Metal-free synthesis of N-fused quinazolino-quinazoline-diones as a RNA triple helix intercalator.

The development of chemical scaffolds that target highly conserved RNA received attention due to its significance in splicing, nuclear organization, and gene expression in disease progression pathways. Here, we synthesized a series of N-fused quinazolino-quinazoline-diones a PIDA-induced C-N coupling methodology to target . Interestingly, compound 2z binds to the UUG pocket of a RNA triple-helix through intercalation, evidenced from molecular docking studies, fluorescence-based assay and CD experiments.

Silica sources for arsenic mitigation in rice: machine learning-based predictive modeling and risk assessment.

Arsenic (As) is a well-known human carcinogen, and the consumption of rice is the main pathway for the South Asian people. The study evaluated the impact of the amendments involving CaSiO, SiO nanoparticles, silica solubilizing bacteria (SSB), and rice straw compost (RSC) on mitigation of As toxicity in rice. The translocation of As from soil to cooked rice was tracked, and the results showed that RSC and its combination with SSB were the most effective in reducing As loading in rice grain by 53.

G4 Sensing Pyridyl-Thiazole Polyamide Represses c-KIT Expression in Leukemia Cells.

Specific sensing and functional tuning of nucleic acid secondary structures remain less explored to date. Herein, we report a thiazole polyamide TPW that binds specifically to c-KIT1 G-quadruplex (G4) with sub-micromolar affinity and ∼1 : 1 stoichiometry and represses c-KIT proto-oncogene expression. TPW shows up to 10-fold increase in fluorescence upon binding with c-KIT1 G4, but shows weak or no quantifiable binding to other G4s and ds26 DNA.

Ionophore constructed from non-covalent assembly of a G-quadruplex and liponucleoside transports K-ion across biological membranes.

The selective transport of ions across cell membranes, controlled by membrane proteins, is critical for a living organism. DNA-based systems have emerged as promising artificial ion transporters. However, the development of stable and selective artificial ion transporters remains a formidable task.

The complete chloroplast genome of , an endangered medicinal orchid from north-east India and its comparison with related species.

The medicinal orchid genus belonging to the Orchidaceae family is a huge genus comprising about 800-1,500 species. To better illustrate the species status in the genus , a comparative analysis of 33 available chloroplast genomes retrieved from NCBI RefSeq database was compared with that of the first complete chloroplast genome of from north-east India based on next-generation sequencing methods (Illumina HiSeq 2500-PE150). Our results provide comparative chloroplast genomic information for taxonomical identification, alignment-free phylogenomic inference and other statistical features of plastomes, which can also provide valuable information on their mutational events and sequence divergence.

G-Quadruplex-Binding Small Molecule Induces Synthetic Lethality in Breast Cancer Cells by Inhibiting c-MYC and BCL2 Expression.

Herein, a prolinamide-derived peptidomimetic that preferentially binds to c-MYC and BCL2 G-quadruplexes present in the promoter regions of apoptosis-related genes (c-MYC and BCL2) over other DNA quadruplexes are described. Biological assays, such as real-time quantitative reverse transcription, western blot, dual luciferase, and small interfering RNA knockdown assays, indicate that the ligand triggers a synthetic lethal interaction by simultaneously inhibiting the expression of c-MYC and BCL2 genes through their promoter G-quadruplexes. The ligand shows antiproliferative activity in MCF-7 cells that overexpress both MYC and BCL2 genes, in comparison to cells that overexpress either of the two.

Water vapor flux in tropical lowland rice.

A field experiment was conducted at Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India in the dry seasons of 2015 and 2016 to assess the water vapor flux (FHO) and its relationship with other climatic variables. The FHO and climatic variables were measured by an eddy covariance system and a micrometeorological observatory. Daily mean FHO during the dry seasons of 2015 and 2016 were 0.

Chemical Regulation of DNA i-Motifs for Nanobiotechnology and Therapeutics.

DNA sequences rich in cytosine have the propensity, under acidic pH, to fold into four-stranded intercalated DNA structures called i-motifs. Recent studies have provided significant breakthroughs that demonstrate how chemists can manipulate these structures for nanobiotechnology and therapeutics. The first section of this Minireview discusses the development of advanced functional nanostructures by synthetic conjugation of i-motifs with organic scaffolds and metal nanoparticles and their role in therapeutics.

Cell penetrating thiazole peptides inhibit c-MYC expression via site-specific targeting of c-MYC G-quadruplex.

The structural differences among different G-quadruplexes provide an opportunity for site-specific targeting of a particular G-quadruplex structure. However, majority of G-quadruplex ligands described thus far show little selectivity among different G-quadruplexes. In this work, we delineate the design and synthesis of a crescent-shaped thiazole peptide that preferentially stabilizes c-MYC quadruplex over other promoter G-quadruplexes and inhibits c-MYC oncogene expression.

Induction of apoptosis, anti-proliferation, tumor-angiogenic suppression and down-regulation of Dalton's Ascitic Lymphoma (DAL) induced tumorigenesis by poly-l-lysine: A mechanistic study.

Purpose: The present study, attempts to validate the molecular mechanism(s) of Poly-l-lysine (PLL) induced apoptosis, anti-proliferative and anti-tumorigenic properties in in-vitro HUVECs cells and Dalton's Ascitic Lymphoma (DAL) and in in-vivo DAL cell bearing BALB/c mice model.

Materials And Methods: The cell proliferation assay and morphological assay was carried out using the MTT assay and Giemsa staining method. The antitumor activity of PLL was evaluated in BALB/c mice at 20 and 40 mg/kg/b.

Enzyme-Regulated DNA-Based Logic Device.

Herein, we report a carbazole (Cz) ligand that displays distinct turn-on fluorescence signals upon interaction with human telomeric G-quadruplex ( h-TELO) and nuclease enzymes. Interestingly, Cz selectively binds and stabilizes the mixed hybrid topology of h-TELO G-quadruplex that withstands digestion by exonucleases and nuclease S1. The distinct fluorescence signatures of Cz-stabilized h-TELO with nucleases are used to design conceptually novel DNA devices for selectively detecting the enzymatic activity of DNase I as well as performing logic operations.

Preferential targeting of i-motifs and G-quadruplexes by small molecules.

i-Motifs and G-quadruplexes are dynamic nucleic acid secondary structures, which are believed to play key roles in gene expression. We herein report two peptidomimetic ligands ( and ) that selectively target i-motifs and G-quadruplexes over double-stranded DNA. These peptidomimetics, regioisomeric with respect to the position of triazole/prolinamide motifs, have been synthesized using a modular method involving Cu(i)-catalyzed azide and alkyne cycloaddition.

Poly-L-Lysine Inhibits Tumor Angiogenesis and Induces Apoptosis in Ehrlich Ascites Carcinoma and in Sarcoma S-180 Tumor.

Background: This study focuses on the role of Poly-L-lysine (PLL), an essential amino acid, on molecular changes of tumor angiogenesis suppression, pro-apoptotic and anti-apoptotic gene expression after treatment on Ehrlich ascites carcinoma (EAC) and solid sarcoma-180 tumor cells bearing mice. Materials and Methods: The cell viability was carried out using MTT assay. The antitumor activity was evaluated by treatment with PLL at 20 and 40mg/kg/b.

Chloroplast Genome Sequence Annotation of (Asparagales: Orchidaceae), an Endangered Medicinal Orchid from Northeast India.

Orchidaceae constitutes one of the largest families of angiosperms. Owing to the significance of orchids in plant biology, market needs and current sustainable technology levels, basic research on the biology of orchids and their applications in the orchid industry is increasing. Although chloroplast (cp) genomes continue to be evolutionarily informative, there is very limited information available on orchid chloroplast genomes in public repositories.

Age estimation for the genus Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) and phylogeographic inference from ancestral area reconstruction.

Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and biogeographers. One such family belonging to angiosperms is Orchidaceae with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and biogeographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are distinctly distributed in tropical to temperate regions.

Complete Chloroplast Genome Sequence of Dendrobium nobile from Northeastern India.

The orchid species Dendrobium nobile belonging to the family Orchidaceae and genus Dendrobium (a vast genus that encompasses nearly 1,200 species) has an herbal medicinal history of about 2000 years in east and south Asian countries. Here, we report the complete chloroplast genome sequence of D. nobile from northeastern India for the first time.

Complete mitochondrial genome annotation of the giant intestinal fluke, (Indian isolate) as revealed by ion torrent and illuminanext-generation sequencing.

The complete mitogenome sequences of the intestinal fluke are presented for the first time in this study. It is 14,119 bp long and is thus the shortest trematode mitochondrial genome sequenced to date. The mtDNA genome has a close resemblance with and has a similar gene order tallying with that of other trematodes.

Northeast India Helminth Parasite Information Database (NEIHPID): Knowledge Base for Helminth Parasites.

Most metazoan parasites that invade vertebrate hosts belong to three phyla: Platyhelminthes, Nematoda and Acanthocephala. Many of the parasitic members of these phyla are collectively known as helminths and are causative agents of many debilitating, deforming and lethal diseases of humans and animals. The North-East India Helminth Parasite Information Database (NEIHPID) project aimed to document and characterise the spectrum of helminth parasites in the north-eastern region of India, providing host, geographical distribution, diagnostic characters and image data.

Small molecule regulated dynamic structural changes of human G-quadruplexes.

The changes in structure and dynamics of oncogenic () and telomeric () G-rich DNA sequences due to the binding of a novel carbazole derivative () are elucidated using single-molecule Förster resonance energy transfer (sm-FRET), fluorescence correlation spectroscopy (FCS) and NMR spectroscopy. In contrast to the previous reports on the binding of ligands to pre-folded G-quadruplexes, this work illustrates how ligand binding changes the conformational equilibria of both unstructured G-rich DNA sequences and K-folded G-quadruplexes. The results demonstrate that K free and exist as unfolded and partially folded conformations.

Selective recognition of c-MYC G-quadruplex DNA using prolinamide derivatives.

Herein we report the design, synthesis, biophysical and biological evaluation of triazole containing prolinamide derivatives as selective c-MYC G-quadruplex binding ligands. A modular synthetic route has been devised for prolinamide derivatives using a copper(i) catalyzed azide-alkyne cycloaddition (CuAAC). The Förster resonance energy transfer (FRET) melting assay indicates that prolinamide trimers can significantly stabilize G-quadruplex structures over duplex DNA compared to prolinamide dimers.

A Nucleus-Imaging Probe That Selectively Stabilizes a Minor Conformation of c-MYC G-quadruplex and Down-regulates c-MYC Transcription in Human Cancer Cells.

The c-MYC proto-oncogene is a regulator of fundamental cellular processes such as cell cycle progression and apoptosis. The development of novel c-MYC inhibitors that can act by targeting the c-MYC DNA G-quadruplex at the level of transcription would provide potential insight into structure-based design of small molecules and lead to a promising arena for cancer therapy. Herein we report our finding that two simple bis-triazolylcarbazole derivatives can inhibit c-MYC transcription, possibly by stabilizing the c-MYC G-quadruplex.

Environment-sensitive probes containing a 2,6-diethynylpyridine motif for fluorescence turn-on detection and induction of nanoarchitectures of human telomeric quadruplex.

Bis(phenylethynyl)pyridylcarboxamides with amide side chains at the para position of the NH2 group possess strong solvatochromic properties compared with the meta analogues. Fluorescence binding titrations show that these probes exhibit remarkable fluorescence turn-on responses upon interacting with the human telomeric G-quadruplex (h-TELO). Förster resonance energy transfer melting analysis shows the high selectivity of these probes for h-TELO over duplex DNA.

A small molecule peptidomimetic that binds to c-KIT1 G-quadruplex and exhibits antiproliferative properties in cancer cells.

A modular synthesis of l-proline derived peptidomimetics has been developed using the Cu(I) catalyzed Huisgen cycloaddition between an azido prolinamide with pyridine and benzene dicarboxamide containing dialkynes. Förster Resonance Energy Transfer (FRET) melting assay provided an initial indication that the pyridyl analogue can stabilize the c-KIT1 quadruplex DNA. A competitive FRET-melting assay and Fluorescent Intercalator Displacement (FID) assay suggest that the pyridyl ligand shows excellent selectivity for c-KIT1 quadruplex over duplex DNA and other investigated G-quadruplexes.

Preparation of low toxic fluorescent chitosan-graft-polyethyleneimine copolymer for gene carrier.

Fluorescent chitosan-graft-polyethyleneimine (PEI) copolymer was prepared by incorporating PEI molecule onto chitosan backbone through naphthalimide moiety by simple substitution reaction. 4-Bromo-1,8-naphthalic anhydride was used as fluorescent probe due to its strong fluorescence and good photo-stability property and the presence of a fine tunable bromide functional group in the naphthalimide ring, in this work. The copolymer was characterized by FTIR, elemental analysis and XRD.