The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

Thomas R. Cech - One of the best experts on this subject based on the ideXlab platform.

  • Dynamics of human telomerase recruitment depend on template- telomere Base Pairing.
    Molecular biology of the cell, 2018
    Co-Authors: Jens C. Schmidt, Arthur J. Zaug, Regina Kufer, Thomas R. Cech
    Abstract:

    The reverse transcriptase telomerase adds telomeric repeats to chromosome ends to counteract telomere shortening and thereby assures genomic stability in dividing human cells. Key parameters in telomere homeostasis are the frequency with which telomerase engages the chromosome end and the number of telomeric repeats it adds during each association event. To study telomere elongation in vivo, we have established a live-cell imaging assay to track individual telomerase ribonucleoproteins in CRISPR-edited HeLa cells. Using this assay and the drug imetelstat, which is a competitive inhibitor of telomeric DNA binding, we demonstrate that stable association of telomerase with the single-stranded overhang of the chromosome end requires telomerase-DNA Base Pairing. Furthermore, we show that telomerase processivity contributes to telomere elongation in vivo. Together, these findings provide new insight into the dynamics of telomerase recruitment and the importance of processivity in maintaining telomere length in human cancer cells.

  • Dynamics of human telomerase recruitment depend on template-telomere Base-Pairing
    2017
    Co-Authors: Jens C. Schmidt, Arthur J. Zaug, Regina Kufer, Thomas R. Cech
    Abstract:

    The reverse transcriptase telomerase adds telomeric repeats to chromosome ends to counteract telomere shortening and thereby assures genomic stability in dividing human cells. Key variables in telomere homeostasis are the frequency with which telomerase engages the chromosome end and the number of telomeric repeats it adds during each association event. To study telomere elongation in vivo we have established a live-cell imaging assay to track individual telomerase RNPs in HeLa cells. Using this assay and the drug imetelstat, which is a competitive inhibitor of telomeric DNA binding, we demonstrate that stable association of telomerase with the single-stranded overhang of the chromosome end requires telomerase-DNA Base-Pairing. Furthermore, we show that telomerase processivity contributes to telomere elongation in vivo. Together, these findings provide new insight into the dynamics of telomerase recruitment and the importance of processivity in maintaining telomere length in human cancer cells.

  • euplotes telomerase evidence for limited Base Pairing during primer elongation and dgtp as an effector of translocation
    Biochemistry, 1998
    Co-Authors: Philip W Hammond, Thomas R. Cech
    Abstract:

    The telomeric sequence repeats at the ends of eukaryotic chromosomes are maintained by the ribonucleoprotein enzyme telomerase. Telomeric DNA primers are bound by telomerase both at the active site, which includes Base-Pairing with the RNA template, and at a second anchor site. The stabilities of Euplotes aediculatus primer-telomerase complexes were determined by measuring their dissociation rates (koff), using an assay involving photo-cross-linking at the anchor site. The primer length was varied, and mismatched substitutions were introduced in a systematic manner. We observed that koff does not scale with primer length as expected for accumulated primer-template Base-Pairing. This suggests that telomerase maintains a more-or-less constant number of Base pairs, similar to the transcription bubble maintained by RNA polymerase. An upper limit was estimated by comparing the experimental koff for the primer-telomerase complex to that of a model DNA-RNA duplex. All the binding energy could be attributed to 10 or 11 Base pairs; alternatively, there could be <10 Base pairs, with the remaining energy contributed by other parts of telomerase. Most primers exhibited biphasic dissociation kinetics, with variations in both the amount in each phase and the rate for each phase. Since the cross-links monitored in the dissociation assay were all formed with the 5' region of the primer, the two phases may arise from different Base-Pairing registers with the RNA template, possibly representing pre- and post-translocation complexes. A shift from slow phase to fast phase dissociation was observed in the presence of dGTP, which may implicate dGTP as a positive effector of translocation.

David Tollervey - One of the best experts on this subject based on the ideXlab platform.

  • Base Pairing between u3 small nucleolar rna and the 5 end of 18s rrna is required for pre rrna processing
    Molecular and Cellular Biology, 1999
    Co-Authors: Kishor Sharma, David Tollervey
    Abstract:

    The loop of a stem structure close to the 5′ end of the 18S rRNA is complementary to the box A region of the U3 small nucleolar RNA (snoRNA). Substitution of the 18S loop nucleotides inhibited pre-rRNA cleavage at site A1, the 5′ end of the 18S rRNA, and at site A2, located 1.9 kb away in internal transcribed spacer 1. This inhibition was largely suppressed by a compensatory mutation in U3, demonstrating functional Base Pairing. The U3–pre-rRNA Base Pairing is incompatible with the structure that forms in the mature 18S rRNA and may prevent premature folding of the pre-rRNA. In the Escherichia coli pre-rRNA the homologous region of the 16S rRNA is also sequestered, in that case by Base Pairing to the 5′ external transcribed spacer (5′ ETS). Cleavage at site A0 in the yeast 5′ ETS strictly requires Base Pairing between U3 and a sequence within the 5′ ETS. In contrast, the U3-18S interaction is not required for A0 cleavage. U3 therefore carries out at least two functionally distinct Base pair interactions with the pre-rRNA. The nucleotide at the site of A1 cleavage was shown to be specified by two distinct signals; one of these is the stem-loop structure within the 18S rRNA. However, in contrast to the efficiency of cleavage, the position of A1 cleavage is not dependent on the U3-loop interaction. We conclude that the 18S stem-loop structure is recognized at least twice during pre-rRNA processing.

  • Base Pairing between u3 and the pre ribosomal rna is required for 18s rrna synthesis
    The EMBO Journal, 1995
    Co-Authors: Monica Beltrame, David Tollervey
    Abstract:

    Abstract The nucleolus, the site of pre-ribosomal RNA (pre-rRNA) synthesis and processing in eukaryotic cells, contains a number of small nucleolar RNAs (snoRNAs). Yeast U3 snoRNA is required for the processing of 18S rRNA from larger precursors and contains a region complementary to the pre-rRNA. Substitution mutations in the pre-rRNA which disrupt this Base Pairing potential are lethal and prevent synthesis of 18S rRNA. These mutant pre-rRNAs show defects in processing which closely resemble the effects of genetic depletion of components of the U3 snoRNP. Co-expression of U3 snoRNAs which carry compensatory mutations allows the mutant pre-rRNAs to support viability and synthesize 18S rRNA at high levels. Pre-rRNA processing steps which are blocked by the external transcribed spacer region mutations are largely restored by expression of the compensatory U3 mutants. Pre-rRNA processing therefore requires direct Base Pairing between snoRNA and the substrate. Base Pairing with the substrate is thus a common feature of small RNAs involved in mRNA and rRNA maturation.

Tal Schwartz - One of the best experts on this subject based on the ideXlab platform.

  • light emitting self assembled peptide nucleic acids exhibit both stacking interactions and watson crick Base Pairing
    Nature Nanotechnology, 2015
    Co-Authors: Or Berger, Lihi Adlerabramovich, Assaf Grunwald, Yael Liebespeer, Mor Bachar, Ludmila Buzhansky, Estelle Mossou, Trevor V Forsyth, Michal Levysakin, Tal Schwartz
    Abstract:

    Peptide nucleic acids can self-assemble into ordered architectures that are coordinated by both stacking interactions and Watson–Crick Base Pairing, and exhibit a variety of optical properties.

  • light emitting self assembled peptide nucleic acids exhibit both stacking interactions and watson crick Base Pairing
    Nature Nanotechnology, 2015
    Co-Authors: Or Berger, Lihi Adlerabramovich, Assaf Grunwald, Yael Liebespeer, Mor Bachar, Ludmila Buzhansky, Estelle Mossou, Trevor V Forsyth, Michal Levysakin, Tal Schwartz
    Abstract:

    The two main branches of bionanotechnology involve the self-assembly of either peptides or DNA. Peptide scaffolds offer chemical versatility, architectural flexibility and structural complexity, but they lack the precise Base Pairing and molecular recognition available with nucleic acid assemblies. Here, inspired by the ability of aromatic dipeptides to form ordered nanostructures with unique physical properties, we explore the assembly of peptide nucleic acids (PNAs), which are short DNA mimics that have an amide backbone. All 16 combinations of the very short di-PNA building blocks were synthesized and assayed for their ability to self-associate. Only three guanine-containing di-PNAs-CG, GC and GG-could form ordered assemblies, as observed by electron microscopy, and these di-PNAs efficiently assembled into discrete architectures within a few minutes. The X-ray crystal structure of the GC di-PNA showed the occurrence of both stacking interactions and Watson-Crick Base Pairing. The assemblies were also found to exhibit optical properties including voltage-dependent electroluminescence and wide-range excitation-dependent fluorescence in the visible region.

David Posada - One of the best experts on this subject based on the ideXlab platform.

  • Base-Pairing Versatility Determines Wobble Sites in tRNA Anticodons of Vertebrate Mitogenomes
    2016
    Co-Authors: Miguel M. Fonseca, Sara Rocha, David Posada
    Abstract:

    Background: Vertebrate mitochondrial genomes typically have one transfer RNA (tRNA) for each synonymous codon family. This limited anticodon repertoire implies that each tRNA anticodon needs to wobble (establish a non-Watson-Crick Base Pairing between two nucleotides in RNA molecules) to recognize one or more synonymous codons. Different hypotheses have been proposed to explain the factors that determine the nucleotide composition of wobble sites in vertebrate mitochondrial tRNA anticodons. Until now, the two major postulates – the ‘‘codon-anticodon adaptation hypothesis’ ’ and the ‘‘wobble versatility hypothesis’ ’ – have not been formally tested in vertebrate mitochondria because both make the same predictions regarding the composition of anticodon wobble sites. The same is true for the more recent ‘‘wobble cost hypothesis’’. Principal Findings: In this study we have analyzed the occurrence of synonymous codons and tRNA anticodon wobble sites in 1553 complete vertebrate mitochondrial genomes, focusing on three fish species with mtDNA codon usage bias reversal (L-strand is GT-rich). These mitogenomes constitute an excellent opportunity to study the evolution of the wobble nucleotide composition of tRNA anticodons because due to the reversal the predictions for the anticodon wobble sites differ between the existing hypotheses. We observed that none of the wobble sites of tRNA anticodons in these unusual mitochondrial genomes coevolved to match the new overall codon usage bias, suggesting that nucleotides at the wobbl

  • Base-Pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.
    PLOS ONE, 2012
    Co-Authors: Miguel Fonseca, Sara Rocha, David Posada
    Abstract:

    Background Vertebrate mitochondrial genomes typically have one transfer RNA (tRNA) for each synonymous codon family. This limited anticodon repertoire implies that each tRNA anticodon needs to wobble (establish a non-Watson-Crick Base Pairing between two nucleotides in RNA molecules) to recognize one or more synonymous codons. Different hypotheses have been proposed to explain the factors that determine the nucleotide composition of wobble sites in vertebrate mitochondrial tRNA anticodons. Until now, the two major postulates – the “codon-anticodon adaptation hypothesis” and the “wobble versatility hypothesis” – have not been formally tested in vertebrate mitochondria because both make the same predictions regarding the composition of anticodon wobble sites. The same is true for the more recent “wobble cost hypothesis”.

Mitsuhiko Shionoya - One of the best experts on this subject based on the ideXlab platform.

  • site specific polymerase incorporation of consecutive ligand containing nucleotides for multiple metal mediated Base Pairing
    Chemical Communications, 2021
    Co-Authors: Takahiro Nakama, Yusuke Takezawa, Mitsuhiko Shionoya
    Abstract:

    An enzymatic method has been developed for the synthesis of DNA oligomers containing consecutive artificial ligand-type nucleotides. Three hydroxypyridone ligand-containing nucleotides forming CuII-mediated unnatural Base pairs were continuously incorporated at a pre-specified position by a lesion-bypass Dpo4 polymerase. This enzymatic synthesis was applied to the development of a CuII-responsive DNAzyme. Accordingly, this research will open new routes for the construction of metal-responsive DNA architectures that are manipulated by multiple metal-mediated Base Pairing.

  • artificial dna Base Pairing mediated by diverse metal ions
    Chemistry Letters, 2017
    Co-Authors: Yusuke Takezawa, Jens Muller, Mitsuhiko Shionoya
    Abstract:

    Metal-mediated artificial DNA Base pairs, consisting of two ligand-type nucleosides and a bridging metal ion, are promising building units for constructing DNA-Based supermolecules. Metallo-Base Pairing allows the thermal stabilization and site-specific functionalization of DNA duplexes. In this review, representative examples of the metallo-Base pairs are classified according to the metal species, and their structures and properties are highlighted. Recent applications including polymerase synthesis are also overviewed to illustrate the future directions of this research field.

  • bifacial Base Pairing behaviors of 5 hydroxyuracil dna Bases through hydrogen bonding and metal coordination
    Chemistry: A European Journal, 2015
    Co-Authors: Yusuke Takezawa, Kotaro Nishiyama, Tsukasa Mashima, Masato Katahira, Mitsuhiko Shionoya
    Abstract:

    A novel bifacial ligand-bearing nucleoBase, 5-hydroxyuracil (UOH), which forms both a hydrogen-bonded Base pair (UOH–A) and a metal-mediated Base pair (UOH–M–UOH) has been developed. The UOH–M–UOH Base pairs were quantitatively formed in the presence of lanthanide ions such as GdIII when UOH–UOH pairs were consecutively incorporated into DNA duplexes. This result established metal-assisted duplex stabilization as well as DNA-templated assembly of lanthanide ions. Notably, a duplex possessing UOH–A Base pairs was destabilized by addition of GdIII ions. This observation suggests that the hybridization behaviors of the UOH-containing DNA strands are altered by metal complexation. Thus, the UOH nucleoBase with a bifacial Base-Pairing property holds great promise as a component for metal-responsive DNA materials.

  • metal mediated dna Base Pairing alternatives to hydrogen bonded watson crick Base pairs
    Accounts of Chemical Research, 2012
    Co-Authors: Yusuke Takezawa, Mitsuhiko Shionoya
    Abstract:

    With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely Based on highly specific molecular recognition between nucleoBases through the specific hydrogen bonds in the Watson–Crick Base Pairing system. While the native Base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative Base Pairing systems in recent decades. Most of these new systems were designed Based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA Base Pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme ...

  • metal Base Pairing in dna
    Coordination Chemistry Reviews, 2010
    Co-Authors: Guido H Clever, Mitsuhiko Shionoya
    Abstract:

    Abstract The use of DNA as a molecular wire in nanoscale electronic architectures would greatly benefit from its capability of sequence-specific self-assembly. Although single electrons and positive charges have been shown to be transmitted by natural DNA over a distance of several Base pairs, the high ohmic resistance of unmodified oligonucleotides imposes a serious obstacle. Exchanging some or all of the Watson–Crick Base pairs in DNA by metal complexes may solve this problem and evolve DNA-like materials with superior conductivity for future nano-electronic applications. The so-called metal–Base pairs are formed from suitable transition metal ions and ligand-like nucleosides which are introduced into both of the two Pairing strands by automated DNA synthesis. This review illustrates the basic concepts of metal–Base Pairing and highlights recent developments in the field.