Rapid and efficient hybridization-triggered crosslinking within a DNA duplex by an oligodeoxyribonucleotide bearing a conjugated cyclopropapyrroloindole.


:The antitumor antibiotic CC-1065 binds in the minor groove of double-stranded DNA, and the cyclopropapyrroloindole (CPI) subunit of the drug alkylates adjacent adenines at their N-3 position. We have attached racemic CPI to oligodeoxyribonucleotides (ODNs) via a terminal phosphorothioate at either the 3'- or 5'-end of the ODNs. These conjugates were remarkably stable in aqueous solution at neutral pH even in the presence of strong nucleophiles. When a 3'-CPI-ODN conjugate was hybridized to a complementary DNA strand at 37 degrees C, the CPI moiety alkylated nearby adenine bases of the complement efficiently and rapidly, with a half-life of a few minutes. The 4'-CPR- ODN conjugate showed very little reactivity within the duplex. CPI-ODN conjugates should be highly effective sequence-specific inhibitors of single-stranded viral DNA replication or gene selective inhibitors of transcription initiation.


Nucleic Acids Res


Nucleic acids research


Lukhtanov EA,Podyminogin MA,Kutyavin IV,Meyer RB,Gamper HB




Has Abstract


1996-02-15 00:00:00














  • Distinct roles of XRCC4 and Ku80 in non-homologous end-joining of endonuclease- and ionizing radiation-induced DNA double-strand breaks.

    abstract::Non-homologous end-joining (NHEJ) of DNA double-strand breaks (DSBs) is mediated by two protein complexes comprising Ku80/Ku70/DNA-PKcs/Artemis and XRCC4/LigaseIV/XLF. Loss of Ku or XRCC4/LigaseIV function compromises the rejoining of radiation-induced DSBs and leads to defective V(D)J recombination. In this study, we...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Schulte-Uentrop L,El-Awady RA,Schliecker L,Willers H,Dahm-Daphi J

    更新日期:2008-05-01 00:00:00

  • Allosteric DNAzyme-based DNA logic circuit: operations and dynamic analysis.

    abstract::Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zheng X,Yang J,Zhou C,Zhang C,Zhang Q,Wei X

    更新日期:2019-02-20 00:00:00

  • Photomodulating RNA cleavage using photolabile circular antisense oligodeoxynucleotides.

    abstract::Caged antisense oligodeoxynucleotides (asODNs) are synthesized by linking two ends of linear oligodeoxynucleotides using a photocleavable linker. Two of them (H30 and H40) have hairpin-like structures which show a large difference in thermal stability (Delta T(m) = 17.5 degrees C and 11.6 degrees C) comparing to uncag...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Tang X,Su M,Yu L,Lv C,Wang J,Li Z

    更新日期:2010-06-01 00:00:00

  • Ordered processing of Escherichia coli 23S rRNA in vitro.

    abstract::In an RNase III-deficient strain of E. coli 23S pre-rRNA accumulates unprocessed in 50S ribosomes and in polysomes. These ribosomes provide a substrate for the analysis of rRNA maturation in vitro. S1 nuclease protection analysis of the products obtained in in vitro processing reactions demonstrates that 23S rRNA proc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sirdeshmukh R,Schlessinger D

    更新日期:1985-07-25 00:00:00

  • Polynucleotides. XL. Synthesis and properties of poly 2'-azido-2'-deoxyadenylic acid.

    abstract::Poly 2'-azido-2'-deoxyadenylic acid (Poly Az) was synthesized from 2'-azido-2'-deoxyadenosine diphosphate by polynucleotide phosphorylase. Poly (Az) has U.V. absorption properties similar to poly (A) and hypochromicity of 40% at 0.1 M Na+ and neutrality. CD curve also resembled to that of poly (A), but has smaller ell...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ikehara M,Fukui T,Kakiuchi N

    更新日期:1976-08-01 00:00:00

  • Improved specificity of gene silencing by siRNAs containing unlocked nucleobase analogs.

    abstract::siRNAs confer sequence specific and robust silencing of mRNA. By virtue of these properties, siRNAs have become therapeutic candidates for disease intervention. However, their use as therapeutic agents can be hampered by unintended off-target effects by either or both strands of the siRNA duplex. We report here that u...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Vaish N,Chen F,Seth S,Fosnaugh K,Liu Y,Adami R,Brown T,Chen Y,Harvie P,Johns R,Severson G,Granger B,Charmley P,Houston M,Templin MV,Polisky B

    更新日期:2011-03-01 00:00:00

  • Isolation and characterization of plasmids carrying a partially defective Escherichia coli replication origin.

    abstract::The replication origin (oriC) of the Escherichia coli chromosome has been cloned and the region essential for chromosomal replication has been delimited to 245 base pairs. In previous studies the ability of recombinants between oriC and ColE1-type vectors, to transform E. coli polA- strains was used to determine which...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Stuitje AR,Meijer M

    更新日期:1983-11-25 00:00:00

  • mRNA transfection of a novel TAL effector nuclease (TALEN) facilitates efficient knockout of HIV co-receptor CCR5.

    abstract::Homozygosity for a natural deletion variant of the HIV-coreceptor molecule CCR5, CCR5Δ32, confers resistance toward HIV infection. Allogeneic stem cell transplantation from a CCR5Δ32-homozygous donor has resulted in the first cure from HIV ('Berlin patient'). Based thereon, genetic disruption of CCR5 using designer nu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mock U,Machowicz R,Hauber I,Horn S,Abramowski P,Berdien B,Hauber J,Fehse B

    更新日期:2015-06-23 00:00:00

  • Transcription Regulatory Regions Database (TRRD):its status in 1999.

    abstract::The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes, the regulatory elements they contain, i.e., transcription factor binding sites, promoters, enhancers, silencers, etc., and expression patterns of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kolchanov NA,Ananko EA,Podkolodnaya OA,Ignatieva EV,Stepanenko IL,Kel-Margoulis OV,Kel AE,Merkulova TI,Goryachkovskaya TN,Busygina TV,Kolpakov FA,Podkolodny NL,Naumochkin AN,Romashchenko AG

    更新日期:1999-01-01 00:00:00

  • Protection of (dA.dT) cluster regions in the DNAase I cleavage of DNA by specific interaction with netropsin.

    abstract::The specific DNA binding ligand netropsin selectively blocks dA-dT base pairs in clusters containing two or more consecutive thymine residues at the dNAase I cleavage sites of DNA. Using CD and UV absorption measurements it is shown, that at various ratios of netropsin to nucleotide concentrations and even at satuatio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zimmer C,Luck G,Nüske R

    更新日期:1980-07-11 00:00:00

  • Unexpected behavior of H2Kb mutant DNAs in denaturing gradient gel electrophoresis.

    abstract::Denaturing gradient gel electrophoresis (DGGE) is based upon the different melting behaviors of DNA molecules in a chemical denaturant gradient according to their sequences. This technique has recently become a widespread tool to detect mutations. The introduction of a GC-clamp enables the detection of most single bas...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Weber CK,Shaffer DJ,Sidman CL

    更新日期:1991-06-25 00:00:00

  • Wide-ranging and unexpected consequences of altered Pol II catalytic activity in vivo.

    abstract::Here we employ a set of RNA Polymerase II (Pol II) activity mutants to determine the consequences of increased or decreased Pol II catalysis on gene expression in Saccharomyces cerevisiae. We find that alteration of Pol II catalytic rate, either fast or slow, leads to decreased Pol II occupancy and apparent reduction ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Malik I,Qiu C,Snavely T,Kaplan CD

    更新日期:2017-05-05 00:00:00

  • NetVenn: an integrated network analysis web platform for gene lists.

    abstract::Many lists containing biological identifiers, such as gene lists, have been generated in various genomics projects. Identifying the overlap among gene lists can enable us to understand the similarities and differences between the data sets. Here, we present an interactome network-based web application platform named N...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wang Y,Thilmony R,Gu YQ

    更新日期:2014-07-01 00:00:00

  • Two zinc finger proteins from Xenopus laevis bind the same region of 5S RNA but with different nuclease protection patterns.

    abstract::Immature oocytes from Xenopus laevis contain a 42S ribonucleoprotein particle (RNP) containing 5S RNA, tRNA, a 43 kDa protein, and a 48 kDa protein. A particle containing 5S RNA and the 43 kDa protein (p43-5S) liberated from the 42S particle upon brief treatment with urea can be purified by anion exchange chromatograp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sands MS,Bogenhagen DF

    更新日期:1991-04-25 00:00:00

  • Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions.

    abstract::Conserved segments in DNA or protein sequences are strong candidates for functional elements and thus appropriate methods for computing them need to be developed and compared. We describe five methods and computer programs for finding highly conserved blocks within previously computed multiple alignments, primarily fo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Stojanovic N,Florea L,Riemer C,Gumucio D,Slightom J,Goodman M,Miller W,Hardison R

    更新日期:1999-10-01 00:00:00

  • The FSSP database: fold classification based on structure-structure alignment of proteins.

    abstract::The FSSP database presents a continuously updated classification of 3-D protein folds based on an all-against-all comparison of structures currently in the Protein Data Bank (PDB) [Bernstein et al. (1977) J. Mol. Biol., 112, 535- 542]. The database currently contains an extended structural family for each of 600 repre...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Holm L,Sander C

    更新日期:1996-01-01 00:00:00

  • A G-tract element in apoptotic agents-induced alternative splicing.

    abstract::Alternative splicing of a single pre-mRNA transcript can produce protein isoforms that promote either cell growth or death. Here we show that Ro-31-8220 (Ro), an apoptotic agent that inhibits protein kinase C and activates the c-Jun N terminal kinase, decreased the proportion of the cell growth-promoting Bcl-xL splice...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hai Y,Cao W,Liu G,Hong SP,Elela SA,Klinck R,Chu J,Xie J

    更新日期:2008-06-01 00:00:00

  • Nuclear dynamics of topoisomerase IIβ reflects its catalytic activity that is regulated by binding of RNA to the C-terminal domain.

    abstract::DNA topoisomerase II (topo II) changes DNA topology by cleavage/re-ligation cycle(s) and thus contributes to various nuclear DNA transactions. It is largely unknown how the enzyme is controlled in a nuclear context. Several studies have suggested that its C-terminal domain (CTD), which is dispensable for basal relaxat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Onoda A,Hosoya O,Sano K,Kiyama K,Kimura H,Kawano S,Furuta R,Miyaji M,Tsutsui K,Tsutsui KM

    更新日期:2014-08-01 00:00:00

  • Primary organization of nucleosomal core particles is invariable in repressed and active nuclei from animal, plant and yeast cells.

    abstract::A refined map for the linear arrangement of histones along DNA in nucleosomal core particles has been determined by DNA-protein crosslinking. On one strand of 145-bp core DNA, histones are aligned in the following order: (5') H2B25,35-H455,65-H375,85,95/H488-H2B105,11 5-H2A118-H3135,145/H2A145 (3') (the subscripts giv...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bavykin SG,Usachenko SI,Lishanskaya AI,Shick VV,Belyavsky AV,Undritsov IM,Strokov AA,Zalenskaya IA,Mirzabekov AD

    更新日期:1985-05-24 00:00:00

  • Oncogene activation of HIV-LTR-driven expression via the NF-kappa B binding sites.

    abstract::The Raf-1 proto-oncogene product is a highly regulated serine/threonine kinase that functions in signal transduction downstream from growth factor receptors and upstream from nuclear proto-oncogene products. Using a transient cotransfection assay we have found that activated Raf-1 activates expression from the HIV-LTR...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bruder JT,Heidecker G,Tan TH,Weske JC,Derse D,Rapp UR

    更新日期:1993-11-11 00:00:00

  • Transcription activation by the siderophore sensor Btr is mediated by ligand-dependent stimulation of promoter clearance.

    abstract::Bacterial transcription factors often function as DNA-binding proteins that selectively activate or repress promoters, although the biochemical mechanisms vary. In most well-understood examples, activators function by either increasing the affinity of RNA polymerase (RNAP) for the target promoter, or by increasing the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gaballa A,MacLellan S,Helmann JD

    更新日期:2012-04-01 00:00:00

  • Identification of residues required for stalled-ribosome rescue in the codon-independent release factor YaeJ.

    abstract::The YaeJ protein is a codon-independent release factor with peptidyl-tRNA hydrolysis (PTH) activity, and functions as a stalled-ribosome rescue factor in Escherichia coli. To identify residues required for YaeJ function, we performed mutational analysis for in vitro PTH activity towards rescue of ribosomes stalled on ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kogure H,Handa Y,Nagata M,Kanai N,Güntert P,Kubota K,Nameki N

    更新日期:2014-03-01 00:00:00

  • ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis.

    abstract::Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction data...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Obayashi T,Kinoshita K,Nakai K,Shibaoka M,Hayashi S,Saeki M,Shibata D,Saito K,Ohta H

    更新日期:2007-01-01 00:00:00

  • See me, feel me: methods to concurrently visualize and manipulate single DNA molecules and associated proteins.

    abstract::Direct visualization of DNA and proteins allows researchers to investigate DNA-protein interactions with great detail. Much progress has been made in this area as a result of increasingly sensitive single-molecule fluorescence techniques. At the same time, methods that control the conformation of DNA molecules have be...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审


    authors: van Mameren J,Peterman EJ,Wuite GJ

    更新日期:2008-08-01 00:00:00

  • Masking repeats while clustering ESTs.

    abstract::A problem in EST clustering is the presence of repeat sequences. To avoid false matches, repeats have to be masked. This can be a time-consuming process, and it depends on available repeat libraries. We present a fast and effective method that aims to eliminate the problems repeats cause in the process of clustering. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Schneeberger K,Malde K,Coward E,Jonassen I

    更新日期:2005-04-14 00:00:00

  • Identification of pseudogenes in the Drosophila melanogaster genome.

    abstract::Pseudogenes are copies of genes that cannot produce a protein. They can be detected from disruptions to their apparent coding sequence, caused by frameshifts and premature stop codons. They are classed as either processed pseudogenes (made by reverse transcription from an mRNA) or duplicated pseudogenes, arising from ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Harrison PM,Milburn D,Zhang Z,Bertone P,Gerstein M

    更新日期:2003-02-01 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

  • Structural and mechanistic insights into Helicobacter pylori NikR activation.

    abstract::NikR is a transcriptional metalloregulator central in the mandatory response to acidity of Helicobacter pylori that controls the expression of numerous genes by binding to specific promoter regions. NikR/DNA interactions were proposed to rely on protein activation by Ni(II) binding to high-affinity (HA) and possibly s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bahlawane C,Dian C,Muller C,Round A,Fauquant C,Schauer K,de Reuse H,Terradot L,Michaud-Soret I

    更新日期:2010-05-01 00:00:00

  • An adaptation of the LMS method to determine expression variations in profiling data.

    abstract::One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expressio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chuchana P,Marchand D,Nugoli M,Rodriguez C,Molinari N,Garcia-Sanz JA

    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