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DNA structure review

Marçal Pastor-Anglada, Sandra Pérez-Torras
Since human Nucleoside Transporters (hNTs) were identified by their activity as transport systems, extensive work has been done to fully characterize them at the molecular and physiological level. Many efforts have been addressed to the identification of their selectivity for natural substrates and nucleoside analogs used to treat several diseases. hNTs belong to two different gene families, SLC28 and SLC29 , encoding human Concentrative Nucleoside Transporters (hCNTs) and human Equilibrative Nucleoside Transporters (hENTs), respectively...
2018: Frontiers in Pharmacology
Carlo Maria Di Liegro, Gabriella Schiera, Italia Di Liegro
H1 linker histones are a class of DNA-binding proteins involved in the formation of supra-nucleosomal chromatin higher order structures. Eleven non-allelic subtypes of H1 are known in mammals, seven of which are expressed in somatic cells, while four are germ cell-specific. Besides having a general structural role, H1 histones also have additional epigenetic functions related to DNA replication and repair, genome stability, and gene-specific expression regulation. Synthesis of the H1 subtypes is differentially regulated both in development and adult cells, thus suggesting that each protein has a more or less specific function...
June 20, 2018: Genes
Tamaki Suganuma, Jerry L Workman
Chromatin is a mighty consumer of cellular energy generated by metabolism. Metabolic status is efficiently coordinated with transcription and translation, which also feed back to regulate metabolism. Conversely, suppression of energy utilization by chromatin processes may serve to preserve energy resources for cell survival. Most of the reactions involved in chromatin modification require metabolites as their cofactors or coenzymes. Therefore, the metabolic status of the cell can influence the spectra of posttranslational histone modifications and the structure, density and location of nucleosomes, impacting epigenetic processes...
June 20, 2018: Annual Review of Biochemistry
Gareth Bloomfield
Sex in social amoebae (or dictyostelids) has a number of striking features. Dictyostelid zygotes do not proliferate but grow to a large size by feeding on other cells of the same species, each zygote ultimately forming a walled structure called a macrocyst. The diploid macrocyst nucleus undergoes meiosis, after which a single meiotic product survives to restart haploid vegetative growth. Meiotic recombination is generally initiated by the Spo11 enzyme, which introduces DNA double-strand breaks. Uniquely, as far as is known among sexual eukaryotes, dictyostelids lack a SPO11 gene...
June 20, 2018: Annual Review of Microbiology
Xing Wang, Arun Richard Chandrasekaran, Zhiyong Shen, Yoel P Ohayon, Tong Wang, Megan E Kizer, Ruojie Sha, Chengde Mao, Hao Yan, Xiaoping Zhang, Shiping Liao, Baoquan Ding, Banani Chakraborty, Natasha Jonoska, Dong Niu, Hongzhou Gu, Jie Chao, Xiang Gao, Yuhang Li, Tanashaya Ciengshin, Nadrian C Seeman
Over the past 35 years, DNA has been used to produce various nanometer-scale constructs, nanomechanical devices, and walkers. Construction of complex DNA nanostructures relies on the creation of rigid DNA motifs. Paranemic crossover (PX) DNA is one such motif that has played many roles in DNA nanotechnology. Specifically, PX cohesion has been used to connect topologically closed molecules, to assemble a three-dimensional object, and to create two-dimensional DNA crystals. Additionally, a sequence-dependent nanodevice based on conformational change between PX and its topoisomer, JX2 , has been used in robust nanoscale assembly lines, as a key component in a DNA transducer, and to dictate polymer assembly...
June 18, 2018: Chemical Reviews
Mauro Ravera, Elsa Moreno-Viguri, Rocio Paucar, Silvia Pérez-Silanes, Elisabetta Gabano
The development of safe and affordable antiparasitic agents effective against neglected tropical diseases is a big challenge of the drug discovery. The drugs currently employed have limitations such as poor efficacy, drug resistance or side effects. Thus, the search for new promising drugs is more and more crucial. Metal complexes and, in particular, organometallic compounds may expand the list of the drug candidates due to the peculiar attributes that the presence of the metal core add to the organic fragment (e...
June 1, 2018: European Journal of Medicinal Chemistry
Anirban Basu, Gopinatha Suresh Kumar
BACKGROUND: Nucleic acids are now important targets for therapeutic intervention. Alkaloids are an important class of molecules that have myriad therapeutic utility. Isoquinoline and benzophenanthridine alkaloids exhibit multiple pharmacological activities which are often related to their strong nucleic acid binding abilities. Therefore, a review of their interaction aspects with varying nucleic acid structures is essential for rational design and development as therapeutic agents. SCOPE OF THE REVIEW: This work reviews the interaction of various therapeutically important isoquinoline and benzophenanthridine alkaloids with nucleic acids...
June 13, 2018: Biochimica et Biophysica Acta
Paulo Tavares
Many icosahedral viruses use a specialized portal vertex for genome encapsidation in the viral capsid (or head). This structure then controls release of the viral genetic information to the host cell at the beginning of infection. In tailed bacteriophages, the portal system is connected to a tail device that delivers their genome to the bacterial cytoplasm. The head-to-tail interface is a multiprotein complex that locks the viral DNA inside the phage capsid correctly positioned for egress and that controls its ejection when the viral particle interacts with the host cell receptor...
2018: Sub-cellular Biochemistry
Duane P Grandgenett, Hideki Aihara
Integration of the reverse-transcribed viral cDNA into the host's genome is a critical step in the lifecycle of all retroviruses. Retrovirus integration is carried out by integrase (IN), a virus-encoded enzyme that forms an oligomeric 'intasome' complex with both ends of the linear viral DNA to catalyze their concerted insertions into the backbones of the host's DNA. IN also forms a complex with host proteins, which guides the intasome to the host's chromosome. Recent structural studies have revealed remarkable diversity as well as conserved features among the architectures of the intasome assembly from different genera of retroviruses...
2018: Sub-cellular Biochemistry
Jason Greenwald, Witek Kwiatkowski, Roland Riek
How life can emerge from non-living matter is one of the fundamental mysteries of the universe. A bottom-up approach to this problem focuses on the potential chemical precursors of life, in particular the nature of the first replicative molecules. Such thinking has led to the currently most popular idea: that a RNA-like molecule played a central role as the first replicative and catalytic molecule. Here, we review an alternative hypothesis that has recently gained experimental support, focusing on the role of amyloidogenic peptides rather than nucleic acids, in what has been by some termed "the amyloid-world" hypothesis...
June 8, 2018: Journal of Molecular Biology
Thomas O Mason, Ulyana Shimanovich
Protein self-assembly processes, by which polypeptides interact and independently form multimeric structures, lead to a wide array of different endpoints. Structures formed range from highly ordered molecular crystals to amorphous aggregates. Order arises in the system from a balance between many low-energy processes occurring due to a set of interactions between residues in a chain, between residues in different chains, and between solute and solvent. In Nature, self-assembling protein systems have evolved over millions of years to organize into supramolecular structures, optimized for specific functions, with this propensity determined by the sequence of their constituent amino acids, of which only 20 are encoded in DNA...
June 8, 2018: Advanced Materials
Nelle Varoquaux
The development of new ways to probe samples for the three-dimensional (3D) structure of DNA paves the way for in depth and systematic analyses of the genome architecture. 3C-like methods coupled with high-throughput sequencing can now assess physical interactions between pairs of loci in a genome-wide fashion, thus enabling the creation of genome-by-genome contact maps. The spreading of such protocols creates many new opportunities for methodological development: how can we infer 3D models from these contact maps? Can such models help us gain insights into biological processes? Several recent studies applied such protocols to P...
June 7, 2018: International Journal of Biostatistics
S W Pipe
Recombinant DNA technology has led to accelerating introduction of novel therapeutics for the treatment of haemophilia. This technology has driven the development of recombinant clotting factors, extended half-life clotting factors, alternative biologics to promote haemostasis and enabled the launch of the gene therapy era for haemophilia. At the core of this technology is the ability to study the structure and function of the native molecules and to apply rational bioengineering to overcome limitations to the existing therapies...
May 2018: Haemophilia: the Official Journal of the World Federation of Hemophilia
Jolie D Barter, Thomas C Foster
Gene expression in the aging brain depends on transcription signals generated by senescent physiology, interacting with genetic and epigenetic programs. In turn, environmental factors influence epigenetic mechanisms, such that an epigenetic-environmental link may contribute to the accumulation of cellular damage, susceptibility or resilience to stressors, and variability in the trajectory of age-related cognitive decline. Epigenetic mechanisms, DNA methylation and histone modifications, alter chromatin structure and the accessibility of DNA...
June 1, 2018: Neuroscientist: a Review Journal Bringing Neurobiology, Neurology and Psychiatry
Dacheng Yang, Xinwei Jiang, Jianxia Sun, Xia Li, Xusheng Li, Rui Jiao, Ziyao Peng, Yuqi Li, Weibin Bai
Zearalenone is commonly generated from moldy cereal grain, which is toxic to the development of gametogenesis and embryo in human and animals. The zearalenone-induced reproductive damage is mainly attributed to four mechanisms. Firstly, zearalenone as an oestrogen-like compound binds to estrogen receptor and causes damage to germ cells and testicular structure. Secondly, zearalenone disrupts the blood-testis barrier, and causes the damage to germ cells. Thirdly, zearalenone elevates oxidative stress, which increases the production of lipid peroxides, and results in the damage to the antioxidant defense system...
June 1, 2018: Food and Chemical Toxicology
Austin T Raper, Andrew J Reed, Zucai Suo
Faithful transmission and maintenance of genetic material is primarily fulfilled by DNA polymerases. During DNA replication, these enzymes catalyze incorporation of deoxynucleotides into a DNA primer strand based on Watson-Crick complementarity to the DNA template strand. Through the years, research on DNA polymerases from every family and reverse transcriptases has revealed structural and functional similarities, including a conserved domain architecture and purported two-metal-ion mechanism for nucleotidyltransfer...
June 4, 2018: Chemical Reviews
Wataru Sakamoto, Tsuneaki Takami
Endosymbiotically originated chloroplast DNA (cpDNA) encodes part of the genetic information needed to fulfill chloroplast function, including fundamental processes such as photosynthesis. In the last two decades, advances in genome analysis led to the identification of a considerable number of cpDNA sequences from various species. While these data provided the consensus features of cpDNA organization and chloroplast evolution in plants, how cpDNA is maintained through development and is inherited remains to be fully understood...
June 1, 2018: Plant & Cell Physiology
Karissa L Paquin, Niall G Howlett
Chromatin is a highly compact structure that must be rapidly rearranged in order for DNA repair proteins to access sites of damage and facilitate timely and efficient repair. Chromatin plasticity is achieved through multiple processes, including the post-translational modification of histone tails. In recent years, the impact of histone post-translational modification on the DNA damage response has become increasingly well recognized, and chromatin plasticity has been firmly linked to efficient DNA repair. One particularly important histone post-translational modification process is methylation...
June 1, 2018: Molecular Cancer Research: MCR
Yixing Gou, Yixuan Jia, Peng Wang, Changku Sun
Inertial microfluidics has become a popular topic in microfluidics research for its good performance in particle manipulation and its advantages of simple structure, high throughput, and freedom from an external field. Compared with traditional microfluidic devices, the flow field in inertial microfluidics is between Stokes state and turbulence, whereas the flow is still regarded as laminar. However, many mechanical effects induced by the inertial effect are difficult to observe in traditional microfluidics, making particle motion analysis in inertial microfluidics more complicated...
June 1, 2018: Sensors
H Steven Seifert
Advances in understanding mechanisms of nucleic acids have revolutionized molecular biology and medicine, but understanding of nontraditional nucleic acid conformations is less developed. The guanine quadruplex (G4) alternative DNA structure was first described in the 1960s, but the existence of G4 structures (G4-S) and their participation in myriads of biological functions are still underappreciated. Despite many tools to study G4s and many examples of roles for G4s in eukaryotic molecular processes and issues with uncontrolled G4-S formation, there is relatively little knowledge about the roles of G4-S in viral or prokaryotic systems...
May 31, 2018: Annual Review of Microbiology
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