Nucleic Acids Symposium Series (Nucleic Acids Symp)

Publisher: Oxford University Press

Journal description

The Nucleic Acids Symposium Series consists of the proceedings of the Symposium on Nucleic Acids Chemistry held annually in Japan.

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Additional details

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Website Nucleic Acids Symposium Series website
Other titles Nucleic acids symposium series (Online), Nucleic acids research., Nucleic acids research
ISSN 0261-3166
OCLC 60639222
Material type Conference publication, Document, Series, Internet resource
Document type Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details

Oxford University Press

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author cannot archive a post-print version
  • Restrictions
    • 12 months embargo on science, technology, medicine articles
    • 2 years embargo on arts and humanities articles
    • Some titles may have different embargoes
  • Conditions
    • Pre-print can only be posted prior to acceptance
    • Pre-print must be accompanied by set statement (see link)
    • Pre-print must not be replaced with post-print, instead a link to published version with amended set statement should be made
    • Pre-print on author's personal website, employer website, free public server or pre-prints in subject area
    • Post-print in Institutional repositories or Central repositories
    • Publisher version cannot be used except for Nucleic Acids Research articles
    • Published source must be acknowledged
    • Must link to publisher version
    • Set phrase to accompany archived copy (see policy)
    • Articles in some journals can be made Open Access on payment of additional charge
    • Eligible UK authors may deposit in OpenDepot
    • Publisher will deposit on behalf of NIH funded authors to PubMed Central, Nucleic Acids Research authors must pay their fee first
    • Some titles may use different policies
  • Classification
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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: DNA damage was monitored by fluorescent microscopy observations of DNA fluorescent images after hydrodynamic stretching on a microscope glass. DNA double-strand breaks lead to a decrease of the average length of observed fluorescent DNA molecules. Compared to conventional methods such as electrophoresis, the proposed method allows for the analysis of the DNA damage at very low DNA breaking frequency. In particular, this method was used to study DNA damage by weak UV irradiation in solutions of quantum dots.
    Nucleic Acids Symposium Series 09/2009; DOI:10.1093/nass/nrp024
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    ABSTRACT: The novel multi-arm DNA structures were designed using 2D-DNA Origami method, and these structures were folded into 3D hollow prism structures by introduction of connection strands into the arms. The opening of the prism structures were examined by a high-speed AFM, which showed the dissociation events of the connecting arms in the 3D-structures.
    Nucleic Acids Symposium Series 09/2009; DOI:10.1093/nass/nrp041
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    ABSTRACT: Triplex-forming oligonucleotides bind in the major groove of duplex DNA, generating three stranded structures containing T.AT and C+.GC triplets. Their sequence specific binding has potential uses in gene targeting but is limited by their low affinity, the requirement for low pH and the need for oligopurine targets. We have prepared nucleotide analogues to overcome these limitations and can now target some sequences that contain pyrimidine interruptions at physiological pH. We have tested the biological activity of these modified oligonucleotides. TFOs that contain multiple substitutions with positively charged groups bind with high affinity and we have explored how they interact with secondary sites.
    Nucleic Acids Symposium Series 09/2009; DOI:10.1093/nass/nrp036
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    ABSTRACT: Over the past few years, molecular oncology research has revealed that abnormalities in both protein coding genes (PCGs) and noncoding RNAs (ncRNAs) can be identified in tumors and that the interplay between PCGs and ncRNAs is causally involved in the initiation, progression and metastases of human cancers. MicroRNAs (miRNAs), which are among the most studied ncRNAs, are small 19- to 25-nucleotide genes involved in the regulation of PCGs and other ncRNAs. With the recent findings of miRNAs' involvement in cancer, miRNAs are strongly associated with the pathogenesis in human cancers. In this review, we focus on the possible mechanisms of miRNAs in cancer pathogenesis.
    Nucleic Acids Symposium Series 09/2009; DOI:10.1093/nass/nrp013
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    ABSTRACT: In transtranslation, ribosome switches the template for protein synthesis from an mRNA to tmRNA. The molecular mechanism of transtranslation remains mysterious. In order to clarify how tmRNA move through the ribosome, we developedinvitrosystems to monitor transtranslation as well as translation, which are composed of ribosome, elongation factors, tmRNA and SmpB all from Thermusthermophilus. In these systems, the early steps of transtranslation including transtransfer and the resume codon decoding could be monitored. Using these systems, the function of ribosomal protein S1 which has been suggested to be involved intranstranslation was investigated.
    Nucleic Acids Symposium Series 11/2007; DOI:10.1093/nass/nrm185
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    ABSTRACT: We present a combined experimental and theoretical approach, whereby a comparison of calculated and experimental 15N NMR chemical shifts allows the elucidation of hydrogen-bond structure in a ligand-nucleobase complex inside duplex DNA. In this work, we focus on the highly selective interaction of 2-amino-7-methyl-1,8-naphthyridine (AMND) to cytosine (C) base opposite the abasic site in DNA duplexes, despite the hydrogen-bond array of neutral AMND being fully complementary to guanine (G). Examination of the salt dependence of the binding constants reveals that the effective number of charges on the ligand is +1.0, indicating protonated AMND does bind to C. This is clearly supported by 15N NMR measurements, where the drastic changes in chemical shift are observed for the aromatic nitrogens on the ligand when binding to C. Furthermore, from the complexation-induced changes in chemical shift at 15N1 (83.1 ppm upfield), 15N8 (14.1 ppm upfield), and 15NH2 (18.3 ppm downfield) on AMND, the ligand is found to bind to C via three point hydrogen-bonds. The chemical shifts of the AMND-C complex, calculated by gauge-independent atomic orbital-DFT method, are in fair agreement with the experimental values. These results clearly explain the selective binding of AMND to C over G in abasic site-containing duplex DNA.
    Nucleic Acids Symposium Series 02/2005; DOI:10.1093/nass/49.1.255
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    ABSTRACT: As a part of our recent studies of RNA cleavage using antisense oligonucleotide–metal complex(es) conjugates, we prepared self-complementary 2′- O -methyl oligonucleotides with a terpyridine·Cu(II) complex, which was attached to the sugar portion of the 5′-end or 3′-end. The thermal stabilities of the formed duplexes, as compared with those of the unmodified 2′- O -methyl duplexes, revealed that both the 5′- and 3′-complexes greatly enhanced the duplex stability.
    Nucleic Acids Symposium Series 09/2003; DOI:10.1093/nass/3.1.135
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    ABSTRACT: Oligonucleotides containing photocleavable protecting groups at thymine bases were synthesized to induce the duplex formation by photo-irradiation. 6-Nitroveratryloxycarbonyl (NVOC) group was used for the photocleavable protecting group at N3 position of thymidine. An oligonucleotide containing NVOC groups (NVOC-ODN2:5'-dATG CAC CAT(NVOC) TCT(NVOC)GTC TGT-3') was synthesized by phosphoramidite method. The NVOC groups were found to be removable by UV irradiation at wavelength of 365 nm for 5 h. UV-melting temperature (Tm value) analysis indicated that the duplex of NVOC-ODN2 with the complementary RNA was significantly unstable compared with the unmodified DNA/RNA duplex (delta Tm=-13 degrees C). After UV irradiation at 365 nm, the Tm value of the mixture increased to the almost same as that of the unmodified duplex. These results suggest that the RNA binding ability of the NVOC-ODN2 can be induced by photocleavage of the NVOC groups.
    Nucleic Acids Symposium Series 09/2003; 3(1):61-62. DOI:10.1093/nass/3.1.61
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    ABSTRACT: Experimental strategies involving in vitro selection, designed to test the validity of the "RNA World Hypothesis", have demonstrated a significantly broader catalytic range for RNA (and, nucleic acids in general) than found in naturally occurring ribozymes. We wished to explore whether photochemical reactions could be catalyzed by nucleic acid enzymes. In vitro selection experiments were carried out to obtain "photolyase" deoxyribozymes, capable of photoreversing thymine cyclobutane dimers in the presence of a cofactor, serotonin. During in vitro selection from a thymine-dimer containing random DNA library, irradiated with light >300 nm, two pools of catalytic nucleic molecules emerged--one that required serotonin for activity, and another pool that, surprisingly, did not. Characterization of the serotonin-independent clones indicated the optimal wavelength for its repair activity (approximately 1,400-fold) to be approximately 300 nm, notably red-shifted from the absorption maximum of the DNA itself. The folded enzyme may contain a G-quadruplex (whose spectra have red-shifted tails relative to duplex absorbance), and our hypothesis has the folded enzyme as an antenna for the efficient channelling of light or electrons to the thymine dimer, much in the manner of protein photolyases.
    Nucleic Acids Symposium Series 09/2003; DOI:10.1093/nass/3.1.217
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    ABSTRACT: A novel bridged nucleic acid, 3'-amino-2'-deoxy-3',4'-BNA, having an N3'-->P5' phosphoramidate linkage and an S-type conformation, was successfully synthesized. It showed selective hybridization ability toward ssDNA complements, and high enzymatic stability against snake venom phosphodiesterase.
    Nucleic Acids Symposium Series 09/2003; DOI:10.1093/nass/3.1.87
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    ABSTRACT: The data set of the crystal structure of a self-complementary RNA duplex r(ggcggucgcu)2 with terminal and tandem G·U wobble base-pairs has been collected to 2.3 Å resolution. Crystals belong to the tetragonal space group P 4 1 2 1 2 or P 4 3 2 1 2; a = b = 50.0 Å, c = 102.7 Å, and α = β = γ = 90°, with two duplexes in the asymmetric unit. The structural analysis using the MAD method is currently in progress.
    Nucleic Acids Symposium Series 09/2003; DOI:10.1093/nass/3.1.225
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    ABSTRACT: Isolation of the designated genome region of Bacillus subtilis was investigated using a B. subtilis recombinational transfer (BReT) system. Two DNA sequences flanking the precise genome region are cloned in the BReT vector. The BReT plasmid recovered the predicted genome sequence as large as 100 kb with high fidelity. The result indicates that the BReT system originally developed to recover the non-cognate segments cloned in the B. subtilis genome vector can be applied to the cognate sequence.
    Nucleic Acids Symposium Series 02/2003; DOI:10.1093/nass/3.1.295
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    ABSTRACT: Development of peptide/protein synthesis is very important for investigating the functions of peptides and proteins. The advantages of cell-free synthesis, which has been extensively developed, include the ability to synthesize toxic proteins, aggregated proteins and proteins containing unnatural amino acids. However, this promising approach does not have a high reaction yield. In this study, we examine whether the rolling synchronization system, which produces long RNAs with a repeated sequence encoded by very small circular ssDNAs without the promoter sequence for RNA polymerase, can be used for cell-free peptide synthesis to improve the reaction yield. As a result, we have found that rolling synchronization is useful for large-scale cell-free peptide/protein synthesis.
    Nucleic Acids Symposium Series 02/2003; DOI:10.1093/nass/3.1.311
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    ABSTRACT: The ODNs containing (MD)A, which effectively mediate hole transport, were enzymatically ligated, and photo-induced hole transport reaction proceeded efficiently through a ligated long duplex. The ligated duplex showed high hole transport efficiency.
    Nucleic Acids Symposium Series 02/2003; DOI:10.1093/nass/3.1.39