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














  • Two-dimensional conformation-dependent electrophoresis (2D-CDE) to separate DNA fragments containing unmatched bulge from complex DNA samples.

    abstract::DNA fragments containing mispaired and modified bases, bulges, lesions and specific sequences have altered conformation. Methods for separating complex samples of DNA fragments based on conformation but independent of length have many applications, including (i) separation of mismatched or unmatched DNA fragments from...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gunnarsson GH,Thormar HG,Gudmundsson B,Akesson L,Jonsson JJ

    更新日期:2004-02-03 00:00:00

  • The conformation of adenovirus VAI-RNA in solution.

    abstract::The secondary structure of an adenovirus associated low molecular weight RNA (VAI-RNA) has been studied by partial digestion with T1-RNase and S1-endonuclease followed by T1-fingerprint analysis. The empirical secondary structure has been compared with two computer generated models based on minimal free energy of the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Monstein HJ,Philipson L

    更新日期:1981-09-11 00:00:00

  • Summarizing and correcting the GC content bias in high-throughput sequencing.

    abstract::GC content bias describes the dependence between fragment count (read coverage) and GC content found in Illumina sequencing data. This bias can dominate the signal of interest for analyses that focus on measuring fragment abundance within a genome, such as copy number estimation (DNA-seq). The bias is not consistent b...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Benjamini Y,Speed TP

    更新日期:2012-05-01 00:00:00

  • Modeling of DNA local parameters predicts encrypted architectural motifs in Xenopus laevis ribosomal gene promoter.

    abstract::We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Roux-Rouquie M,Marilley M

    更新日期:2000-09-15 00:00:00

  • CK2 kinase-mediated PHF8 phosphorylation controls TopBP1 stability to regulate DNA replication.

    abstract::ATR functions as a master regulator of the DNA-damage response. ATR activation requires the ATR activator, topoisomerase IIβ-binding protein 1 (TopBP1). However, the underlying mechanism of TopBP1 regulation and how its regulation affects DNA replication remain unknown. Here, we report a specific interaction between T...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Feng H,Lu J,Song X,Thongkum A,Zhang F,Lou L,Reizes O,Almasan A,Gong Z

    更新日期:2020-11-04 00:00:00

  • A diminutive and specific RNA binding site for L-tryptophan.

    abstract::Selection for amino acid affinity by elution of RNAs from tryptophan-Sepharose using free L-tryptophan evokes one sequence predominantly (K(D) = 12 microM), a symmetrical internal loop of 3 nt per side. Though we have also isolated larger sequences with affinity for tryptophan, successively squeezed selection in rando...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Majerfeld I,Yarus M

    更新日期:2005-09-25 00:00:00

  • Structure of recombinant rat UBF by electron image analysis and homology modelling.

    abstract::We have studied the structure of recombinant rat UBF (rrUBF), an RNA polymerase I transcription factor, by electron microscopy and image analysis of single particles contrasted with methylamine tungstate. Recombinant rat UBF appeared to be a flat, U-shaped protein with a central region of low density. In the dominant ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Neil KJ,Ridsdale RA,Rutherford B,Taylor L,Larson DE,Glibetic M,Rothblum LI,Harauz G

    更新日期:1996-04-15 00:00:00

  • Archaebacterial reverse gyrase cleavage-site specificity is similar to that of eubacterial DNA topoisomerases I.

    abstract::ATP-dependent type I topoisomerases from extremely thermophilic archaebacteria--reverse gyrases--drive positive supercoiling of DNA. We showed that reverse gyrase from Desulfurococcus amylolyticus breaks the DNA at specific sites and covalently binds to the 5' end. In 30 out of 31 sites located in pBR322 DNA fragments...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kovalsky OI,Kozyavkin SA,Slesarev AI

    更新日期:1990-05-11 00:00:00

  • Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL.

    abstract::The surface accessibility of macromolecules plays a key role in modulating molecular recognition events. RNA is a complex and dynamic molecule involved in many aspects of gene expression. However, there are few experimental methods available to measure the accessible surface of RNA. Here, we investigate the accessible...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Venditti V,Niccolai N,Butcher SE

    更新日期:2008-03-01 00:00:00

  • Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity.

    abstract::PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct arch...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Qiu C,Dutcher RC,Porter DF,Arava Y,Wickens M,Hall TMT

    更新日期:2019-09-19 00:00:00

  • Genome engineering of isogenic human ES cells to model autism disorders.

    abstract::Isogenic pluripotent stem cells are critical tools for studying human neurological diseases by allowing one to study the effects of a mutation in a fixed genetic background. Of particular interest are the spectrum of autism disorders, some of which are monogenic such as Timothy syndrome (TS); others are multigenic suc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Martinez RA,Stein JL,Krostag AR,Nelson AM,Marken JS,Menon V,May RC,Yao Z,Kaykas A,Geschwind DH,Grimley JS

    更新日期:2015-05-26 00:00:00

  • Invadolysin acts genetically via the SAGA complex to modulate chromosome structure.

    abstract::Identification of components essential to chromosome structure and behaviour remains a vibrant area of study. We have previously shown that invadolysin is essential in Drosophila, with roles in cell division and cell migration. Mitotic chromosomes are hypercondensed in length, but display an aberrant fuzzy appearance....

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rao SG,Janiszewski MM,Duca E,Nelson B,Abhinav K,Panagakou I,Vass S,Heck MM

    更新日期:2015-04-20 00:00:00

  • Human testis expresses a specific poly(A)-binding protein.

    abstract::In testis mRNA stability and translation initiation are extensively under the control of poly(A)-binding proteins (PABP). Here we have cloned a new human testis-specific PABP (PABP3) of 631 amino acids (70.1 kDa) with 92.5% identical residues to the ubiquitous PABP1. A northern blot of multiple human tissues hybridise...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Féral C,Guellaën G,Pawlak A

    更新日期:2001-05-01 00:00:00

  • The metabolic pathway collection: an update.

    abstract::The Metabolic Pathway Collection from EMP is an extraction of data from the larger Enzymes and Metabolic Pathways database (EMP). This extraction has been made publicly available in the hope that others will find it useful for a variety of purposes. The original release in October 1995 contained 1814 distinct pathways...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Selkov E,Galimova M,Goryanin I,Gretchkin Y,Ivanova N,Komarov Y,Maltsev N,Mikhailova N,Nenashev V,Overbeek R,Panyushkina E,Pronevitch L,Selkov E Jr

    更新日期:1997-01-01 00:00:00

  • The Signal Recognition Particle Database (SRPDB).

    abstract::The signal recognition particle database (SRPDB) is located at the University of Texas Health Science Center at Tyler and includes tabulations of SRP RNA, SRP protein and SRP receptor sequences. The sequences are annotated with links to the primary databases. They are ordered alphabetically or phylogenetically and are...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Samuelsson T,Zwieb C

    更新日期:1999-01-01 00:00:00

  • Sense and antisense transcription are associated with distinct chromatin architectures across genes.

    abstract::Genes from yeast to mammals are frequently subject to non-coding transcription of their antisense strand; however the genome-wide role for antisense transcription remains elusive. As transcription influences chromatin structure, we took a genome-wide approach to assess which chromatin features are associated with nasc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Murray SC,Haenni S,Howe FS,Fischl H,Chocian K,Nair A,Mellor J

    更新日期:2015-09-18 00:00:00

  • Quadruplex formation is necessary for stable PNA invasion into duplex DNA of BCL2 promoter region.

    abstract::Guanine-rich sequences are highly abundant in the human genome, especially in regulatory regions. Because guanine-rich sequences have the unique ability to form G-quadruplexes, these structures may play a role in the regulation of gene transcription. In previous studies, we demonstrated that formation of G-quadruplexe...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Onyshchenko MI,Gaynutdinov TI,Englund EA,Appella DH,Neumann RD,Panyutin IG

    更新日期:2011-09-01 00:00:00

  • Combined SSCP/duplex analysis by capillary electrophoresis for more efficient mutation detection.

    abstract::SSCP and heteroduplex analysis (HA) continue to be the most popular methods of mutation detection due to their simplicity, high sensitivity and low cost. The advantages of these methods are most clearly visible when large genes, such as BRCA1 and BRCA2, are scanned for scattered unknown mutations and/or when a large n...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kozlowski P,Krzyzosiak WJ

    更新日期:2001-07-15 00:00:00

  • A computer program to enter DNA gel reading data into a computer.

    abstract::This paper describes a simple program that uses a digitizing device to enter DNA sequences directly from autoradiographs into a computer. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Staden R

    更新日期:1984-01-11 00:00:00

  • Solution studies of the dimerization initiation site of HIV-1 genomic RNA.

    abstract::Dimerization of HIV-1 genomic RNA is an essential step of the viral cycle, initiated at a conserved stem-loop structure which forms a 'kissing complex' involving loop-loop interactions (dimerization initiation site, DIS). A 19mer RNA oligonucleotide (DIS-19) has been synthesized which forms a stable symmetrical dimer ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dardel F,Marquet R,Ehresmann C,Ehresmann B,Blanquet S

    更新日期:1998-08-01 00:00:00

  • Triplet repeat RNA structure and its role as pathogenic agent and therapeutic target.

    abstract::This review presents detailed information about the structure of triplet repeat RNA and addresses the simple sequence repeats of normal and expanded lengths in the context of the physiological and pathogenic roles played in human cells. First, we discuss the occurrence and frequency of various trinucleotide repeats in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审


    authors: Krzyzosiak WJ,Sobczak K,Wojciechowska M,Fiszer A,Mykowska A,Kozlowski P

    更新日期:2012-01-01 00:00:00

  • Conditional degradation of SDE2 by the Arg/N-End rule pathway regulates stress response at replication forks.

    abstract::Multiple pathways counteract DNA replication stress to prevent genomic instability and tumorigenesis. The recently identified human SDE2 is a genome surveillance protein regulated by PCNA, a DNA clamp and processivity factor at replication forks. Here, we show that SDE2 cleavage after its ubiquitin-like domain generat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rageul J,Park JJ,Jo U,Weinheimer AS,Vu TTM,Kim H

    更新日期:2019-05-07 00:00:00

  • Sequence determination of nucleic acids containing 5-methylisocytosine and isoguanine: identification and insight into polymerase replication of the non-natural nucleobases.

    abstract::Nucleobase analogs 5-methylisocytosine ((Me)isoC) and isoguanine (isoG) form a non-natural base pair in duplex nucleic acids with base pairing specificity orthogonal to the natural nucleobase pairs. Sequencing reactions were conducted with oligodeoxyribonucleotides (ODNs) containing d(Me)isoC and disoG using modified ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ahle JD,Barr S,Chin AM,Battersby TR

    更新日期:2005-06-02 00:00:00

  • Telomere processing in Euplotes.

    abstract::In Euplotes crassus millions of telomeres are synthesized during the sexual phase of the life cycle. Since these newly synthesized telomeres are longer than normal macronuclear telomeres, they must be trimmed to the mature size. We have examined the timing and mechanism of this trimming step. We have shown that a sudd...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Vermeesch JR,Williams D,Price CM

    更新日期:1993-11-25 00:00:00

  • Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification.

    abstract::MicroRNAs are a class of small non-coding RNAs that serve as important regulators of gene expression at the posttranscriptional level. They are stable in body fluids and pose great potential to serve as biomarkers. Here, we present a highly specific, sensitive and cost-effective system to quantify miRNA expression bas...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Androvic P,Valihrach L,Elling J,Sjoback R,Kubista M

    更新日期:2017-09-06 00:00:00

  • Nanoscopic structure of DNA condensed for gene delivery.

    abstract::Scanning force microscopy was used to examine DNA condensates prepared with varying stoichiometries of lipospermine or polyethylenimine in physiological solution. For the first time, individual DNA strands were clearly visualized in incomplete condensates without drying. Using lipospermine at sub-saturating concentrat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dunlap DD,Maggi A,Soria MR,Monaco L

    更新日期:1997-08-01 00:00:00

  • Multiply damaged sites in DNA: interactions with Escherichia coli endonucleases III and VIII.

    abstract::Bursts of free radicals produced by ionization of water in close vicinity to DNA can produce clusters of opposed DNA lesions and these are termed multiply damaged sites (MDS). How MDS are processed by the Escherichia coli DNA glycosylases, endonuclease (endo) III and endo VIII, which recognize oxidized pyrimidines, is...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Harrison L,Hatahet Z,Purmal AA,Wallace SS

    更新日期:1998-02-15 00:00:00

  • Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.

    abstract::Many DNA modification and repair enzymes require access to DNA bases and therefore flip nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within or in the vicinity of the target recognition site and do not require base extrusion for the sequence readout and catalysis. Therefore, the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Tamulaitis G,Zaremba M,Szczepanowski RH,Bochtler M,Siksnys V

    更新日期:2007-01-01 00:00:00

  • JSNP: a database of common gene variations in the Japanese population.

    abstract::JSNP is a repository of Japanese Single Nucleotide Polymorphism (SNP) data, begun in 2000 and developed through the Prime Minister's Millennium Project. The aim of this undertaking is to identify and collate up to 150 000 SNPs from the Japanese population, located in genes or in adjacent regions that might influence t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hirakawa M,Tanaka T,Hashimoto Y,Kuroda M,Takagi T,Nakamura Y

    更新日期:2002-01-01 00:00:00

  • Transcription of cloned Moloney murine leukemia proviral DNA injected into Xenopus laevis oocytes.

    abstract::We have microinjected genomic DNA clones containing the Moloney murine leukemia virus (M-MuLV) proviral genome and flanking mouse sequences from Mov-3, Mov-7 and Mov-10 mice into Xenopus laevis oocytes and analyzed the virus-specific transcription and translation products. These mouse strains carry a proviral genome c...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Breindl M,Kalthoff H,Jaenisch R

    更新日期:1983-06-25 00:00:00