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1.
Phys Chem Chem Phys ; 21(32): 17971-17977, 2019 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-31384846

RESUMO

The electron-hole injection from a family of spiropyran photoswitches into A/T-duplex DNA has been investigated at the molecular level for the first time. Multiscale computations coupled with automatized quantitative wavefunction analysis reveal a pronounced directionality and regioselectivity towards the template strand of the duplex DNA. Our findings suggest that this directional and regioselective photoinduced electron-hole transfer could thus be exploited to tailor the charge transport processes in DNA in specific applications.


Assuntos
Benzopiranos/química , DNA/química , Indóis/química , Substâncias Intercalantes/química , Nitrocompostos/química , Transporte de Elétrons , Luz , Modelos Moleculares , Conformação de Ácido Nucleico , Oxirredução , Processos Fotoquímicos , Prótons , Termodinâmica
2.
Chem Commun (Camb) ; 55(67): 9955-9958, 2019 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-31364619

RESUMO

A silver nanocluster-based ratiometric fluorescent nanosensor was developed for the determination of ATP in the cerebrospinal fluid of a mouse brain. Using this useful tool with good stability and high selectivity as well as a wide linear detection range, it was found that the ATP concentration in a mouse brain with Alzheimer's disease was 2300-fold higher than that in a normal one.


Assuntos
Trifosfato de Adenosina/líquido cefalorraquidiano , Química Encefálica , DNA/química , Corantes Fluorescentes/química , Nanopartículas Metálicas/química , Doença de Alzheimer/metabolismo , Doença de Alzheimer/patologia , Animais , Encéfalo/citologia , Encéfalo/patologia , Córtex Cerebral/química , Hipocampo/química , Camundongos , Conformação de Ácido Nucleico , Prata/química , Espectrometria de Fluorescência/métodos
3.
J Phys Chem A ; 123(32): 7087-7103, 2019 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-31323178

RESUMO

The Cremer-Pople ring puckering analysis and the Konkoli-Cremer local mode analysis supported by the topological analysis of the electron density were applied for the first comprehensive analysis of the interplay between deoxyribose ring puckering and intramolecular H-bonding in 2'-deoxycytidine, 2'-deoxyadenosine, 2'-deoxythymidine, and 2'-deoxyguanosine. We mapped for each deoxyribonucleoside the complete conformational energy surface and the corresponding pseudorotation path. We found only incomplete pseudorotation cycles, caused by ring inversion, which we coined as pseudolibration paths. On each pseudolibration path a global and a local minimum separated by a transition state were identified. The investigation of H-bond free deoxyribonucleoside analogs revealed that removal of the H-bond does not restore the full conformational flexibility of the sugar ring. Our work showed that ring puckering predominantly determines the conformational energy; the larger the puckering amplitude, the lower the conformational energy. In contrast no direct correlation between conformational energy and H-bond strength was found. The longest and weakest H-bonds are located in the local minimum region, whereas the shortest and strongest H-bonds are located outside the global and local minimum regions at the turning points of the pseudolibration paths, i.e., H-bonding determines the shape and length of the pseudolibration paths. In addition to the H-bond strength, we evaluated the covalent/electrostatic character of the H-bonds applying the Cremer-Kraka criterion of covalent bonding. H-bonding in the puric bases has a more covalent character whereas in the pyrimidic bases the H-bond character is more electrostatic. We investigated how the mutual orientation of the CH2OH group and the base influences H-bond formation via two geometrical parameters describing the rotation of the substituents perpendicular to the sugar ring and their tilting relative to the ring center. According to our results, rotation is more important for H-bond formation. In addition we assessed the influence of the H-bond acceptor, the lone pair (N, respectively O), via the delocalization energy. We found larger delocalization energies corresponding to stronger H-bonds for the puric bases. The global minimum conformation of 2'-deoxyguanosine has the strongest H-bond of all conformers investigated in this work with a bond strength of 0.436 which is even stronger than the H-bond in the water dimer (0.360). The application of our new analysis to DNA deoxyribonucleotides and to unnatural base pairs, which have recently drawn a lot of attention, is in progress.


Assuntos
Desoxirribonucleosídeos/química , DNA/química , Ligações de Hidrogênio , Conformação de Ácido Nucleico , Termodinâmica
4.
Chem Commun (Camb) ; 55(65): 9709-9712, 2019 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-31353371

RESUMO

We functionalize nucleic acid nanostructures with click chemistry (for attachment of cargos) and a photocleavable linker (for release). We demonstrate cargo attachment using a fluorescein dye and release using UV trigger from an RNA three-way junction, a DNA star motif and a DNA tetrahedron. Such multifunctional nucleic acid nanostructures have potential in targeted drug delivery.


Assuntos
DNA/química , Portadores de Fármacos/química , Fluoresceínas/química , Corantes Fluorescentes/química , Nanoestruturas/química , RNA/química , Animais , Fagos Bacilares/genética , Sequência de Bases , Bovinos , Química Click , DNA/sangue , DNA/síntese química , DNA/efeitos da radiação , Portadores de Fármacos/síntese química , Portadores de Fármacos/efeitos da radiação , Fluorescência , Nanoestruturas/efeitos da radiação , Conformação de Ácido Nucleico , RNA/sangue , RNA/síntese química , RNA/efeitos da radiação , Raios Ultravioleta
5.
J Chem Theory Comput ; 15(8): 4660-4672, 2019 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-31282669

RESUMO

DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. While the wormlike chain model provides a good description of small to moderate bending fluctuations, it is expected to break down for large bending. Recent cyclization experiments on strongly bent shorter molecules indeed suggest enhanced flexibility over and above that expected from the wormlike chain. Here, we use a coarse-grained model of DNA to investigate the subtle thermodynamics of DNA cyclization for molecules ranging from 30 to 210 base pairs. As the molecules get shorter, we find increasing deviations between our computed equilibrium j-factor and the classic wormlike chain predictions of Shimada and Yamakawa for a torsionally aligned looped molecule. These deviations are due to sharp kinking, first at nicks, and only subsequently in the body of the duplex. At the shortest lengths, substantial fraying at the ends of duplex domains is the dominant method of relaxation. We also estimate the dynamic j-factor measured in recent FRET experiments. We find that the dynamic j-factor is systematically larger than its equilibrium counterpart-with the deviation larger for shorter molecules-because not all the stress present in the fully cyclized state is present in the transition state. These observations are important for the interpretation of recent cyclization experiments, suggesting that measured anomalously high j-factors may not necessarily indicate non-WLC behavior in the body of duplexes.


Assuntos
DNA Circular/química , Pareamento de Bases , Ciclização , Elasticidade , Modelos Moleculares , Método de Monte Carlo , Conformação de Ácido Nucleico , Termodinâmica
6.
Phys Rev Lett ; 122(21): 218101, 2019 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-31283336

RESUMO

Base-pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule fluorescence resonance energy transfer, we measured the lifetimes of tightly bent DNA loops with and without base-pair mismatch. Surprisingly, for loops captured by stackable sticky ends which leave single-stranded DNA breaks (or nicks) upon annealing, the mismatch decreased the loop lifetime despite reducing the overall bending stress, and the decrease was largest when the mismatch was placed at the DNA midpoint. These findings suggest that base-pair mismatch increases bending stress at the opposite side of the loop through an allosteric mechanism known as cooperative kinking. Based on this mechanism, we present a three-state model that explains the apparent dichotomy between thermodynamic and kinetic stability.


Assuntos
Pareamento Incorreto de Bases , DNA/química , Transferência Ressonante de Energia de Fluorescência , Cinética , Modelos Químicos , Conformação de Ácido Nucleico , Termodinâmica
7.
Chem Commun (Camb) ; 55(61): 8951-8954, 2019 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-31289799

RESUMO

A new reconfigurable DNA nanocage based on a DNA origami method has been constructed to capture a tobacco mosaic virus (TMV) disk. We used a hairpin to control the transformation of the nanocage and a strand of TMV RNA to attract the TMV disk. Our design could inspire new DNA-protein complex designs.


Assuntos
DNA/química , Nanoestruturas/química , Vírus do Mosaico do Tabaco/química , Sequência de Bases , DNA/síntese química , DNA/genética , Sequências Repetidas Invertidas , Conformação de Ácido Nucleico , Hibridização de Ácido Nucleico , RNA Viral/química
8.
Talanta ; 202: 520-525, 2019 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-31171216

RESUMO

A rapid, cost-effective and quencher-free fluorescence-based analytical method for sensitive detection of l-cysteine (Cys) based on 2-aminopurine (2-AP) labeled DNA probe and exonuclease I (Exo I) activity was developed. 2-AP labeled DNA probe includes two thymine (T)-T mismatches, which can bind with Hg2+ to form T-Hg2+-T pairing bases, resulting in stable hairpin with five base pairs in its stem. The target Cys can remove Hg2+ from the stem of the hairpin probe based on the high affinity of Cys with Hg2+, leading to the unfolding of the hairpin probe. At last, by adding Exo I, the resulted single-stranded DNA (ssDNA) will be digested to release free 2-AP with strong fluorescence. Under the optimal conditions, the sensing system exhibited a good and wider linear range from 0.4 to 400 nM (R2 = 0.997) and a detection limit as low as 0.16 nM for Cys. Furthermore, other amino acids without reductive sulfur group did not generate obvious change in fluorescence signals. Finally, the sensor can be used in diluted real samples with a good recovery rate, showing promising application in food, environmental and medical analysis.


Assuntos
2-Aminopurina/química , Cisteína/análise , Sondas de DNA/química , Fluorescência , Conformação de Ácido Nucleico
9.
Nat Commun ; 10(1): 2544, 2019 06 11.
Artigo em Inglês | MEDLINE | ID: mdl-31186424

RESUMO

Cas13d, the type VI-D CRISPR-Cas effector, is an RNA-guided ribonuclease that has been repurposed to edit RNA in a programmable manner. Here we report the detailed structural and functional analysis of the uncultured Ruminococcus sp. Cas13d (UrCas13d)-crRNA complex. Two hydrated Mg2+ ions aid in stabilizing the conformation of the crRNA repeat region. Sequestration of divalent metal ions does not alter pre-crRNA processing, but abolishes target cleavage by UrCas13d. Notably, the pre-crRNA processing is executed by the HEPN-2 domain. Furthermore, both the structure and sequence of the nucleotides U(-8)-C(-1) within the repeat region are indispensable for target cleavage, and are specifically recognized by UrCas13d. Moreover, correct base pairings within two separate spacer regions (an internal and a 3'-end region) are essential for target cleavage. These findings provide a framework for the development of Cas13d into a tool for a wide range of applications.


Assuntos
Proteínas de Bactérias/metabolismo , Proteínas Associadas a CRISPR/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Ribonucleases/metabolismo , Ruminococcus/genética , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas Associadas a CRISPR/química , Proteínas Associadas a CRISPR/metabolismo , Sistemas CRISPR-Cas , Conformação de Ácido Nucleico , Domínios Proteicos , Processamento Pós-Transcricional do RNA , RNA Bacteriano/genética , RNA Bacteriano/metabolismo , RNA Guia/genética , Ribonucleases/química , Ribonucleases/genética , Ruminococcus/enzimologia
10.
Phys Chem Chem Phys ; 21(23): 12566-12575, 2019 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-31149680

RESUMO

For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The ds-DNA is modeled by a mesoscopic Hamiltonian which accounts for the three dimensional helical structure and incorporates fluctuational effects at the level of the base pair. The computational method assumes that the base pair fluctuations are temperature dependent trajectories whose amplitudes can be spatially modulated according to the crowders distribution. We show that the molecular elongation, as measured by the end-to-end distance, varies non-monotonically with the strength of the confinement. Furthermore it is found that, if the crowders mostly confine the DNA mid-chain, the helix over-twists and its end-to-end distance grows in the strong confinement regime. Instead, if the crowders mostly pin one chain end, the helix untwists while the molecule stretches for large confinement strengths. Thus, our results put forward a peculiar relation between stretching and twisting which significantly depends on the crowders profile. The method could be applied to design specific DNA shapes by controlling the environment which constrains the molecule.


Assuntos
DNA/química , Conformação de Ácido Nucleico , Pareamento de Bases , Tamanho da Partícula , Termodinâmica
11.
J Photochem Photobiol B ; 196: 111497, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31154276

RESUMO

Systematic identification and quantification of active radical sites in a small molecule, pyrazolium 3,5-dinitrobenzoate:3,5-dinitrobenzoic acid as well as in the stable free radical (DPPH•) were carried out by Fukui functions calculation using DFT functional with B3LYP/6-311++G(d,p) level of basis set. Bioactive Lewis acid-base compound, pyrazolium 3,5-dinitrobenzoate:3,5-dinitrobenzoic acid (PDNB:DNBA) has been synthesized and crystallized by slow evaporation - solution method at 30 °C. Various functional groups and the structural arrangements were ascertained from spectral and XRD analyses, respectively. UV-vis spectral analysis was used to find out the stability of the anticipated drug for about 60 min using methanol as a solvent. Stabilization of the compound was linked to the presence of enormous N-H…O, O-H…O and C-H…O hydrogen bonding interactions identified through Hirshfeld surface analysis. Chemical stability and reactivity of the drug were validated from theoretical optimization and HOMO-LUMO analysis. Active nucleophilic, electrophilic and radical sites of PDNB:DNBA were also identified from molecular electrostatic potential analysis. Inhibition of growth of pathogens in screening experiments by the proposed drug attests its suitability in biological applications. Antioxidant activity of the compound, PDNB:DNBA, endorses its aptness for scavenging reactive radicals. Fluorimetry experiments confirm hyperchromism in DNA binding analysis proving groove mode of binding. Molecular docking explored the various modes of intermolecular interactions of the drug with microbes as well as DNA.


Assuntos
DNA/química , Nitrobenzoatos/química , Pirazóis/química , Animais , Antioxidantes/química , Aspergillus niger/efeitos dos fármacos , Sítios de Ligação , Bovinos , DNA/metabolismo , Conformação Molecular , Simulação de Acoplamento Molecular , Nitrobenzoatos/metabolismo , Nitrobenzoatos/farmacologia , Conformação de Ácido Nucleico , Teoria Quântica , Eletricidade Estática
12.
J Chem Phys ; 150(21): 215102, 2019 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-31176328

RESUMO

A central question in epigenetics is how histone modifications influence the 3D structure of eukaryotic genomes and, ultimately, how this 3D structure is manifested in gene expression. The wide range of length scales that influence the 3D genome structure presents important challenges; epigenetic modifications to histones occur on scales of angstroms, yet the resulting effects of these modifications on genome structure can span micrometers. There is a scarcity of computational tools capable of providing a mechanistic picture of how molecular information from individual histones is propagated up to large regions of the genome. In this work, a new molecular model of chromatin is presented that provides such a picture. This new model, referred to as 1CPN, is structured around a rigorous multiscale approach, whereby free energies from an established and extensively validated model of the nucleosome are mapped onto a reduced coarse-grained topology. As such, 1CPN incorporates detailed physics from the nucleosome, such as histone modifications and DNA sequence, while maintaining the computational efficiency that is required to permit kilobase-scale simulations of genomic DNA. The 1CPN model reproduces the free energies and dynamics of both single nucleosomes and short chromatin fibers, and it is shown to be compatible with recently developed models of the linker histone. It is applied here to examine the effects of the linker DNA on the free energies of chromatin assembly and to demonstrate that these free energies are strongly dependent on the linker DNA length, pitch, and even DNA sequence. The 1CPN model is implemented in the LAMMPS simulation package and is distributed freely for public use.


Assuntos
Cromatina/química , Modelos Químicos , Montagem e Desmontagem da Cromatina , DNA/química , Epigênese Genética , Histonas/química , Conformação de Ácido Nucleico , Nucleossomos/química
13.
Gene ; 710: 399-405, 2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31200088

RESUMO

Iron-responsive elements (IREs) are ~35-nucleotide (nt) stem-loop RNA structures located in 5' or 3' untranslated regions (UTRs) of mRNAs that mediate post-transcriptional regulation by their association with IRE-binding proteins (IRPs). IREs are characterized by their apical 6-nt loop motif 5'-CAGWGH-3' (W = A or U and H = A, C or U), the so-called pseudotriloop, of which the loop nts C1 and G5 are paired, and the none-paired C between the two stem regions. In this study, the yeast three-hybrid (Y3H) system was used to investigate the relevance of the pseudotriloop structure of ferritin light chain (FTL) for the IRE-IRP interaction and the binding affinities between variant IRE(-like) structures and the two IRP isoforms, IRP1 and 2. Destabilization of the pseudotriloop structure by a G5-to-A mutation reduced binding of IRP1 and 2, while restoring the pseudotriloop conformation by the compensatory C1-to-U mutation, restored binding to both IRPs. In particular, IRP1 showed even stronger binding to the C1U-G5A mutant than to the wildtype FTL IRE. On the other hand, deletion of the bulged-out U6 of the pseudotriloop did not significantly affect its binding to either IRP1 or 2, but substitution with C particularly enhanced the binding to IRP1. In comparison to FTL IRE, IRE-like structures of 5'-aminolevulinate synthase 2 (ALAS2) and SLC40A1 (also known as ferroportin-1) showed similar or, in the case of endothelial PAS domain protein 1 (EPAS1) IRE, slightly weaker binding affinity to IRPs. SLC11A2 (a.k.a. divalent metal transporter-1) IRE exhibited relatively weak binding to IRP1 and medium binding to IRP2. Notably, the IRE-like structure of α-synuclein showed no detectable binding to either IRP under the conditions used in this Y3H assay. Our results indicate that Y3H can be used to characterize binding between IRPs and various IRE-like structures in vivo.


Assuntos
Apoferritinas/química , Apoferritinas/genética , Proteína 1 Reguladora do Ferro/metabolismo , Proteína 2 Reguladora do Ferro/metabolismo , 5-Aminolevulinato Sintetase/química , 5-Aminolevulinato Sintetase/genética , 5-Aminolevulinato Sintetase/metabolismo , Animais , Apoferritinas/metabolismo , Fatores de Transcrição Hélice-Alça-Hélice Básicos/química , Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Proteínas de Transporte de Cátions/química , Proteínas de Transporte de Cátions/genética , Proteínas de Transporte de Cátions/metabolismo , Proteína 1 Reguladora do Ferro/genética , Proteína 2 Reguladora do Ferro/genética , Mutação , Conformação de Ácido Nucleico , Técnicas do Sistema de Duplo-Híbrido , Regiões não Traduzidas
14.
World J Microbiol Biotechnol ; 35(7): 97, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31222457

RESUMO

Endophytic Streptomyces sp. SSD49 inhibited eight pathogens, including the human opportunistic pathogenic microorganisms, the plant pathogenic fungi and bacteria. The growth of soybeans, tomatoes, peppers and Populus tomentosa seedings inoculated with SSD49 are remarkably promoted. Here, we constructed two P. tomentosa seedling microRNA (miRNA) libraries inoculated with (PS30d) and without SSD49 (PC30d) to explore the molecular regulatory roles in the plant response to the beneficial bacteria. Totals of 314 known and 144 novel miRNAs were identified, among which 27 known and 11 novel miRNA had significantly different expression. The targets of up-regulated miR160, miR156, ptc114 and down-regulated miR319 and other differential expressed miRNAs primarily regulated genes encoding transcription factors (auxin response factor, small auxin-up RNA, and GRAS proteins), disease resistance proteins, phytohormone oxidase, and response regulators, which could promote plant growth, influence disease resistance and miRNA biosynthesis in P. tomentosa. This is the first report on the genome-wide identification of biocontrol endophytic Streptomyces inoculation-responsive miRNAs using small RNA sequencing in P. tomentosa and these findings provide new insight into understanding the biocontrol effects of endophytic Streptomyces.


Assuntos
MicroRNAs/genética , Reguladores de Crescimento de Planta , Populus/genética , RNA de Plantas/isolamento & purificação , Streptomyces/metabolismo , Agentes de Controle Biológico , Regulação da Expressão Gênica de Plantas , Biblioteca Gênica , Sequenciamento de Nucleotídeos em Larga Escala , MicroRNAs/metabolismo , Conformação de Ácido Nucleico , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Populus/metabolismo , Populus/microbiologia , RNA de Plantas/genética , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/isolamento & purificação , Análise de Sequência de RNA
15.
Genome Biol ; 20(1): 120, 2019 06 11.
Artigo em Inglês | MEDLINE | ID: mdl-31186073

RESUMO

BACKGROUND: The three-dimensional (3D) organization of chromosomes is linked to epigenetic regulation and transcriptional activity. However, only few functional features of 3D chromatin architecture have been described to date. The KNOT is a 3D chromatin structure in Arabidopsis, comprising 10 interacting genomic regions termed KNOT ENGAGED ELEMENTs (KEEs). KEEs are enriched in transposable elements and associated small RNAs, suggesting a function in transposon biology. RESULTS: Here, we report the KNOT's involvement in regulating invasive DNA elements. Transgenes can specifically interact with the KNOT, leading to perturbations of 3D nuclear organization, which correlates with the transgene's expression: high KNOT interaction frequencies are associated with transgene silencing. KNOT-linked silencing (KLS) cannot readily be connected to canonical silencing mechanisms, such as RNA-directed DNA methylation and post-transcriptional gene silencing, as both cytosine methylation and small RNA abundance do not correlate with KLS. Furthermore, KLS exhibits paramutation-like behavior, as silenced transgenes can lead to the silencing of active transgenes in trans. CONCLUSION: Transgene silencing can be connected to a specific feature of Arabidopsis 3D nuclear organization, namely the KNOT. KLS likely acts either independent of or prior to canonical silencing mechanisms, such that its characterization not only contributes to our understanding of chromosome folding but also provides valuable insights into how genomes are defended against invasive DNA elements.


Assuntos
Arabidopsis/genética , Inativação Gênica , Genoma de Planta , Conformação de Ácido Nucleico , Transgenes , Elementos de DNA Transponíveis
16.
Chem Commun (Camb) ; 55(50): 7211-7214, 2019 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-31165808

RESUMO

A label-free and universal photosensitization colorimetric assay based on target-induced dsDNA termini switching has been developed for the analysis of nucleic acids, proteins, small molecules and metal ions. This strategy is highly sensitive and versatile, the principle of which will be desirable for various biosensor developments and applications.


Assuntos
Colorimetria/métodos , DNA/química , Metais/química , Ácidos Nucleicos/química , Proteínas/química , Bioensaio/métodos , Conformação de Ácido Nucleico , Conformação Proteica
17.
J Phys Chem Lett ; 10(14): 3985-3990, 2019 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-31241956

RESUMO

Trinucleotide repeat (TNR) sequences, which are responsible for several neurodegenerative genetic diseases, fold into hairpins that interfere with the protein machinery in replication or repair, thus leading to dynamic mutation -abnormal expansions of the genome. Despite their high thermodynamic stability, these hairpins can undergo configurational rearrangements, which may be crucial for continuous dynamic mutation. Here, we used CTG repeats as a model system to study their structural dynamics at the single-molecule level. A unique dynamic two-state configuration interchange was discovered over a wide range of odd-numbered CTG repeat sequences. Employing repeat-number-dependent kinetic analysis, we proposed a bulge translocation model, which is driven by the local instability and can be extended reasonably to longer (pathologically relevant) hairpins, implying the potential role in error accumulation in repeat expansion.


Assuntos
DNA/química , DNA/genética , Conformação de Ácido Nucleico , Repetições de Trinucleotídeos/genética , Simulação de Dinâmica Molecular , Método de Monte Carlo , Termodinâmica
18.
DNA Res ; 26(3): 273-286, 2019 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-31231763

RESUMO

The intergenic spacer (IGS) of rDNA is frequently built of long blocks of tandem repeats. To estimate the intragenomic variability of such knotty regions, we employed PacBio sequencing of the Cucurbita moschata genome, in which thousands of rDNA copies are distributed across a number of loci. The rRNA coding regions are highly conserved, indicating intensive interlocus homogenization and/or high selection pressure. However, the IGS exhibits high intragenomic structural diversity. Two repeated blocks, R1 (300-1250 bp) and R2 (290-643 bp), account for most of the IGS variation. They exhibit minisatellite-like features built of multiple periodically spaced short GC-rich sequence motifs with the potential to adopt non-canonical DNA conformations, G-quadruplex-folded and left-handed Z-DNA. The mutual arrangement of these motifs can be used to classify IGS variants into five structural families. Subtle polymorphisms exist within each family due to a variable number of repeats, suggesting the coexistence of an enormous number of IGS variants. The substantial length and structural heterogeneity of IGS minisatellites suggests that the tempo of their divergence exceeds the tempo of the homogenization of rDNA arrays. As frequently occurring among plants, we hypothesize that their instability may influence transcription regulation and/or destabilize rDNA units, possibly spreading them across the genome.


Assuntos
Cucurbita/genética , DNA Espaçador Ribossômico/genética , Variação Genética , Repetições Minissatélites , Conformação de Ácido Nucleico , DNA Espaçador Ribossômico/química , DNA Espaçador Ribossômico/metabolismo , Análise de Sequência de DNA
19.
J Photochem Photobiol B ; 197: 111516, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31170508

RESUMO

In the search for new therapeutic agents we have synthesized 13 new organotin(IV) carboxylate derivatives of (E)-4-((4-methoxy-2-nitrophenyl)amino)-4-oxobut-2-enoic acid. The synthesized complexes were characterized by several spectroscopic techniques. A chelating or bridging bidentate nature of the carboxylate ligand was suggested from the solid state FT-IR results. Solution state multinuclear NMR (1H, 13C and 119Sn) results reveal that the geometry around the Sn atom in triorganotin(IV) complexes is trigonal bipyramidal and in diorganotin(IV) complexes is octahedral. The ligand, (E)-4-((4-methoxy-2-nitrophenyl)amino)-4-oxobut-2-enoic acid, complex 1 and complex 2 were also analyzed by single crystal X-ray technique and the results fully supports the spectroscopic data. For 1 and 2 the geometry optimized by the single crystal X-ray analyses is distorted trigonal bipyramidal. The interaction of the studied compounds with SS-DNA was investigated by UV-Vis. Spectroscopy and Molecular docking showing an intercalative mode of binding. The evaluation of the screened compounds for cancer treatment displays even higher than that of the vincristine used as a standard drug. Similarly the performance of the tested compounds as an antileishmanial agent considers them very close in activity to the standard drug, amphotericin B. The antibacterial results show that the most of the compounds have a moderate sensitivity against the studied bacterial pathogens.


Assuntos
Complexos de Coordenação/química , Compostos Orgânicos de Estanho/química , Sítios de Ligação , Ácidos Carboxílicos/química , Linhagem Celular , Proliferação de Células/efeitos dos fármacos , Complexos de Coordenação/síntese química , Complexos de Coordenação/farmacologia , Cristalografia por Raios X , DNA/química , DNA/metabolismo , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Positivas/efeitos dos fármacos , Humanos , Leishmania tropica/efeitos dos fármacos , Ligantes , Espectroscopia de Ressonância Magnética , Conformação Molecular , Simulação de Acoplamento Molecular , Conformação de Ácido Nucleico , Espectroscopia de Infravermelho com Transformada de Fourier
20.
J Phys Chem A ; 123(29): 6229-6240, 2019 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-31241337

RESUMO

4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone is a potent nicotine-based carcinogen that generates many DNA lesions, including the HOCH2-C, HOCH2-G, and HOCH2-A hydroxymethyl adducts. Despite all lesions containing an altered exocyclic amino group, which allows the hydroxymethyl group to be directed away from the Watson-Crick binding face, only the most persistent adenine adduct is mutagenic. As a first step toward understanding this differential mutagenicity, density functional theory (DFT) and molecular dynamics (MD) simulations were used to gain atomic-level structural details of these DNA damage products. DFT calculations reveal that all three lesions exhibit conformational diversity. However, regardless of the hydroxymethyl-nucleobase orientation, both DFT and MD simulations highlight that HOCH2-C and HOCH2-G form pairs with the canonical complementary base (G and C, respectively) that are structural and energetically preferred over mispairs. In contrast, depending on the hydroxymethyl-nucleobase orientation, the Watson-Crick HOCH2-A:T pair can become significantly destabilized relative to undamaged A:T. As a result, HOCH2-A mispairs with G, C, and A are energetically accessible and maintain key geometrical features of canonical DNA. Overall, our data directly correlate with the reported differential mutagenicity of the hydroxylmethyl lesions and will encourage future studies to further uncover the cellular impact of the most persistent adenine lesion.


Assuntos
Adutos de DNA/química , Formaldeído/química , Adenina/química , Pareamento de Bases , Citosina/química , Adutos de DNA/genética , Teoria da Densidade Funcional , Guanina/química , Ligações de Hidrogênio , Modelos Químicos , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico
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