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 been improving constantly. The combination of both techniques has appealed to researchers ever since single-molecule measurements have become possible and indeed first implementations of such combined approaches have proven useful in the study of several DNA-binding proteins in real time. Here, we describe the technical state-of-the-art of various integrated manipulation-and-visualization methods. We first discuss methods that allow only little control over the DNA conformation, such as DNA combing. We then describe DNA flow-stretching approaches that allow more control, and end with the full control on position and extension obtained by manipulating DNA with optical tweezers. The advantages and limitations of the various techniques are discussed, as well as several examples of applications to biophysical or biochemical questions. We conclude with an outlook describing potential future technical developments in combining fluorescence microscopy with DNA micromanipulation technology.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
van Mameren J,Peterman EJ,Wuite GJdoi
10.1093/nar/gkn412subject
Has Abstractpub_date
2008-08-01 00:00:00pages
4381-9issue
13eissn
0305-1048issn
1362-4962pii
gkn412journal_volume
36pub_type
杂志文章,评审abstract：:Nuclei from frozen calf thymus suspended in buffer were analyzed for metal content prior to and after repeated washing. After three such extractions about 0.1 micrograms Zn/mg DNA and 0.025 micrograms Cu/mg DNA remained tightly associated with chromatin. This level of metal was essentially unchanged with subsequent wa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.21.5811
更新日期：1981-11-11 00:00:00
abstract：:Hg-UMP-containing transcripts made from chick erythroid chromatins with E. coli RNA polymerase hybridize to chick globin cDNA. Contamination with endogenous globin RNA has been largely removed by purification on SH-agarose columns at 55 degrees C. Some endogenous globin mRNA sequences remain, probably as hybrids with ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.4.1237
更新日期：1978-04-01 00:00:00
abstract：:p53 is thought to function in the maintenance of genomic stability by modulating transcription and interacting with cellular proteins to influence the cell cycle, DNA repair and apoptosis. p53 mutations occur in >50% of human cancers, and cells which lack wild type p53 accumulate karyotypic abnormalities such as ampli...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.19.3868
更新日期：1997-10-01 00:00:00
abstract：:We have sequenced 14 introns from the ciliate Tetrahymena thermophila and include these in an analysis of the 27 intron sequences available from seven T. thermophila protein-encoding genes. Consensus 5' and 3' splice junctions were determined and found to resemble the junctions of other nuclear pre-mRNA introns. Uniqu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.17.5133
更新日期：1990-09-11 00:00:00
abstract：:Bacteriophage T4 Dda helicase has recently been shown to be active as a monomer for unwinding of short duplex oligonucleotides and for displacing streptavidin from 3'-biotinylated oligonucleotides. However, its activity for streptavidin displacement and DNA unwinding has been shown to increase as the number of Dda mol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl369
更新日期：2006-05-31 00:00:00
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
doi：10.1093/nar/18.10.2917
更新日期：1990-05-25 00:00:00
abstract：:The DNA sequence of a 225.4 kilobase segment of the Escherichia coli K-12 genome is described here, from 76.0 to 81.5 minutes on the genetic map. This brings the total of contiguous sequence from the E.coli genome project to 725.1 kb (76.0 to 92.8 minutes). We found 191 putative coding genes (ORFs) of which 72 genes w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.13.2576
更新日期：1994-07-11 00:00:00
abstract：:Molecular replacement (MR) is the method of choice for X-ray crystallography structure determination when structural homologues are available in the Protein Data Bank (PDB). Although the success rate of MR decreases sharply when the sequence similarity between template and target proteins drops below 35% identical res...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh400
更新日期：2004-07-01 00:00:00
abstract：:PKR is a doubled-stranded RNA-dependent protein kinase which is implicated in the regulation of several cellular processes, including cell proliferation. PKR undergoes phosphorylation and activation in mouse embryonic 3T3-F442A cells in response to endogenous RNA(s). Activation of PKR is related to growth and differen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.13.2672
更新日期：1997-07-01 00:00:00
abstract：:The death of sympathetic neurons after nerve growth factor (NGF) withdrawal requires de novo gene expression. Dp5 was one of the first NGF withdrawal-induced genes to be identified and it encodes a proapoptotic BH3-only member of the Bcl-2 family. To study how dp5 transcription is regulated by NGF withdrawal we cloned...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp175
更新日期：2009-05-01 00:00:00
abstract：:The novel deoxyribonucleotide alpha-[d(CpCpTpTpCpC)] and its complement beta-[d(GpGpApApGpG)] were synthesized by the phosphotriester method. 1H-NMR-NOE examination of the alpha-hexamer revealed that the cytosine and thymine bases appear to adopt anti conformations in this strand. In addition the deoxyribose of the th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.12.5019
更新日期：1986-06-25 00:00:00
abstract：:We recently developed a new type of pyrrole (Py)-imidazole (Im) polyamide-tetrahydrocyclopropabenzindolone (CBI) conjugate with an indole linker as a stable sequence-specific alkylating agent. In this study, we investigated the gene silencing activities of polyamides A, B and C, which selectively alkylate specific seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl005
更新日期：2006-02-25 00:00:00
abstract：:The primary structure of the E. coli rpoC gene (5321 base pairs) coding the beta'-subunit of RNA polymerase as well as its adjacent segment have been determined. The structure analysis of the peptides obtained by cleavage of the protein with cyanogen bromide and trypsin has confirmed the amino acid sequence of the bet...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.13.4035
更新日期：1982-07-10 00:00:00
abstract：:The editing function of aminoacyl-tRNA synthetases (aaRSs) is indispensible for formation of the correct aminoacyl-tRNAs. Editing deficiency may lead to growth inhibition and the pathogenesis of various diseases. Herein, we confirmed that norvaline (Nva) but not isoleucine or valine is the major threat to the editing ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx487
更新日期：2017-07-07 00:00:00
abstract：:The structure of eukaryotic chromatin has been investigated by isolating and analyzing the "accessible" DNA fraction of rat liver chromatin. This DNA fraction has been isolated by titrating the chromatin with the protese-resistant D isomer of polylysine to bind the "accessible" DNA sites. After removal of chromosomal ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.5.667
更新日期：1975-05-01 00:00:00
abstract：:It has been postulated that a myriad of long noncoding RNAs (lncRNAs) contribute to gene regulation. In fission yeast, glucose starvation triggers lncRNA transcription across promoter regions of stress-responsive genes including fbp1 (fructose-1,6-bisphosphatase1). At the fbp1 promoter, this transcription promotes chr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw142
更新日期：2016-06-20 00:00:00
abstract：:A new procedure has been developed for the efficient cloning of complex PCR mixtures, resulting in libraries exclusively consisting of recombinant clones. Recombinants are generated between PCR products and a PCR-amplified plasmid vector. The procedure does not require the use of restriction enzymes, T4 DNA ligase or ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.20.6069
更新日期：1990-10-25 00:00:00
abstract：:A simplified and economical method for the attachment of 2'-deoxyribo, ribo and arabinonucleosides onto long-chain alkylamidopropanoic acid controlled-pore glass (LCAAP-CPG, P-3) is described. In this procedure, 5'-O-tritylated nucleosides are coupled directly to LCAAP-CPG in excellent yields using 1-(3-dimethylaminop...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.13.3813
更新日期：1990-07-11 00:00:00
abstract：:A differential effect is found of various bivalent cations (Ba2+, Ca2+, Mg2+, Cd2+, Co2+, Mn2+, Ni2+, Zn2+ and Hg2+) on stability of intermolecular Py-Pu-Pu triplex with different sequence of base triads. Ca2+, Mg2+, Cd2+, Co2+, Mn2+, Ni2+ and Zn2+ do stabilize the d(C)n d(G)n d(G)n triplex whereas Ba2+ and Hg2+ do no...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.3.585
更新日期：1993-02-11 00:00:00
abstract：:Invariance of temporal order of genome replication in eukaryotic cells and its correlation with gene activity has been well-documented. However, recent data suggest a relax control of replication timing. To evaluate replication schedule accuracy, we detailed the replicational organization of the developmentally regula...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm586
更新日期：2007-01-01 00:00:00
abstract：:The Dnd (DNA degradation) phenotype, reflecting a novel DNA modification by sulfur in Streptomyces lividans 1326, was strongly aggravated when one (dndB) of the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear change...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm176
更新日期：2007-01-01 00:00:00
abstract：:Non-coding RNAs (ncRNAs) have diverse essential biological functions in all organisms, and in eukaryotes, two such classes of ncRNAs are the small nucleolar (sno) and small nuclear (sn) RNAs. In this study, we have identified and characterized a collection of sno and snRNAs in Giardia lamblia, by exploiting our discov...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks887
更新日期：2012-11-01 00:00:00
abstract：:Human telomerase reverse transcriptase (hTERT), the catalytic subunit of human telomerase, contains conserved motifs common to retroviral reverse transcriptases and telomerases. Within the C motif of hTERT is the Leu866-Val867-Asp868-Asp869 tetrapeptide that includes a catalytically essential aspartate dyad. Site-dire...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm002
更新日期：2007-01-01 00:00:00
abstract：:Fifteen years elapsed between the discovery of the double helix (1953) and the first DNA sequencing (1968). Modern DNA sequencing began in 1977, with development of the chemical method of Maxam and Gilbert and the dideoxy method of Sanger, Nicklen and Coulson, and with the first complete DNA sequence (phage X174), whi...
journal_title：Nucleic acids research
pub_type： 历史文章,杂志文章
doi：10.1093/nar/gkm688
更新日期：2007-01-01 00:00:00
abstract：:Insertion of the T3 DNA polymerase thioredoxin binding domain (TBD) into the distantly related thermostable Taq DNA polymerase at an analogous position in the thumb domain, converts the Taq DNA polymerase from a low processive to a highly processive enzyme. Processivity is dependent on the presence of thioredoxin. The...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg667
更新日期：2003-08-15 00:00:00
abstract：:The chromatin structure of yeast ribosomal DNA was analyzed in vivo by crosslinking intact cells with psoralen. We found that in exponentially growing cultures the regions coding for the 35S rRNA precursor fall into two distinct classes. One class was highly accessible to psoralen and associated with nascent RNAs, cha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.10.2331
更新日期：1993-05-25 00:00:00
abstract：:We have investigated the attachment of the DNA to the nuclear matrix during the division cycle of the plasmodial slime mold Physarum polycephalum. The DNA of plasmodia was pulse labelled at different times during the S phase and the label distribution was studied by graded DNase digestion of the matrix-DNA complexes p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.4.1181
更新日期：1983-02-25 00:00:00
abstract：:The nucleotide sequence of the faeD gene of Escherichia coli and the amino acid sequence of its product is presented. The faeD product is an outer membrane protein required for transport of K88ab fimbrial subunits across the outer membrane. The protein is synthesized as a precursor containing a signal peptide, and the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.6.2443
更新日期：1986-03-25 00:00:00
abstract：:In the present study, the relationship between short interfering RNA (siRNA) sequence and RNA interference (RNAi) effect was extensively analyzed using 62 targets of four exogenous and two endogenous genes and three mammalian and Drosophila cells. We present the rules that may govern siRNA sequence preference and in a...
journal_title：Nucleic acids research
pub_type： 指南,杂志文章
doi：10.1093/nar/gkh247
更新日期：2004-02-09 00:00:00
abstract：:The transcriptional shift from repression to activation of target genes is crucial for the fidelity of Notch responses through incompletely understood mechanisms that likely involve chromatin-based control. To activate silenced genes, repressive chromatin marks are removed and active marks must be acquired. Histone H3...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw105
更新日期：2016-06-02 00:00:00
