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














  • The Pfam protein families database.

    abstract::Pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (, the USA ( and Sweden ( Here, we report on changes that ha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Punta M,Coggill PC,Eberhardt RY,Mistry J,Tate J,Boursnell C,Pang N,Forslund K,Ceric G,Clements J,Heger A,Holm L,Sonnhammer EL,Eddy SR,Bateman A,Finn RD

    更新日期:2012-01-01 00:00:00

  • Ribosomal protein eL24, involved in two intersubunit bridges, stimulates translation initiation and elongation.

    abstract::Interactions between subunits in the Saccharomyces cerevisiae ribosome are mediated by universal and eukaryote-specific intersubunit bridges. Universal bridges are positioned close to the ribosomal functional centers, while eukaryote-specific bridges are mainly located on the periphery of the ribosome. Two bridges, eB...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kisly I,Remme J,Tamm T

    更新日期:2019-01-10 00:00:00

  • A highly specific sodium aptamer probed by 2-aminopurine for robust Na+ sensing.

    abstract::Sodium is one of the most abundant metals in the environment and in biology, playing critical ecological and physiological roles. Na+ is also the most common buffer salt for nucleic acids research, while its specific interaction with DNA has yet to be fully studied. Herein, we probe a highly selective and robust Na+ a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhou W,Ding J,Liu J

    更新日期:2016-12-01 00:00:00

  • Altered expression and editing of miRNA-100 regulates iTreg differentiation.

    abstract::RNA editing of miRNAs, especially in the seed region, adds another layer to miRNA mediated gene regulation which can modify its targets, altering cellular signaling involved in important processes such as differentiation. In this study, we have explored the role of miRNA editing in CD4(+) T cell differentiation. CD4(+...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Negi V,Paul D,Das S,Bajpai P,Singh S,Mukhopadhyay A,Agrawal A,Ghosh B

    更新日期:2015-09-18 00:00:00

  • Broad range of missense error frequencies in cellular proteins.

    abstract::Assessment of the fidelity of gene expression is crucial to understand cell homeostasis. Here we present a highly sensitive method for the systematic Quantification of Rare Amino acid Substitutions (QRAS) using absolute quantification by targeted mass spectrometry after chromatographic enrichment of peptides with miss...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Garofalo R,Wohlgemuth I,Pearson M,Lenz C,Urlaub H,Rodnina MV

    更新日期:2019-04-08 00:00:00

  • Structural analysis of an RNA molecule involved in replication control of plasmid R1.

    abstract::The replication control circuit of the FII plasmids R1, R100 and R6-5 involves a small untranslated RNA molecule of about 93 nucleotides. This RNA, designated CopA RNA in plasmid R1, acts in vivo as a post-transcriptional inhibitor of the expression of the RepA protein whose synthesis is required for each round of pla...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gerhart E,Wagner H,Nordström K

    更新日期:1986-03-25 00:00:00

  • Apurinic endonucleases from Saccharomyces cerevisiae.

    abstract::Three endonuclease activities have been partially purified from Saccharomyces cerevisiae on the basis of their activity against x-irradiated closed-circular supercoiled bacteriophage PM2 DNA. These endonucleases also nick apurinic DNA and two out of the three activities incise DNA UV-irradiated with high doses. The en...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Armel PR,Wallace SS

    更新日期:1978-09-01 00:00:00

  • Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities.

    abstract::An intronic hexanucleotide UGCAUG has been shown to play a critical role in the regulation of tissue-specific alternative splicing of pre-mRNAs in a wide range of tissues. Vertebrate Fox-1 has been shown to bind to this element, in a highly sequence-specific manner, through its RNA recognition motif (RRM). In mammals,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Nakahata S,Kawamoto S

    更新日期:2005-04-11 00:00:00

  • Regulation of polysome assembly on the endoplasmic reticulum by a coiled-coil protein, p180.

    abstract::A coiled-coil microtubule-bundling protein, p180, was originally identified as one of the ribosome receptor candidates on the rough endoplasmic reticulum (ER) and is highly expressed in secretory tissues. Recently, we reported that p180 plays crucial roles in upregulating collagen biosynthesis, mainly by facilitating ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ueno T,Kaneko K,Sata T,Hattori S,Ogawa-Goto K

    更新日期:2012-04-01 00:00:00

  • c-Myc/Max heterodimers bind cooperatively to the E-box sequences located in the first intron of the rat ornithine decarboxylase (ODC) gene.

    abstract::The oncoprotein c-Myc plays an important role in cell proliferation, transformation, inhibition of differentiation and apoptosis. These functions most likely result from the transcription factor activity of c-Myc. As a heterodimer with Max, the c-Myc protein binds to the E-box sequence (CACGTG), which is also recogniz...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Walhout AJ,Gubbels JM,Bernards R,van der Vliet PC,Timmers HT

    更新日期:1997-04-15 00:00:00

  • Unique organization of the human BCR gene promoter.

    abstract::The promoter of the human BCR gene, regulating the transcription of the chimeric BCR/ABL mRNA in leukemia, has been isolated and characterized. A region of 1.1 kb immediately 5' to the transcription start site was analyzed in detail by sequencing, DNase 1 footprinting, gel retardation and functional studies. These exp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhu QS,Heisterkamp N,Groffen J

    更新日期:1990-12-11 00:00:00

  • 5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy.

    abstract::(19)F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondar...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Puffer B,Kreutz C,Rieder U,Ebert MO,Konrat R,Micura R

    更新日期:2009-12-01 00:00:00

  • Evolutionary changes in the Leishmania eIF4F complex involve variations in the eIF4E-eIF4G interactions.

    abstract::Translation initiation in eukaryotes is mediated by assembly of the eIF4F complex over the m(7)GTP cap structure at the 5'-end of mRNAs. This requires an interaction between eIF4E and eIF4G, two eIF4F subunits. The Leishmania orthologs of eIF4E are structurally diverged from their higher eukaryote counterparts, since ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Yoffe Y,Léger M,Zinoviev A,Zuberek J,Darzynkiewicz E,Wagner G,Shapira M

    更新日期:2009-06-01 00:00:00

  • The FurA regulon in Anabaena sp. PCC 7120: in silico prediction and experimental validation of novel target genes.

    abstract::In the filamentous cyanobacterium Anabaena sp. PCC 7120, the ferric uptake regulator FurA functions as a global transcriptional regulator. Despite several analyses have focused on elucidating the FurA-regulatory network, the number of target genes described for this essential transcription factor is limited to a handf...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: González A,Angarica VE,Sancho J,Fillat MF

    更新日期:2014-04-01 00:00:00

  • Nucleocapsid protein-mediated maturation of dimer initiation complex of full-length SL1 stemloop of HIV-1: sequence effects and mechanism of RNA refolding.

    abstract::Specific binding of HIV-1 viral protein NCp7 to a unique 35-base RNA stem-loop SL1 is critical for formation and packaging of the genomic RNA dimer found within HIV-1 virions. NCp7 binding stimulates refolding of SL1 from a metastable kissing dimer (KD) into thermodynamically stable linear dimer (LD). Using UV melting...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mujeeb A,Ulyanov NB,Georgantis S,Smirnov I,Chung J,Parslow TG,James TL

    更新日期:2007-01-01 00:00:00

  • A study of the interaction between ethidium bromide and rye chromatin: comparison with calf thymus chromatin.

    abstract::We studied the interaction of ethidium bromide with rye and calf thymus chromatin. Both types of chromatin have the same dye accessibility, which is about 50% of that of DNA. From this result we conclude that the molecular structure of these two chromatins is similar. For rye, the extraction of H1 produces no change i...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: LaRue H,Pallotta D

    更新日期:1976-09-01 00:00:00

  • Direct interaction between Rsc6 and Rsc8/Swh3,two proteins that are conserved in SWI/SNF-related complexes.

    abstract::The RSC complex of Saccharomyces cerevisiae is closely related to the SWI/SNF complex. Both complexes are involved in remodeling chromatin structure and they share conserved components. The RSC proteins Sth1, Rsc8/Swh3, Sfh1 and Rsc6 are homologs of the SWI/SNF proteins Swi2/Snf2, Swi3, Snf5 and Swp73 respectively. To...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Treich I,Ho L,Carlson M

    更新日期:1998-08-15 00:00:00

  • Cyclic mismatch binding ligand CMBL4 binds to the 5'-T-3'/5'-GG-3' site by inducing the flipping out of thymine base.

    abstract::A newly designed cyclic bis-naphthyridine carbamate dimer CMBL4: with a limited conformational flexibility was synthesized and characterized. Absorption spectra revealed that two naphthyridines in CMBL4: were stacked on each other in aqueous solutions. The most efficient binding of CMBL4: to DNA was observed for the s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mukherjee S,Dohno C,Asano K,Nakatani K

    更新日期:2016-09-06 00:00:00

  • Nucleotide sequence of the 3'-terminal tRNA-like structure in barley stripe mosaic virus genome.

    abstract::This paper describes the sequence of 257 nucleotides from the 3' end of RNA 2 of barley stripe mosaic virus ( BSMV , strain Argentina Mild) including an internal oligo (A) tract localized at a distance of 236 nucleotides from the 3' end, and the 3' terminal tRNA-like structure accepting tyrosine. This sequence is show...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kozlov YuV,Rupasov VV,Adyshev DM,Belgelarskaya SN,Agranovsky AA,Mankin AS,Morozov SYu,Dolja VV,Atabekov JG

    更新日期:1984-05-11 00:00:00

  • Different dynamics in nuclear entry of subunits of the repair/transcription factor TFIIH.

    abstract::We report here the different ways in which four subunits of the basal transcription/repair factor TFIIH (XPB, XPD, p62 and p44) and the damage recognition XPC repair protein can enter the nucleus. We examined their nuclear localization by transiently expressing the gene products tagged with the enhanced green fluoresc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Santagati F,Botta E,Stefanini M,Pedrini AM

    更新日期:2001-04-01 00:00:00

  • The cellular mismatch repair system is able to repair mismatches within MLV retroviral double-stranded DNA at a low frequency.

    abstract::Eukaryotic cells possess several distinct mismatch repair pathways. A mismatch can be introduced in retroviral double-stranded DNA by a pre-existing mutation within the primer binding site (PBS) of the viral RNA genome. In order to evaluate mismatch repair of retroviral double-stranded DNA, Moloney leukemia virus (MLV...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Tang LY,Zhang J

    更新日期:2000-06-15 00:00:00

  • Aicardi-Goutières syndrome protein TREX1 suppresses L1 and maintains genome integrity through exonuclease-independent ORF1p depletion.

    abstract::Maintaining genome integrity is important for cells and damaged DNA triggers autoimmunity. Previous studies have reported that Three-prime repair exonuclease 1(TREX1), an endogenous DNA exonuclease, prevents immune activation by depleting damaged DNA, thus preventing the development of certain autoimmune diseases. Con...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Li P,Du J,Goodier JL,Hou J,Kang J,Kazazian HH Jr,Zhao K,Yu XF

    更新日期:2017-05-05 00:00:00

  • Modulating role of RNA structure in alternative splicing of a critical exon in the spinal muscular atrophy genes.

    abstract::Humans have two nearly identical copies of the survival motor neuron (SMN ) gene, SMN1 and SMN2. Homozygous loss of SMN1 causes spinal muscular atrophy (SMA). SMN2 is unable to prevent the disease due to skipping of exon 7. Using a systematic approach of in vivo selection, we have previously demonstrated that a weak 5...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Singh NN,Singh RN,Androphy EJ

    更新日期:2007-01-01 00:00:00

  • Two protein-protein interaction sites on the spliceosome-associated human cyclophilin CypH.

    abstract::Cyclophilins are a family of proteins that share a common, highly conserved sequence motif. Cyclophilins bind transiently to other proteins and facilitate their folding. One member of the family, hCypH, is part of the human spliceosomal [U4/U6.U5] tri-snRNP complex; it associates specifically and stably with the U4/U6...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ingelfinger D,Göthel SF,Marahiel MA,Reidt U,Ficner R,Lührmann R,Achsel T

    更新日期:2003-08-15 00:00:00

  • Regulation of the herpes simplex virus type 1 late (gamma 2) glycoprotein C gene: sequences between base pairs -34 to +29 control transient expression and responsiveness to transactivation by the products of the immediate early (alpha) 4 and 0 genes.

    abstract::The glycoprotein C (gC) gene of herpes simplex virus type 1 is a true late gene, in that its expression occurs late in infection with a strict requirement for viral DNA replication. Recently, we reported on gC expression during infection with mutant viruses carrying deletions in the gC gene promoter. Analysis of RNA e...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shapira M,Homa FL,Glorioso JC,Levine M

    更新日期:1987-04-10 00:00:00

  • The GAA*TTC triplet repeat expanded in Friedreich's ataxia impedes transcription elongation by T7 RNA polymerase in a length and supercoil dependent manner.

    abstract::Large expansions of the trinucleotide repeat GAA*TTC within the first intron of the X25 (frataxin) gene cause Friedreich's ataxia, the most common inherited ataxia. Expansion leads to reduced levels of frataxin mRNA in affected individuals. Here we show that GAA*TTC tracts, in the absence of any other frataxin gene se...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Grabczyk E,Usdin K

    更新日期:2000-07-15 00:00:00

  • The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b.

    abstract::ymf39 is a conserved hypothetical protein-coding gene found in mitochondrial genomes of land plants and certain protists. We speculated earlier, based on a weak sequence similarity between Ymf39 from a green alga and the atpF gene product from Bradyrhizobium, that ymf39 might code for subunit b of mitochondrial F(0)F(...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Burger G,Lang BF,Braun HP,Marx S

    更新日期:2003-05-01 00:00:00

  • Incorporation of 2'-amido-nucleosides in oligodeoxynucleotides and oligoribonucleotides as a model for 2'-linked conjugates.

    abstract::The functionalisation of oligodeoxynucleotides and oligoribonucleotides by incorporation of 2'-amido-2'-deoxyribonucleosides, possibly containing a reporter group via the 2'-amido bond, was examined. Therefore 2'-acetamido-ribonucleosides containing a small methyl group at the 2'-amido bond were synthesized as model c...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hendrix C,Devreese B,Rozenski J,van Aerschot A,De Bruyn A,Van Beeumen J,Herdewijn P

    更新日期:1995-01-11 00:00:00

  • Histone variant H3.3 provides the heterochromatic H3 lysine 9 tri-methylation mark at telomeres.

    abstract::In addition to being a hallmark at active genes, histone variant H3.3 is deposited by ATRX at repressive chromatin regions, including the telomeres. It is unclear how H3.3 promotes heterochromatin assembly. We show that H3.3 is targeted for K9 trimethylation to establish a heterochromatic state enriched in trimethylat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Udugama M,M Chang FT,Chan FL,Tang MC,Pickett HA,R McGhie JD,Mayne L,Collas P,Mann JR,Wong LH

    更新日期:2015-12-02 00:00:00

  • Structural and biochemical characterization of HP0315 from Helicobacter pylori as a VapD protein with an endoribonuclease activity.

    abstract::VapD-like virulence-associated proteins have been found in many organisms, but little is known about this protein family including the 3D structure of these proteins. Recently, a relationship between the Cas2 family of ribonucleases associated with the CRISPR system of microbial immunity and VapD was suggested. Here, ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kwon AR,Kim JH,Park SJ,Lee KY,Min YH,Im H,Lee I,Lee KY,Lee BJ

    更新日期:2012-05-01 00:00:00