Abstract:
:The inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson-Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates for investigations of DNA-interacting enzymes. More recently, strategies for synthesis of more complex two-dimensional (2D) and 3D DNA structures have emerged. However, the building of such structures is still in progress and more experiences from different research groups and different fields of expertise are necessary before complex DNA structures can be routinely designed for the use in basal science and/or biotechnology. Here we present the design, construction and structural analysis of a covalently closed and stable 3D DNA structure with the connectivity of an octahedron, as defined by the double-stranded DNA helices that assembles from eight oligonucleotides with a yield of approximately 30%. As demonstrated by Small Angle X-ray Scattering and cryo-Transmission Electron Microscopy analyses the eight-stranded DNA structure has a central cavity larger than the apertures in the surrounding DNA lattice and can be described as a nano-scale DNA cage, Hence, in theory it could hold proteins or other bio-molecules to enable their investigation in certain harmful environments or even allow their organization into higher order structures.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Andersen FF,Knudsen B,Oliveira CL,Frøhlich RF,Krüger D,Bungert J,Agbandje-McKenna M,McKenna R,Juul S,Veigaard C,Koch J,Rubinstein JL,Guldbrandtsen B,Hede MS,Karlsson G,Andersen AH,Pedersen JS,Knudsen BRdoi
10.1093/nar/gkm1124subject
Has Abstractpub_date
2008-03-01 00:00:00pages
1113-9issue
4eissn
0305-1048issn
1362-4962pii
gkm1124journal_volume
36pub_type
杂志文章abstract::Multiplexed tandem PCR (MT-PCR) is a process for highly multiplexed gene expression profiling. In the first step, multiple primer pairs are added to the RNA to be analysed together with reverse transcriptase and Taq DNA polymerase. Following reverse transcription, the multiplexed amplicons are simultaneously amplified...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni182
更新日期:2005-11-24 00:00:00
abstract::Laser-Raman spectra of poly(rI) show the formation of an ordered complex in aqueous solutions of high ionic strength. This structure exhibits the A-helix geometry, contains stacked bases and is apparently stabilized by specific hydrogen bonding involving hypoxanthine C6=0 groups. Thermal dissociation of the poly(rI) c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.7.2407
更新日期:1977-07-01 00:00:00
abstract::DAP-like kinase (Dlk, also termed ZIP kinase) is a leucine zipper-containing serine/threonine-specific protein kinase with as yet unknown biological function(s). Interaction partners so far identified are either transcription factors or proteins that can support or counteract apoptosis. Thus, Dlk might be involved in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.6.1408
更新日期:2002-03-15 00:00:00
abstract::Most proteins from higher organisms are known to be multi-domain proteins and contain substantial numbers of intrinsically disordered (ID) regions. To analyse such protein sequences, those from human for instance, we developed a special protein-structure-prediction pipeline and accumulated the products in the Structur...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1057
更新日期:2011-01-01 00:00:00
abstract::Variable (diversity) joining [V(D)J] recombination of immune gene loci proceeds in an ordered manner with D to J portions recombining first and then an upstream V joins that recombinant. We present evidence that the non-core domain of recombination activating gene (RAG) protein 2 is involved in the regulation of recom...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn553
更新日期:2008-10-01 00:00:00
abstract::A simple, reproducible affinity chromatography method has been adapted for separation of high molecular weight supercoiled circular molecules from mammalian cells. Electron microscopic analysis of EB viral DNA obtained by this method, from the non-producer Burkitt's lymphoma line Raji, revealed monomer-sized viral mol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.24.10345
更新日期:1987-12-23 00:00:00
abstract::In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Ut...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1172
更新日期:2011-01-01 00:00:00
abstract::Release of phosphorothioate antisense oligonucleotides (PS-ASOs) from late endosomes (LEs) is a rate-limiting step and a poorly defined process for productive intracellular ASO drug delivery. Here, we examined the role of Golgi-endosome transport, specifically M6PR shuttling mediated by GCC2, in PS-ASO trafficking and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1171
更新日期:2020-02-20 00:00:00
abstract::Yeast tRNA Lys2 codes preferentially for AAA and contains a 2-thiouridine derivative (U) at the 5'-position of the anticodon. Removal of the 2-thio group from U by treatment with CNBr did not affect the amino acid accepting activity of the modified tRNA Lys2. CNBr treated tRNA Lys2 was active in protein synthesis but ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.3.523
更新日期:1976-03-01 00:00:00
abstract::The Génolevures online database (http://cbi.labri.fr/Genolevures/ and http://genolevures.org/) provides exploratory tools and curated data sets relative to nine complete and seven partial genome sequences determined and manually annotated by the Génolevures Consortium, to facilitate comparative genomic studies of Hemi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn859
更新日期:2009-01-01 00:00:00
abstract::MicroRNAs (miRNAs) are small noncoding RNAs that attenuate expression of their mRNA targets. Here, we developed a new method and an R package, to easily infer candidate miRNA-mRNA target interactions that could be functional during a given biological process. Using this method, we described, for the first time, a comp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx327
更新日期:2017-06-02 00:00:00
abstract::The chloroplast ribosomal protein CS1 is an essential component of the plastids translational machinery involved in translation initiation. Southern analysis suggests that the corresponding nuclear gene is present in one copy in the spinach genome. We have isolated and sequenced the gene (rps1) to study its expression...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.16.4153
更新日期:1992-08-25 00:00:00
abstract::Bacterial small regulatory RNAs (sRNAs) are the most abundant class of post-transcriptional regulators and have been well studied in Gram-negative bacteria. Little is known about the functions and mechanisms of sRNAs in high GC Gram-positive bacteria including Mycobacterium and Streptomyces. Here, we performed an in-d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz149
更新日期:2019-05-07 00:00:00
abstract::DNA bearing lambda operator sequences was methylated by dimethyl sulfate (DMS) in the presence or absence of lambda repressor. Under the experimental conditions, DMS methylates only the purine residues. The presence of lambda repressor affects only the methylation of certain G residues in the operators. Repressor bloc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.5.1595
更新日期:1977-01-01 00:00:00
abstract::A vast amount of research on the regulation of gene expression has relied on plasmid reporter assays. In this study, we show that plasmids widely used for this purpose constitutively produce substantial amounts of RNA from a TATA-containing cryptic promoter within the origin of replication. Readthrough of these RNAs i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks451
更新日期:2012-08-01 00:00:00
abstract::Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt030
更新日期:2013-04-01 00:00:00
abstract::MobA protein, encoded by the broad host-range plasmid R1162, is required for conjugal mobilization of this plasmid. The protein is an essential part of the relaxosome, and is also necessary for the termination of strand transfer. In vitro, MobA is a nuclease specific for one of the two DNA strands of the origin of tra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.19.4563
更新日期:1993-09-25 00:00:00
abstract::Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt915
更新日期:2014-01-01 00:00:00
abstract::The structure in solution of an RNA fragment (218 nucleotides long) containing part of E. coli 16S rRNA domain 2 has been studied using the intrinsic photoaffinity probe 4-thiouridine (s4U). In vitro transcription with T7 polymerase, in the presence of s4U triphosphate yielded complete RNA molecules. An affinity elect...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.13.3653
更新日期:1991-07-11 00:00:00
abstract::DNA sequences, that control expression of the spliced leader (SL) RNA gene in the parasitic protozoan Leishmania amazonensis, were mapped by block substitution mutagenesis. In the absence of a functional in vitro system for transcription, no promoter elements have yet been identified in this organism. We therefore dev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.11.1959
更新日期:1994-06-11 00:00:00
abstract::Infrared and UV spectroscopies have been used to study the assembly of a hairpin nucleotide sequence (nucleotides 3-30) of the 5' non-coding region of the hepatitis C virus RNA (5'-GGCGGGGAUUAUCCCCGCUGUGAGGCGG-3') with a RNA 20mer ligand (5'-CCGCCUCACAAAGGUGGGGU-3') in the presence of magnesium ion and spermidine. The...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.6.1333
更新日期:2002-03-15 00:00:00
abstract::The speed of the new DNA sequencing techniques has created a need for computer programs to handle the data produced. This paper describes simple programs designed specifically for use by people with little or no computer experience. The programs are for use on small computers and provide facilities for storage, editin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.11.4037
更新日期:1977-11-01 00:00:00
abstract::A repeat sequence 682 base pairs (bp) long produced by cleavage of human DNA with Xba I restriction enzyme is composed of four tandemly arranged subunits with lengths of 171, 170, 171, and 170 bp each. The sequence organization of the 682 bp Xba I repeat bears a striking resemblance to other complex satellite DNAs of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.2.521
更新日期:1985-01-25 00:00:00
abstract::In order to investigate the possible role of RNA secondary structure in determining the efficiency and specificity of mRNA splicing, the structures of sequences at three acceptor splice sites in adenovirus were studied. Transcripts spanning intron-exon junctions were synthesized using SP6 RNA polymerase and analyzed u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.22.8437
更新日期:1984-11-26 00:00:00
abstract::Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interacti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1011
更新日期:2018-01-04 00:00:00
abstract::alpha2-Macroglobulin covalently linked to poly(L)-lysine can be used as a vehicle for receptor-mediated gene transfer. This modified alpha2-macroglobulin maintains its ability to bind to the alpha2-macroglobulin receptor, and was shown to introduce a luciferase reporter gene plasmid into HepG2 human hepatoma cells in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.19.3873
更新日期:1996-10-01 00:00:00
abstract::Various strategies employed in genomic DNA cloning by subtractive hybridization have been examined by computer simulations, with the comparison between the predictions and the published results. The result shows that the efficiency of target sequence enrichment and the sensitivity to experimental conditions depend str...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.6.1440
更新日期:1998-03-15 00:00:00
abstract::Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding g...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw843
更新日期:2016-11-16 00:00:00
abstract::Eukaryotic topoisomerase II (topo II) is the essential decatenase of newly replicated chromosomes and the main relaxase of nucleosomal DNA. Apart from these general tasks, topo II participates in more specialized functions. In mammals, topo IIα interacts with specific RNA polymerases and chromatin-remodeling complexes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt707
更新日期:2013-11-01 00:00:00
abstract::Programmed ribosomal frameshifting provides a mechanism to decode information located in two overlapping reading frames by diverting a proportion of translating ribosomes into a second open reading frame (ORF). The result is the production of two proteins: the product of standard translation from ORF1 and an ORF1-ORF2...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl531
更新日期:2006-01-01 00:00:00