Abstract:
:We have determined the stability of intramolecular DNA quadruplexes in which the four G(3)-tracts are connected by non-nucleosidic linkers containing propanediol, octanediol or hexaethylene glycol, replacing the TTA loops in the human telomeric repeat sequence. We find that these sequences all fold to form intramolecular complexes, which are stabilized by lithium < sodium < potassium. Quadruplex stability increases in the order propanediol < hexaethylene glycol < octanediol. The shallower shape of the melting profile with propanediol linkers and its lower dependency on potassium concentration suggests that this complex contains fewer stacks of G-quartets. The sequence with octanediol linkers displays a biphasic melting profile, suggesting that it can adopt more than one stable structure. All these complexes display melting temperatures above 310 K in the presence of 10 mM lithium, without added potassium, in contrast to the telomeric repeat sequence. These complexes also fold much faster than the telomeric repeat and there is little or no hysteresis between their melting and annealing profiles. In contrast, the human telomeric repeat sequence and a complex containing two hexaethylene glycol groups in each loop, are less stable and fold more slowly. The melting and annealing profiles for the latter sequence show significant differences, even when heated at 0.2 degrees C min(-1). CD spectra for the oligonucleotides containing non-nucleosidic linkers show positive maxima at 264 nm, with negative minima approximately 244 nm, which are characteristic of parallel quadruplex structures. These results show that the structure and stability of intramolecular quadruplexes is profoundly influenced by the length and composition of the loops.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Risitano A,Fox KRdoi
10.1093/nar/gkh598keywords:
subject
Has Abstractpub_date
2004-05-11 00:00:00pages
2598-606issue
8eissn
0305-1048issn
1362-4962pii
32/8/2598journal_volume
32pub_type
杂志文章abstract::Pulsed field gel electrophoresis was used to determine the location of the tumour necrosis factor (TNF) alpha and beta genes. They were shown to be linked to the HLA-B locus; analogous to their location in mouse, between the complement (class III) region and H-2D. However, the distance between the TNF genes and the cl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.21.8957
更新日期:1987-11-11 00:00:00
abstract::Guanine-rich DNA sequences tend to form four-stranded G-quadruplex structures. Characteristic glycosidic conformational patterns along the G-strands, such as the 5'-syn-anti-syn-anti pattern observed with the Oxytricha nova telomeric G-quadruplexes, have been well documented. However, an explanation for these featured...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr031
更新日期:2011-05-01 00:00:00
abstract::Expressed Sequence Tag-based gene expression profiling can be used to discover functionally associated genes on a large scale. Currently available web servers and tools focus on finding differentially expressed genes in different samples or tissues rather than finding co-expressed genes. To fill this gap, we have deve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki480
更新日期:2005-07-01 00:00:00
abstract::The essential and universal N(6)-threonylcarbamoyladenosine (t(6)A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon-anticodon interaction. In Escherichia coli, the YgjD (TsaD), YeaZ (Tsa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1397
更新日期:2015-02-18 00:00:00
abstract::The reported binding preference of human hnRNP protein A1 for the 3'-splice site of some introns (Swanson and Dreyfuss (1988) EMBO J. 7, 3519-3529; Mayrand and Pederson (1990) Nucleic Acids Res. 18, 3307-3318) was tested by assaying in vitro the binding of purified recombinant A1 protein (expressed in bacteria) to syn...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.22.6595
更新日期:1990-11-25 00:00:00
abstract::The RNA degradosome is a multi-enzyme assembly that contributes to key processes of RNA metabolism, and it engages numerous partners in serving its varied functional roles. Small domains within the assembly recognize collectively a diverse range of macromolecules, including the core protein components, the cytoplasmic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks739
更新日期:2012-11-01 00:00:00
abstract::We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt605
更新日期:2013-09-01 00:00:00
abstract::The deoxyoctanucleotide 5'd (AAGGAGGT) which is complementary to the 3' terminus of 16S RNA has been used as a probe to measure the potential of this rRNA region to engage in intermolecular basepairing. The site specific binding of the octanucleotide is shown by labeling 16S RNA in situ at its 3' end with [32P]pCp and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.6.1425
更新日期:1981-03-25 00:00:00
abstract::The rpoH genes encoding homologs of Escherichia coli sigma 32 (heat shock sigma factor) were isolated and sequenced from five gram negative proteobacteria (gamma or alpha subgroup): Enterobacter cloacae (gamma), Serratia marcescens (gamma), Proteus mirabilis (gamma), Agrobacterium tumefaciens (alpha) and Zymomonas mob...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:
更新日期:1995-11-11 00:00:00
abstract::In this study, we show that silencing of CITED2 using small-hairpin RNA (shCITED2) induced DNA damage and reduction of ERCC1 gene expression in HEK293, HeLa and H1299 cells, even in the absence of cisplatin. In contrast, ectopic expression of ERCC1 significantly reduced intrinsic and induced DNA damage levels, and res...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv934
更新日期:2015-12-15 00:00:00
abstract::Loop-loop tertiary interactions play a key role in the folding and catalytic activity of natural hammerhead ribozymes. Using a combination of NMR spectroscopy, site-directed mutagenesis and kinetic and infectivity analyses, we have examined the structure and function of loops 1 and 2 of the (+) and (-) hammerheads of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn918
更新日期:2009-02-01 00:00:00
abstract::The thumb subdomain, located in various family B DNA polymerases in the C-terminal region, has been shown in their crystal structures to move upon binding of DNA, changing its conformation to nearly completely wrap around the DNA. It has therefore been involved in DNA binding. In agreement with this, partial proteolys...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh184
更新日期:2004-01-16 00:00:00
abstract::Recent research hints at an underappreciated complexity in pre-miRNA processing and regulation. Global profiling of pre-miRNA and its potential to increase understanding of the pre-miRNA landscape is impeded by overlap with highly expressed classes of other non coding (nc) RNA. Here, we present a data set excluding th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr903
更新日期:2012-02-01 00:00:00
abstract::Analysis of haplotypes is an important tool in population genetics, familial heredity and gene mapping. Determination of haplotypes of multiple single nucleotide polymorphisms (SNPs) or other simple mutations is time consuming and expensive when analyzing large populations, and often requires the help of computational...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnf062
更新日期:2002-06-15 00:00:00
abstract::eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 euka...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1085
更新日期:2019-01-08 00:00:00
abstract::DNase I and MPE.Fe (II) footprinting both employ partial cleavage of ligand-protected DNA restriction fragments and Maxam-Gilbert sequencing gel methods of analysis. One method utilizes the enzyme, DNase I, as the DNA cleaving agent while the other employs the synthetic molecule, methidium-propyl-EDTA (MPE). For actin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.16.5555
更新日期:1983-08-25 00:00:00
abstract::2'-Deoxyoligonucleotides with 5-fluorocytosine residues incorporated at specific positions of the nucleotide sequence are tools of great potential in the study of the catalytic mechanism by which DNA cytosine methyltransferases methylate the 5-position of DNA cytosine residues in specific sequence contexts. Chemical s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.10.2421
更新日期:1992-05-25 00:00:00
abstract::MiRNAs are important regulators of gene expression and are frequently deregulated under pathologic conditions. They are highly stable in bodily fluids which makes them feasible candidates to become minimally invasive biomarkers. In fact, several studies already proposed circulating miRNA-based biomarkers for different...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky981
更新日期:2019-01-08 00:00:00
abstract::We described here an approach for mapping proteins on any sequence of genomic DNA. UV-induced DNA-protein crosslinking within whole cells and the 'protein image' hybridization technique (1) were applied to test the proteins bound to different regions of the D. melanogaster hsp-70 gene. The histone H1-DNA association w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.4.1031
更新日期:1993-02-25 00:00:00
abstract::Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we discover an HRP2-DPF3a-BAF epigenetic pathway that coordinates methylated histone H3 ly...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa441
更新日期:2020-07-09 00:00:00
abstract::Scanning tunneling microscopy (STM) reveals nanometer scale details of hydrated DNA but the interpretation of the images is controversial because of substrate artifacts and the lack of a theory for image contrast. We demonstrate that we have overcome these problems by identifying five DNA samples by their STM images a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.25.5896
更新日期:1993-12-25 00:00:00
abstract::Studies of bacterial chromosomes and plasmids indicate that their replication initiator proteins bind to origins of replication at many double-stranded sites and also at AT-rich regions where single-stranded DNA is exposed during origin opening. Single-strand binding apparently promotes origin opening by stabilizing a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa826
更新日期:2020-11-04 00:00:00
abstract::The immunoglobulin heavy chain intronic transcriptional enhancer (E mu) is part of a complex cis-regulatory DNA region which has notably been shown to modulate V(D)J rearrangements of associated variable gene segments. We have used recombination substrates comprised of the E mu enhancer together with various lengths o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.5.792
更新日期:1994-03-11 00:00:00
abstract::Saccharomyces cerevisiae Pif1 (ScPif1) is known as an ATP-dependent DNA helicase that plays critical roles in a number of important biological processes such as DNA replication, telomere maintenance and genome stability maintenance. Besides its DNA helicase activity, ScPif1 is also known as a single-stranded DNA (ssDN...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz541
更新日期:2019-08-22 00:00:00
abstract::Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interacti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1016
更新日期:2017-01-04 00:00:00
abstract::RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic molecular biology experiments, and recently also from high-throughput genomic methodologies. We curated the literature to keep Reg...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1077
更新日期:2019-01-08 00:00:00
abstract::Methylation of miRNAs at the 2'-hydroxyl group on the ribose at 3'-end (2'-O-methylation, 2'Ome) is critical for miRNA function in plants and Drosophila. Whether this methylation phenomenon exists for mammalian miRNA remains unknown. Through LC-MS/MS analysis, we discover that majority of miR-21-5p isolated from human...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa504
更新日期:2020-07-27 00:00:00
abstract::In this paper, we report the cloning and sequencing of the C. elegans histidyl-tRNA synthetase gene. The complete genomic sequence, and most of the cDNA sequence, of this gene is now determined. The gene size including flanking and coding regions is 2230 nucleotides long. Three small introns (45-50 bp long) are found ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.18.4344
更新日期:1993-09-11 00:00:00
abstract::Oxoguanine DNA glycosylase (OGG1) initiates the repair of 8-oxoguanine (8-oxoG), a major oxidative DNA base modification that has been directly implicated in cancer and aging. OGG1 functions in the base excision repair pathway, for which a molecular hand-off mechanism has been proposed. To date, only one functional an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki636
更新日期:2005-06-07 00:00:00
abstract::The tight-binding I12-X86 lac repressor binds to non-operator DNA in a sequence-specific fashion. Using the DNA of the E. coli I gene we have investigated these sequence-specific interactions and compared them to the operator binding of wild-type repressor. The specific, non-operator DNA interactions are sensitive to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.3.487
更新日期:1980-02-11 00:00:00