KRAS Promoter G-Quadruplexes from Sequences of Different Length: A Physicochemical Study

DNA G-quadruplexes (G4s) form in relevant genomic regions and intervene in several biological processes, including the modulation of oncogenes expression, and are potential anticancer drug targets. The human KRAS proto-oncogene promoter region contains guanine-rich sequences able to fold into G4 structures. Here, by using circular dichroism and differential scanning calorimetry as complementary physicochemical methodologies, we compared the thermodynamic stability of the G4s formed by a shorter and a longer version of the KRAS promoter sequence, namely 5′-AGGGCGGTGTGGGAATAGGGAA-3′ (KRAS 22RT) and 5′-AGGGCGGTGTGGGAAGAGGGAAGAGGGGGAGG-3′ (KRAS 32R). Our results show that the unfolding mechanism of KRAS 32R is more complex than that of KRAS 22RT. The different thermodynamic stability is discussed based on the recently determined NMR structures. The binding properties of TMPyP4 and BRACO-19, two well-known G4-targeting anticancer compounds, to the KRAS G4s were also investigated. The present physicochemical study aims to help in choosing the best G4 target for potential anticancer drugs.

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Characterization of a Polymeric Membrane for the Separation of Hydrogen in a Mixture with CO2

The Open Fuels & Energy Science Journal ◽

10.2174/1876973x01609010126 ◽

2016 ◽

Vol 9 (1) ◽

pp. 126-136 ◽

Cited By ~ 1

Author(s):

Dionisio H. Malagón-Romero ◽

Alexander Ladino ◽

Nataly Ortiz ◽

Liliana P. Green

Keyword(s):

Carbon Dioxide ◽

Hydrogen Production ◽

Test Performance ◽

Low Cost ◽

Time Lag ◽

Polymeric Membrane ◽

Biological Processes ◽

Scanning Calorimetry ◽

Environmentally Sustainable ◽

Production Of Hydrogen

Hydrogen is expected to play an important role as a clean, reliable and renewable energy source. A key challenge is the production of hydrogen in an economically and environmentally sustainable way on an industrial scale. One promising method of hydrogen production is via biological processes using agricultural resources, where the hydrogen is found to be mixed with other gases, such as carbon dioxide. Thus, to separate hydrogen from the mixture, it is challenging to implement and evaluate a simple, low cost, reliable and efficient separation process. So, the aim of this work was to develop a polymeric membrane for hydrogen separation. The developed membranes were made of polysulfone via phase inversion by a controlled evaporation method with 5 wt % and 10 wt % of polysulfone resulting in thicknesses of 132 and 239 micrometers, respectively. Membrane characterization was performed using scanning electron microscopy (SEM), differential scanning calorimetry (DSC), atomic force microscopy (AFM), and ASTM D882 tensile test. Performance was characterized using a 23 factorial experiment using the time lag method, comparing the results with those from gas chromatography (GC). As a result, developed membranes exhibited dense microstructures, low values of RMS roughness, and glass transition temperatures of approximately 191.75 °C and 190.43 °C for the 5 wt % and 10 wt % membranes, respectively. Performance results for the given membranes showed a hydrogen selectivity of 8.20 for an evaluated gas mixture 54% hydrogen and 46% carbon dioxide. According to selectivity achieved, H2 separation from carbon dioxide is feasible with possibilities of scalability. These results are important for consolidating hydrogen production from biological processes.

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Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets

Molecules ◽

10.3390/molecules26082118 ◽

2021 ◽

Vol 26 (8) ◽

pp. 2118

Author(s):

Yusuke Hosoya ◽

Junko Ohkanda

Keyword(s):

Drug Targets ◽

Intrinsically Disordered Proteins ◽

Dynamic Control ◽

Disordered Proteins ◽

Biological Processes ◽

Phase Separations ◽

Cellular Processes ◽

Intrinsically Disordered ◽

New Drug ◽

Liquid Phase Separations

Intrinsically disordered proteins (IDPs) are critical players in the dynamic control of diverse cellular processes, and provide potential new drug targets because their dysregulation is closely related to many diseases. This review focuses on several medicinal studies that have identified low-molecular-weight inhibitors of IDPs. In addition, clinically relevant liquid–liquid phase separations—which critically involve both intermolecular interactions between IDPs and their posttranslational modification—are analyzed to understand the potential of IDPs as new drug targets.

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DNA G-quadruplexes for native mass spectrometry in potassium: a database of validated structures in electrospray-compatible conditions

Nucleic Acids Research ◽

10.1093/nar/gkab039 ◽

2021 ◽

Author(s):

Anirban Ghosh ◽

Eric Largy ◽

Valérie Gabelica

Keyword(s):

Mass Spectrometry ◽

Drug Targets ◽

Native Mass Spectrometry ◽

Drug Binding ◽

Quadruplex Dna ◽

Dna Structures ◽

Nmr Structures ◽

G Quadruplex ◽

Screening Assays

Abstract G-quadruplex DNA structures have become attractive drug targets, and native mass spectrometry can provide detailed characterization of drug binding stoichiometry and affinity, potentially at high throughput. However, the G-quadruplex DNA polymorphism poses problems for interpreting ligand screening assays. In order to establish standardized MS-based screening assays, we studied 28 sequences with documented NMR structures in (usually ∼100 mM) potassium, and report here their circular dichroism (CD), melting temperature (Tm), NMR spectra and electrospray mass spectra in 1 mM KCl/100 mM trimethylammonium acetate. Based on these results, we make a short-list of sequences that adopt the same structure in the MS assay as reported by NMR, and provide recommendations on using them for MS-based assays. We also built an R-based open-source application to build and consult a database, wherein further sequences can be incorporated in the future. The application handles automatically most of the data processing, and allows generating custom figures and reports. The database is included in the g4dbr package (https://github.com/EricLarG4/g4dbr) and can be explored online (https://ericlarg4.github.io/G4_database.html).

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Techniques to examine nucleotide binding by pseudokinases

Biochemical Society Transactions ◽

10.1042/bst20130075 ◽

2013 ◽

Vol 41 (4) ◽

pp. 975-980 ◽

Cited By ~ 14

Author(s):

Isabelle S. Lucet ◽

Jeffrey J. Babon ◽

James M. Murphy

Keyword(s):

Signal Transduction ◽

Drug Targets ◽

Nucleotide Binding ◽

Biological Functions ◽

Binding Properties ◽

Catalytic Activities ◽

Functional Studies ◽

Signalling Molecules ◽

Advantages And Disadvantages ◽

Human Kinome

Approximately 10% of the human kinome has been classified as pseudokinases due to the absence of one or more of three motifs known to play key roles in the catalytic activities of protein kinases. Structural and functional studies are now emerging, reclassifying this ‘dead’ kinase family as essential signalling molecules that act as crucial modulators of signal transduction. This raises the prospect that pseudokinases may well represent an as-yet-unexplored class of drug targets. However, the extent to which nucleotide binding and catalytic activity contribute to the biological functions of pseudokinases remains an area of great controversy. In the present review, we discuss the advantages and disadvantages of the different methods employed to characterize the nucleotide-binding properties and activity of pseudokinases.

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Thermodynamic stability and drug-binding properties of oligodeoxyribonucleotide duplexes containing 3-deazaadenine:thymine base pairs

Nucleic Acids Research ◽

10.1093/nar/21.8.1743 ◽

1993 ◽

Vol 21 (8) ◽

pp. 1743-1746 ◽

Cited By ~ 6

Author(s):

Catherine Lever ◽

Xiang Li ◽

Richard Cosstick ◽

Susanne Edel ◽

Tom Brown

Keyword(s):

Thermodynamic Stability ◽

Drug Binding ◽

Base Pairs ◽

Binding Properties

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Identification of Selection Signatures in Commercial Asian Rice Subspecies Deciphered Selection Footprints for Four Overrepresented Biological Processes

10.21203/rs.3.rs-121958/v1 ◽

2020 ◽

Author(s):

Siavash Salek Ardestani ◽

Mahmoud Amiri Roudbar ◽

Mohammad Hossein Banabazi ◽

Seyedeh Fatemeh Mousavi ◽

Madhav Bhatta ◽

...

Keyword(s):

Selection Pressure ◽

Rice Genome ◽

Fixation Index ◽

Biological Processes ◽

Selection Signatures ◽

Genomic Changes ◽

Asian Rice ◽

Genome Level ◽

Window Approach ◽

Genomic Regions

Abstract BackgroundSelective breeding pressures have led to gradual genomic changes in Asian commercial rice, which have shaped selection footprints on its genome level. Tracing genomic selection footprints might be illuminative for better understanding of recent selection breeding objectives, and how breeding strategies have formed the Asian commercial rice genome. ResultsIn this study, the genotypic information (HDRA 700K) of four Asian commercial rice subspecies including Indica (n=498), Aus (n=187), Temperate japonica (n=241), and Tropical japonica (n=361) were downloaded from Rice Diversity Project database (http://www.ricediversity.org) to detect selection signatures by employing the Z-transformed of fixation index and Tajima’s D test, based on a sliding window approach. Although we could not identify overrepresented genomic regions underlying selection pressure among all aforementioned Asian commercial rice subspecies, interestingly, our findings revealed four overrepresented biological processes underlying selection pressure including proteolysis (GO:0006508), phosphorylation (GO:0016310), protein catabolic process (GO:0030163), and transmembrane transport (GO:0055085) that might be associated with immunity, senescing leaves, transporting, and absorption of ions. ConclusionsThese results can provide knowledge on how breeding efforts shaped the Asian commercial rice subspecies genome, and which genomic regions of these subspecies have been targeted in recent decades.

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N-methyl mesoporphyrin IX as a highly selective light-up probe for G-quadruplex DNA

Journal of Porphyrins and Phthalocyanines ◽

10.1142/s1088424619300179 ◽

2019 ◽

Vol 23 (11n12) ◽

pp. 1195-1215 ◽

Cited By ~ 5

Author(s):

Ariana Yett ◽

Linda Yingqi Lin ◽

Dana Beseiso ◽

Joanne Miao ◽

Liliya A. Yatsunyk

Keyword(s):

Optical Properties ◽

Small Molecules ◽

Genomic Stability ◽

Water Soluble ◽

Biological Processes ◽

Binding Properties ◽

Quadruplex Dna ◽

Dna Structures ◽

G Quadruplex ◽

High Fluorescence

[Formula: see text]-methyl mesoporphyrin IX (NMM) is a water-soluble, non-symmetric porphyrin with excellent optical properties and unparalleled selectivity for G-quadruplex (GQ) DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences. They are implicated in genomic stability, longevity, and cancer. The ability of NMM to selectively recognize GQ structures makes it a valuable scaffold for designing novel GQ binders. In this review, we survey the literature describing the GQ-binding properties of NMM as well as its wide utility in chemistry and biology. We start with the discovery of the GQ-binding properties of NMM and the development of NMM-binding aptamers. We then discuss the optical properties of NMM, focusing on the light-switch effect — high fluorescence of NMM induced upon its binding to GQ DNA. Additionally, we examine the affinity and selectivity of NMM for GQs, as well as its ability to stabilize GQ structures and favor parallel GQ conformations. Furthermore, a portion of the review is dedicated to the applications of NMM-GQ complexes as biosensors for heavy metals, small molecules ([Formula: see text] ATP and pesticides), DNA, and proteins. Finally and importantly, we discuss the utility of NMM as a probe to investigate the roles of GQs in biological processes.

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Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires

Journal of Animal Science and Biotechnology ◽

10.1186/s40104-019-0403-0 ◽

2019 ◽

Vol 10 (1) ◽

Author(s):

Gerson A. Oliveira Júnior ◽

Daniel J. A. Santos ◽

Aline S. M. Cesar ◽

Solomon A. Boison ◽

Ricardo V. Ventura ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Fine Mapping ◽

Reproductive Hormones ◽

Sequence Variants ◽

Whole Genome ◽

Biological Processes ◽

Snp Chip ◽

Mesh Terms ◽

Genomic Regions

Abstract Background Impaired fertility in cattle limits the efficiency of livestock production systems. Unraveling the genetic architecture of fertility traits would facilitate their improvement by selection. In this study, we characterized SNP chip haplotypes at QTL blocks then used whole-genome sequencing to fine map genomic regions associated with reproduction in a population of Nellore (Bos indicus) heifers. Methods The dataset comprised of 1337 heifers genotyped using a GeneSeek® Genomic Profiler panel (74677 SNPs), representing the daughters from 78 sires. After performing marker quality control, 64800 SNPs were retained. Haplotypes carried by each sire at six previously identified QTL on BTAs 5, 14 and 18 for heifer pregnancy and BTAs 8, 11 and 22 for antral follicle count were constructed using findhap software. The significance of the contrasts between the effects of every two paternally-inherited haplotype alleles were used to identify sires that were heterozygous at each QTL. Whole-genome sequencing data localized to the haplotypes from six sires and 20 other ancestors were used to identify sequence variants that were concordant with the haplotype contrasts. Enrichment analyses were applied to these variants using KEGG and MeSH libraries. Results A total of six (BTA 5), six (BTA 14) and five (BTA 18) sires were heterozygous for heifer pregnancy QTL whereas six (BTA 8), fourteen (BTA 11), and five (BTA 22) sires were heterozygous for number of antral follicles’ QTL. Due to inadequate representation of many haplotype alleles in the sequenced animals, fine mapping analysis could only be reliably performed for the QTL on BTA 5 and 14, which had 641 and 3733 concordant candidate sequence variants, respectively. The KEGG “Circadian rhythm” and “Neurotrophin signaling pathway” were significantly associated with the genes in the QTL on BTA 5 whereas 32 MeSH terms were associated with the QTL on BTA 14. Among the concordant sequence variants, 0.2% and 0.3% were classified as missense variants for BTAs 5 and 14, respectively, highlighting the genes MTERF2, RTMB, ENSBTAG00000037306 (miRNA), ENSBTAG00000040351, PRKDC, and RGS20. The potential causal mutations found in the present study were associated with biological processes such as oocyte maturation, embryo development, placenta development and response to reproductive hormones. Conclusions The identification of heterozygous sires by positionally phasing SNP chip data and contrasting haplotype effects for previously detected QTL can be used for fine mapping to identify potential causal mutations and candidate genes. Genomic variants on genes MTERF2, RTBC, miRNA ENSBTAG00000037306, ENSBTAG00000040351, PRKDC, and RGS20, which are known to have influence on reproductive biological processes, were detected.

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Does thermodynamic stability of peritoneal collagen change during laparoscopic cholecystectomies? A differential scanning calorimetry (DSC) study

Surgical Endoscopy ◽

10.1007/s00464-014-3513-y ◽

2014 ◽

Vol 28 (9) ◽

pp. 2623-2626 ◽

Cited By ~ 4

Author(s):

Kamil Torres ◽

Hanna Trębacz ◽

Magdalena Bącik-Donica ◽

Agnieszka Atras ◽

Anna Torres ◽

...

Keyword(s):

Differential Scanning Calorimetry ◽

Thermodynamic Stability ◽

Scanning Calorimetry

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The orphan nuclear receptors at their 25-year reunion

Journal of Molecular Endocrinology ◽

10.1530/jme-13-0212 ◽

2013 ◽

Vol 51 (3) ◽

pp. T115-T140 ◽

Cited By ~ 51

Author(s):

Shannon E Mullican ◽

Joanna R DiSpirito ◽

Mitchell A Lazar

Keyword(s):

Nuclear Receptors ◽

Hormone Receptors ◽

Steroid Hormone ◽

Steroid Hormone Receptors ◽

Biological Processes ◽

Orphan Nuclear Receptors ◽

Orphan Receptors ◽

Critical Insight ◽

Genomic Regions ◽

Insight Into

The nuclear receptor superfamily includes many receptors, identified based on their similarity to steroid hormone receptors but without a known ligand. The study of how these receptors are diversely regulated to interact with genomic regions to control a plethora of biological processes has provided critical insight into development, physiology, and the molecular pathology of disease. Here we provide a compendium of these so-called orphan receptors and focus on what has been learned about their modes of action, physiological functions, and therapeutic promise.

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