype numerous areas of an organisms genomic makeup. DNA microarrays needs to evolve beyond these limitations. The novel, next generation DNA and RNA microarrays, i.e., Canonical, and Multistranded, Alternative and Transitional Helical (C‐MATH) Nucleic Acid Microarrays, allow for a completely different approach to studying gene expression [e.g., genes (B‐DNA, Z‐DNA) and telomers (G4‐quadruplex DNA)], based on the different structure of ds‐DNA and RNA, and multi‐stranded DNA and RNA molecules. It also allows for the characterization of different drugs and biologics that can directly bind to nucleic acids and inhibit gene expression (or enhance it). C‐MATH DNA microarrays can enhance the “drug discovery” part of “drug discovery and development”, resulting in new drugs, new uses for old drugs and lower coast for drug‐based research. Recent advances in the novel C‐MATH nucleic acid microarrays allow for more precise quantification of multiple fluorescent signals coming from a single immobilized DNA molecule (fluorescently labelled), i.e., B‐DNA, Z‐DNA and G4‐quadruplex DNA. Fluorescent and colorimetric DNA microarrays scanners were employed. The C‐MATH microarrays allow for superior analysis of colocalization, and permits competitive binding assays involving two or more fluorescently labelled drugs or biologicals binding to a gene sequence. Positive and negative controls involve direct binding by DNA‐binding chemicals and anti‐DNA antibodies. Conventional image analysis software was used, along with the development of novel algorithms to differentiate multiple fluorescence signals and intensity. The C‐MATH DNA and RNA microarrays will allow for development of new classes of DNA and RNA structure‐based drugs, and biologics (e.g., antibody, transcription factors), i.e., sequence‐specific and non‐sequence‐specific DNA and RNA binding therapeutics. Additionally, it will also allow for characterization of nucleic acids under different environmental conditions similar to a cell.

Nucleophilic Thiol Proteins Bind Covalently to Abasic Sites in DNA.

In the course of studies on the enhancement of 1,2-dibromoethane-induced DNA base pair mutations by O6-alkylguanine-DNA alkyltransferase (AGT, MGMT), we discovered the facile reaction of AGT with an abasic site in DNA, leading to covalent cross-linking. The binding of AGT differs from the mechanism reported for the protein HMCES; instead it appears to involve formation of a stable thioglycoside. Facile cross-linking was also observed with the protease papain, which like AGT has a low pKa cysteine, and the tripeptide glutathione.

Effect of Bis‐Dimethylamine Substitution on DNA Binding Property and Cytotoxic Activity of Polyhydroxyxanthone

AbstractA bis‐dimethylamine substituted xanthone (Xan‐2) was obtained by cationic modification of the free C3 and C6 hydroxy groups of 1,3,6‐trihydroxyxanthone (Xan‐1) which was isolated from Polygala hongkongensis Hemsl.. The results of the spectroscopic analysis, melting profiles, electrophoretic migration, PCR assay and molecular docking indicated that the hydrophobic plane of Xan‐1 and Xan‐2 could intercalate into the DNA base pairs meanwhile the basic amine alkyl chain of Xan‐2 could bind with DNA phosphate framework via electrostatic interaction. Thus, Xan‐2 exhibited higher DNA binding affinity than Xan‐1. Further study showed that Xan‐2 could inhibit the proliferation of HeLa, SGC‐7901 and A549 cells effectively by MTT assay and induce apoptosis of HeLa cells as detected by AO/EB staining and flow cytometry assay. Interestingly, Xan‐2 exhibited selective cytotoxicity to cells, which was proved by its relatively low inhibitory effect on Raw 264.7 cell. What these studies mean is that disubstituted amine alkyl chains will play an important role in DNA binding property and cytotoxic activity, providing a direction for the development of novel potential antitumor agents.

Design, synthesis and biological evaluation of 3-arylisoquinoline derivatives as topoisomerase I and II dual inhibitors for the therapy of liver cancer

To explore novel topoisomerase inhibitors with high activity and druggability, 3-aryl isoquinoline alkaloids based on the corydamine modification and preliminary SARs of isoquinoline alkaloids in our previous works were re-designed. Currently, the design strategy is mainly revolved around the rigidity and flexibility of the molecular side chain and the molecular size. Consequently, not only the activity and druggability of the compound could be further improved, also the mechanism behind could been discovered. In vitro pharmacological studies, the outstanding nature with the excellent activity and the researchable depth of azepane-substituted compound 7 has been found through the vitro cytotoxicity test (IC50 = 1.93 μM in HuH7 cells and 2.10 μM in LM9 cells) and topoisomerase test. It was found that compound 7 had dual inhibitory effects on topoisomerase I and II, and its inhibitory activity on topoisomerase II is stronger than the positive drug etoposide. From the perspective of molecular docking, it had been verified that compound 7 could insert between DNA base pairs, which was consistent with the results of the DNA unwinding experiment. And the comet experiment confirmed 7 caused DNA damage. Meanwhile, compound 7 could inhibit cell proliferation, invasion and migration, and induce apoptosis by inhibiting PI3K/Akt/mTOR signaling pathway. Therefore, this study may lay a foundation for the discovery of 3-arylisoquinoline compounds with anti-liver cancer potential.

Supramolecular assembly of hydrophilic Co(III)-porphyrin with bidentate ligands in aqueous buffer media

The processes of hydrophilic Co(III)-tetra(4-sulfonatophenyl)porphyrin supramolecular assembly with 4,4-bipyridyl in aqueous buffer media have been studied by UV–vis, 1D and 2D 1H NMR-spectroscopy. In the case of 1,4-diazabicyclo[2.2.2]octane, pyrazine and piperazine in aqueous solutions, no assembly was observed. Interactions of the hydrophilic Co(III)-tetraarylporphyrin with ionic micelles (cationic surfactants with different alkyl tail lengths) in buffer media were investigated. These studies were performed by the UV–vis, 1D NOESY-spectroscopy and dynamic lightscattering (DLS) methods. The metalloporphyrins were incorporated into the hydrophobic part of micelles, which led to Co(III) reduction to Co(II) in the Co-porphyrinate composition. The rate of Co(III) reduction accompanied by detachment of additional ligands coordinated on Co(III)-porphyrins or disruption of supramolecular dimers and depends on the surfactant concentration and nature. The results obtained indicate the possibility of creating of supramolecular porphyrin-based assembles with the preprogrammed lifetime (from several hours to several days) and could be used in the creation of host–guest systems for recognition, selective binding and prolonged release of bioactive substrates as the means in the designing of biomimetic systems with effective binding affinities to heterocycles, DNA base pairs and RNA.

A Catalogue of Orthogonal Complementary Ligand Pairings for Palladium(II) Complexes.

Molecular recognition is a form of information transfer, seen in the base pairing in DNA which is derived from the identity (acceptor or donor) and number of hydrogen bond sites within each base. Here we report bis‐ligand palladium(II) complexes that exhibit similar complementarity. Pd(II) has square planar four‐coordinate geometry, giving control over ligand orientation and denticity. Pairings were developed using ligand denticity (3 : 1 or 2 : 2), and hydrogen bond capability (AA:DD or AD:DA) or lack thereof. Five pairings were investigated, with two sets of four being found fully orthogonal. The two 3 : 1 pairings exhibited limited ligand exchange. The extent of this exchange varied dependant on solvent from 2 : 1 (desired to undesired) to 6 : 1. A reliable and varied set of ligand pairs have therefore been developed for bis‐ligand coordination sphere engineering in pursuit of sorting for complex molecular architectures and molecular‐level information storage and transfer events.

CRISPR-Cas9 bends and twists DNA to read its sequence.

In bacterial defense and genome editing applications, the CRISPR-associated protein Cas9 searches millions of DNA base pairs to locate a 20-nucleotide, guide-RNA-complementary target sequence that abuts a protospacer-adjacent motif (PAM). Target capture requires Cas9 to unwind DNA at candidate sequences using an unknown ATP-independent mechanism. Here we show that Cas9 sharply bends and undertwists DNA upon PAM binding, thereby flipping DNA nucleotides out of the duplex and toward the guide RNA for sequence interrogation. Cryo-electron-microscopy (EM) structures of Cas9:RNA:DNA complexes trapped at different states of the interrogation pathway, together with solution conformational probing, reveal that global protein rearrangement accompanies formation of an unstacked DNA hinge. Bend-induced base flipping explains how Cas9 “reads” snippets of DNA to locate target sites within a vast excess of non-target DNA, a process crucial to both bacterial antiviral immunity and genome editing. This mechanism establishes a physical solution to the problem of complementarity-guided DNA search and shows how interrogation speed and local DNA geometry may influence genome editing efficiency.

Anti-Cancer and Anti-Inflammatory Potential of Furanocoumarins from Ammi majus L.

Secondary metabolites have potential benefits to human being. They are used in the food, agricultural and pharmaceutical industries. The secondary metabolite of furanocoumarins from different plant sources is essential in various skin-related ailments. Biologically, these chemicals are isolated from different plants in the Apiaceae, Fabaceae, Rutaceae and Moraceae families. Ammi majus L. is one of the most common plants in the family of Apiaceae with a large quantity of derivatives. The furanocoumarin derivatives defend the plant by fighting external enemies by Systemic Acquired Resistance (SAR). Via suppressing or retarding microbial growth in infected parts, these derivatives, along with SAR, help to alleviate inflammation in the human body. Latest evidence of these compounds has been established in the treatment of cancer, but the mechanism that needs to be elaborated is not yet understood. Recent studies have shown that furanocoumarin derivatives bind to DNA base pairs and block DNA replication. This may be a potential pathway that helps to regulate the growth of cancerous cells. This article reflects on the pharmaceutical data of furanocoumarins and their different mechanisms in these cases.

Electrochemical detection of DNA damage caused by novel potential 2-nitroimidazole naphthalimide-based hypoxia tumor-targeting agent with mimimum side effects

In this work, we designed and synthesized two novel 2-nitroimidazole-naphthalimide-derived antitumor agents N-(2-(naphthalimide)ethyl)-2-(2-nitroimidazole)acetamide (D-2) and N-(2-(5-nitro-naphthalimide)ethyl)-2-(2-nitroimidazole)acetamide (D-5). The oxidative damage induced by the interaction between D-2 (D-5) and DNA was investigated by CV and DPV. The efficient electrochemical biosensors were prepared through modifying GCE with calf thymus DNA, poly dA and poly dG, respectively. The redox mechanism of D-2 (D-5) on GCE surface involved the reduction of 2-nitro group on imidazole ring and the oxidation of methylene linked naphthalimide skeleton and 2-nitroimidazole. The results of voltametric evaluation of interaction between antitumor agent and DNA/GCE revealed the oxidative damage of DNA caused by D-2 (D-5). In addition, UV–vis absorption and fluorescence spectra were investigated to further distinguish the interaction mode between D-2 (D-5) and DNA, implying the intercalation mode of D-2 (D-5) toward base pairs of DNA with a high affinity. At last, D-2 and D-5 were proved to have significantly better cell selectivity than mitonafide, the fact indicated that D-2 and D-5 had the potential for becoming lead antitumor agents and eliminating the side effects toward normal cells.

DNP-enhanced solid-state NMR spectroscopy of chromatin polymers

Chromatin is a DNA-protein polymer that represents the functional form of the genome. The main building block of chromatin is the nucleosome, a structure that contains 147 base pairs of DNA and two copies each of the histone proteins H2A, H2B, H3 and H4. Previous work has shown that magic angle spinning (MAS) NMR spectroscopy can capture the nucleosome at high resolution although studies have been challenging due to low sensitivity, the presence of dynamic and rigid components, and the complex interaction networks of nucleosomes within the chromatin polymer. Here, we use dynamic nuclear polarization (DNP) to enhance the sensitivity of MAS NMR experiments of nucleosome arrays at 100 K and show that well-resolved 13C-13C MAS NMR correlations can be obtained much more efficiently. We evaluate the effect of temperature on the chemical shifts and linewidths in the spectra and demonstrate that changes are relatively minimal and clustered in regions of histone-DNA or histone-histone contacts. We also compare samples prepared with and without DNA and show that the low temperature 13C-13C correlations exhibit sufficient resolution to detect chemical shift changes and line broadening for residues that form the DNA-histone interface. On the other hand, we show that the measurement of DNP-enhanced 15N-13C histone-histone interactions within the nucleosome core is complicated by the natural 13C abundance network in the sample. Nevertheless, the enhanced sensitivity afforded by DNP can be used to detect long-range correlations between histone residues and DNA. Overall, our experiments demonstrate that DNP-enhanced MAS NMR spectroscopy of chromatin samples yields spectra with high resolution and sensitivity and can be used to capture functionally relevant protein-DNA interactions that have implications for gene regulation and genome organization.

Site-Specific Labeling Reveals Cas9 Induces Partial Unwinding Without RNA/DNA Pairing in Sequences Distal to the PAM.

CRISPR-Cas9 is an RNA-guided nuclease that has been widely adapted for genome engineering. A key determinant in Cas9 target selection is DNA duplex unwinding to form an R-loop, in which the single-stranded RNA guide hybridizes with one of the DNA strands. To advance understanding on DNA unwinding by Cas9, we combined two types of spectroscopic label, 2-aminopurine and nitroxide spin-label, to investigate unwinding at a specific DNA base pair induced by Streptococcus pyogenes Cas9. Data obtained with RNA guide lengths varying from 13 to 20 nucleotide revealed that the DNA segment distal to the protospacer adjacent motif can adopt a "partial unwinding" state, in which a mixture of DNA-paired and DNA-unwound populations exist in equilibrium. Significant unwinding can occur at positions not supported by RNA/DNA pairing, and the degree of unwinding depends on RNA guide length and modulates DNA cleavage activity. The results shed light on Cas9 target selection and may inform developments of genome-engineering strategies.

Rif1-Dependent Control of Replication Timing.

Successful duplication of the genome requires the accurate replication of billions of base pairs of DNA within a relatively short time frame. Failure to accurately replicate the genome results in genomic instability and a host of diseases. To faithfully and rapidly replicate the genome, DNA replication must be tightly regulated and coordinated with many other nuclear processes. These regulations, however, must also be flexible as replication kinetics can change through development and differentiation. Exactly how DNA replication is regulated and how this regulation changes through development is an active field of research. One aspect of genome duplication where much remains to be discovered is replication timing (RT), which dictates when each segment of the genome is replicated during S phase. All organisms display some level of RT, yet the precise mechanisms that govern RT remain are not fully understood. The study of Rif1, a protein that actively regulates RT from yeast to humans, provides a key to unlock the underlying molecular mechanisms controlling RT. The paradigm for Rif1 function is to delay helicase activation within certain regions of the genome, causing these regions to replicate late in S phase. Many questions, however, remain about the intricacies of Rif1 function. Here, we review the current models for the activity of Rif1 with the goal of trying to understand how Rif1 functions to establish the RT program.

Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone.

The influence of hydrogen bonds in model intercalated systems between guanine‐cytosine and adenine‐thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10‐phenanthroline (phen) and derivatives obtained by substitution with —OH and —NH2 groups in positions 4 and 7. Semiempirical and Density Functional Theory (DFT) methods were used both including dispersion effects: PM6‐DH2, M06‐2X and B3LYP‐D3 along with the recently developed near linear‐scaling coupled cluster method DLPNO‐CCSD(T) for benchmark calculations. Our results given by QTAIM and non‐covalent interaction analysis confirmed the existence of hydrogen bonds created by —OH and —NH2. The trends in the energy decomposition analysis for the interaction energy, ΔE int, showed that the ΔE elstat contributions are equal or even a little bit higher than the values for ΔE disp. Such important ΔE elstat attractive contribution comes mainly from the conventional hydrogen bonds formed by —OH and —NH2 functional groups with DNA not only with bps but specially with the sugar and phosphate backbone. This behavior is very different from that of phen and other classical intercalators that cannot form conventional hydrogen bonds, where the ΔE disp is the most important attractive contribution to the ΔE int. The inclusion of explicit water molecules in molecular dynamics simulations showed, as a general trend, that the hydrogen bonds with the bps disappear during the simulations but those with the sugar and phosphate backbone remain in time, which highlights the important role of the sugar and phosphate backbone in the stabilization of these systems.

Study on the interaction between aflatoxin M1 and DNA and its application in the removal of aflatoxin M1

To reveal the interaction between aflatoxin M1 (AFM1) and DNA, and then explore a new method to remove AFM1, spectroscopy, electrophoresis, and fluorescence microscopy were used. Fluorescence spectra assay showed that AFM1 and ethidium bromide (EB) competed for the intercalation sites in DNA, and the binding constant between AFM1 and DNA was 3.81 ± 0.1 × 107 L mol−1. The comparison of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) in the fluorescence enhancement of AFM1 further proved that the binding sites were between the base pairs of DNA. In the presence of AFM1, the melting temperature of DNA increased by 6.2 ° C, and the circular dichroism of DNA changed. These events were closely related to the intercalation between AFM1 and DNA. The binding between AFM1 and DNA was firm. AFM1 and DNA did not separate in agarose gel electrophoresis. Based on the intercalation between AFM1 and DNA, with DNA as an intermediate medium, AFM1 can be indirectly adsorbed onto magnetic beads. Then, AFM1 could be removed by magnetic separation. At an initial concentration of 10 μg/L, the removal efficiencies were 95.5%±3.7 and 85.5%±3.3 for aqueous solution and milk, respectively. This research result provided a direction in the detoxification of AFM1, which deserves to be developed further.

Deciphering the mechanism of p73 recognition of p53 response elements using the crystal structure of p73-DNA complexes and computational studies

p73 belongs to p53 family transcription factor activating more than 50% of cell fate p53 target genes involved in cell cycle, apoptosis, DNA damage response alongside neuronal system development and differentiation by binding to 20-bp response elements (REs) having sequence motif (PPPC-A/T-T/A-GYYY) where P-purines and Y-pyrimidines with each 10-bp separated by minimum 0 to 13-bp spacer. The promiscuous nature of recognizing both cell fate and development genes and the underlying RE selectivity mechanism by p73 is not well understood. Here, we report the molecular details of p73 recognizing the REs using the crystal structure of p73 DNA binding domain (DBD) in complex with 12 base pair DNA sequence 5'-cAGGCATGCCTg-3′ and molecular dynamics simulations with six different p53 natural promoter sequences. Each 20-base pair natural promoter forms a different major/minor groove due to the presence of nucleotides A/T, A/C, G/G, T/T and G/T at positions 3, 8, 13, 18 uniquely recognized by p73 key residues Lys138 and Arg268. The loops L1 and L3 bearing these residues influence inter-and intra-dimer interfaces interactions and hence p73 forms a unique tetramer with each natural promoter sequence. Structural features of the DNA and the spacing between half-sites influence p73 tetramerization and its transactivation function.