Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.


:In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water-water interactions, (ii) ethylene glycol more effectively disrupted water-water interactions around Watson-Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson-Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions.


Nucleic Acids Res


Nucleic acids research


Nakano M,Tateishi-Karimata H,Tanaka S,Tama F,Miyashita O,Nakano S,Sugimoto N




Has Abstract


2015-12-02 00:00:00














  • Primer Design Assistant (PDA): A web-based primer design tool.

    abstract::Primer Design Assistant (PDA) is a web interface primer design service combined with thermodynamic theory to evaluate the fitness of primers. It runs in a Linux-Apache-MySQL-PHP structure on a PC equipped with dual CPU (Intel Pentium III 1.4 GHz) and 512 Mb of RAM. A succinct user interface of PDA is accomplished by b...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chen SH,Lin CY,Cho CS,Lo CZ,Hsiung CA

    更新日期:2003-07-01 00:00:00

  • Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.

    abstract::Ensembl Genomes ( is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project ( Together, the two resources provide a consistent set of programmatic and interacti...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kersey PJ,Allen JE,Allot A,Barba M,Boddu S,Bolt BJ,Carvalho-Silva D,Christensen M,Davis P,Grabmueller C,Kumar N,Liu Z,Maurel T,Moore B,McDowall MD,Maheswari U,Naamati G,Newman V,Ong CK,Paulini M,Pedro H,Perry E

    更新日期:2018-01-04 00:00:00

  • Complete nucleotide sequence of alfalfa mosaic virus RNA 4.

    abstract::Alfalfa mosaic virus RNA 4, the subgenomic messenger for viral coat protein, was partially digested with RNase T1 or RNase A and the sequence of a number of fragments was deduced by in vitro labeling with polynucleotide kinase and application of RNA sequencing techniques. From overlapping fragments, the complete prima...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Brederode FT,Koper-Zwarthoff EC,Bol JF

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  • Mammalian polyadenylation sites: implications for differential display.

    abstract::Differential display relies on a series of anchored primers to divide the total mRNA population into subsets of roughly equal size. However, this will only occur if the dinucleotide targeted by the anchor region of the anchored primers has a random frequency distribution [i.e. each of the 12 possible dinucleotides pre...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Frost MR,Guggenheim JA

    更新日期:1999-03-01 00:00:00

  • A minor class of 5S rRNA genes in Saccharomyces cerevisiae X2180-1B, one member of which lies adjacent to a Ty transposable element.

    abstract::In Saccharomyces cerevisiae the majority of the genes for 5S rRNA lie within a 9kb rDNA sequence that is present as 100-200 tandemly-repeated copies on Chromosome XII. Following our observations that about 10% of yeast 5S rRNA exists as minor variant sequences, we screened a collection of yeast DNA fragments cloned in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Piper PW,Lockheart A,Patel N

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  • SIC: A tool to detect short inverted segments in a biological sequence.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Robelin D,Richard H,Prum B

    更新日期:2003-07-01 00:00:00

  • ATP insertion opposite 8-oxo-deoxyguanosine by Pol4 mediates error-free tolerance in Schizosaccharomyces pombe.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sastre-Moreno G,Sánchez A,Esteban V,Blanco L

    更新日期:2014-09-01 00:00:00

  • Antisense inhibition of gene expression in cells by oligonucleotides incorporating locked nucleic acids: effect of mRNA target sequence and chimera design.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Braasch DA,Liu Y,Corey DR

    更新日期:2002-12-01 00:00:00

  • Search for differences in post-transcriptional modification patterns of mitochondrial DNA-encoded wild-type and mutant human tRNALys and tRNALeu(UUR).

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Helm M,Florentz C,Chomyn A,Attardi G

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  • Structure and evolution of a mouse tRNA gene cluster encoding tRNAAsp, tRNAGly and tRNAGlu and an unlinked, solitary gene encoding tRNAAsp.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Looney JE,Harding JD

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    pub_type: 杂志文章


    authors: Jeffreys AJ,Wilson V,Kelly R,Taylor BA,Bulfield G

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hardenbol P,Wang JC,Van Dyke MW

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Marangoni E,Foray N,O'Driscoll M,Douc-Rasy S,Bernier J,Bourhis J,Jeggo P

    更新日期:2000-12-01 00:00:00

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    abstract::Cationic aromatic tricyclic compounds including triphenylmethane dyes, phenazines, phenoxazines, acridines, phenothiazines, phenanthridinium compounds, anthracenes and xanthene dyes, which amplify cell killing in phleomycin-treated Escherichia coli B cells also modified phleomycin-induced breakdown of DNA to acid-solu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Grigg GW,Gero AM,Sasse WH,Sleigh MJ

    更新日期:1984-12-11 00:00:00

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    abstract::NMR data from different experiments often contain errors; thus, automated backbone resonance assignment is a very challenging issue. In this paper, we present a method called GANA that uses a genetic algorithm to automatically perform backbone resonance assignment with a high degree of precision and recall. Precision ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lin HN,Wu KP,Chang JM,Sung TY,Hsu WL

    更新日期:2005-08-10 00:00:00

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    abstract::Topoisomerases are ubiquitous proteins found in all three domains of life. They change the topology of DNA via transient breaks on either one or two of the DNA strands to allow passage of another single or double DNA strand through the break. Topoisomerases are classified into two types: type I enzymes cleave one DNA ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审


    authors: Baker NM,Rajan R,Mondragón A

    更新日期:2009-02-01 00:00:00

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    journal_title:Nucleic acids research

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    authors: Antal M,Mougin A,Kis M,Boros E,Steger G,Jakab G,Solymosy F,Branlant C

    更新日期:2000-08-01 00:00:00

  • Single molecule detection of PARP1 and PARP2 interaction with DNA strand breaks and their poly(ADP-ribosyl)ation using high-resolution AFM imaging.

    abstract::PARP1 and PARP2 are implicated in the synthesis of poly(ADP-ribose) (PAR) after detection of DNA damage. The specificity of PARP1 and PARP2 interaction with long DNA fragments containing single- and/or double-strand breaks (SSBs and DSBs) have been studied using atomic force microscopy (AFM) imaging in combination wit...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sukhanova MV,Abrakhi S,Joshi V,Pastre D,Kutuzov MM,Anarbaev RO,Curmi PA,Hamon L,Lavrik OI

    更新日期:2016-04-07 00:00:00

  • Structural basis for RNA-genome recognition during bacteriophage Qβ replication.

    abstract::Upon infection of Escherichia coli by bacteriophage Qβ, the virus-encoded β-subunit recruits host translation elongation factors EF-Tu and EF-Ts and ribosomal protein S1 to form the Qβ replicase holoenzyme complex, which is responsible for amplifying the Qβ (+)-RNA genome. Here, we use X-ray crystallography, NMR spect...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gytz H,Mohr D,Seweryn P,Yoshimura Y,Kutlubaeva Z,Dolman F,Chelchessa B,Chetverin AB,Mulder FA,Brodersen DE,Knudsen CR

    更新日期:2015-12-15 00:00:00

  • An atypical RNA pseudoknot stimulator and an upstream attenuation signal for -1 ribosomal frameshifting of SARS coronavirus.

    abstract::The -1 ribosomal frameshifting requires the existence of an in cis RNA slippery sequence and is promoted by a downstream stimulator RNA. An atypical RNA pseudoknot with an extra stem formed by complementary sequences within loop 2 of an H-type pseudoknot is characterized in the severe acute respiratory syndrome corona...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Su MC,Chang CT,Chu CH,Tsai CH,Chang KY

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  • Cap-independent translation initiation in Xenopus oocytes.

    abstract::Eukaryotic cellular mRNAs contain a cap at their 5'-ends, but some viral and cellular mRNAs bypass the cap-dependent mechanism of translation initiation in favor of internal entry of ribosomes at specific RNA sequences. Cap-dependent initiation requires intact initiation factor eIF4G (formerly eIF-4gamma, eIF-4Fgamma ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Keiper BD,Rhoads RE

    更新日期:1997-01-15 00:00:00

  • The thy pol-2 intein of Thermococcus hydrothermalis is an isoschizomer of PI-TliI and PI-TfuII endonucleases.

    abstract::THY Pol-2 intein, from Thermococcus hydrothermalis, belongs to the same allelic family as TLI Pol-2 (PI-TLII), Tfu Pol-2 (PI-TFUII) and TspTY Pol-3 mini-intein, all inserted at the pol-c site of archaeal DNA polymerase genes. This new intein was cloned, expressed in Escherichia coli and purified. The intein is a speci...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Saves I,Eleaume H,Dietrich J,Masson JM

    更新日期:2000-11-01 00:00:00

  • The integrase family of tyrosine recombinases: evolution of a conserved active site domain.

    abstract::The integrases are a diverse family of tyrosine recombinases which rearrange DNA duplexes by means of conservative site-specific recombination reactions. Members of this family, of which the well-studied lambda Int protein is the prototype, were previously found to share four strongly conserved residues, including an ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Esposito D,Scocca JJ

    更新日期:1997-09-15 00:00:00

  • Linkage of TNF genes to the HLA-B locus.

    abstract::Pulsed field gel electrophoresis was used to determine the location of the tumour necrosis factor (TNF) alpha and beta genes. They were shown to be linked to the HLA-B locus; analogous to their location in mouse, between the complement (class III) region and H-2D. However, the distance between the TNF genes and the cl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Inoko H,Trowsdale J

    更新日期:1987-11-11 00:00:00

  • Translatability of a plant-mRNA strongly influences its accumulation in transgenic plants.

    abstract::Current knowledge of parameters affecting RNA stability is very restricted in plants. Here we investigated factors which might contribute to the stability of a particular plant messenger RNA. To this end, insertion and deletion mutants were made in two different exons and an intron of the transcribed region of a well ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Vancanneyt G,Rosahl S,Willmitzer L

    更新日期:1990-05-25 00:00:00

  • PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes.

    abstract::The PRISM web server enables fast and accurate prediction of protein-protein interactions (PPIs). The prediction algorithm is knowledge-based. It combines structural similarity and accounts for evolutionary conservation in the template interfaces. The predicted models are stored in its repository. Given two protein st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Baspinar A,Cukuroglu E,Nussinov R,Keskin O,Gursoy A

    更新日期:2014-07-01 00:00:00

  • Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Yang W,Soares J,Greninger P,Edelman EJ,Lightfoot H,Forbes S,Bindal N,Beare D,Smith JA,Thompson IR,Ramaswamy S,Futreal PA,Haber DA,Stratton MR,Benes C,McDermott U,Garnett MJ

    更新日期:2013-01-01 00:00:00

  • PrankWeb: a web server for ligand binding site prediction and visualization.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jendele L,Krivak R,Skoda P,Novotny M,Hoksza D

    更新日期:2019-07-02 00:00:00

  • In situ imaging and isolation of proteins using dsDNA oligonucleotides.

    abstract::As proteomics initiatives mature, the need will arise for the multiple visualization of proteins and supramolecular complexes within their true context, in situ. Single-stranded DNA and RNA aptamers can be used for low resolution imaging of cellular receptors and cytoplasmic proteins by light microscopy (LM). These te...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dellaire G,Nisman R,Eskiw CH,Bazett-Jones DP

    更新日期:2004-11-23 00:00:00

  • Association of antisense oligonucleotides with lipoproteins prolongs the plasma half-life and modifies the tissue distribution.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: de Smidt PC,Le Doan T,de Falco S,van Berkel TJ

    更新日期:1991-09-11 00:00:00