Abstract：
:Since its discovery in 1979, left-handed Z-DNA has evolved from an in vitro curiosity to a challenging DNA structure with crucial roles in gene expression, regulation and recombination. A fundamental question that has puzzled researchers for decades is how the transition from B-DNA, the prevalent right-handed form of DNA, to Z-DNA is accomplished. Due to the complexity of the B-Z-DNA transition, experimental and computational studies have resulted in several different, apparently contradictory models. Here, we use molecular dynamics simulations coupled with state-of-the-art enhanced sampling techniques operating through non-conventional reaction coordinates, to investigate the B-Z-DNA transition at the atomic level. Our results show a complex free energy landscape, where several phenomena such as over-stretching, unpeeling, base pair extrusion and base pair flipping are observed resulting in interconversions between different DNA conformations such as B-DNA, Z-DNA and S-DNA. In particular, different minimum free energy paths allow for the coexistence of different mechanisms (such as zipper and stretch-collapse mechanisms) that previously had been proposed as independent, disconnected models. We find that the B-Z-DNA transition--in absence of other molecular partners--can encompass more than one mechanism of comparable free energy, and is therefore better described in terms of a reaction path ensemble.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Moradi M,Babin V,Roland C,Sagui Cdoi
10.1093/nar/gks1003subject
Has Abstractpub_date
2013-01-07 00:00:00pages
33-43issue
1eissn
0305-1048issn
1362-4962pii
gks1003journal_volume
41pub_type
杂志文章abstract：:A fluoride-cleavable phosphoramidite for biotinylation was designed, synthesized and coupled efficiently to the 5'-end of DNA on an automatic synthesizer. The diisopropylsilyl acetal functionality was used to link the biotin moiety through a tertiary hydroxide group to the 5'-end of DNA. This linkage proved to be comp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg130
更新日期：2003-01-15 00:00:00
abstract：:In an extensive analysis, using a range of restriction endonucleases, HinfI and TaqI were found to differentiate satellites I, II and III & IV. Satellite I is resistant to digestion by TaqI, but is cleaved by HinfI to yield three major fragments of approximate size 770, 850 and 950bp, associated in a single length of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.2.547
更新日期：1982-01-22 00:00:00
abstract：:Synthetic biology seeks to envision living cells as a matter of engineering. However, increasing evidence suggests that the genetic load imposed by the incorporation of synthetic devices in a living organism introduces a sort of unpredictability in the design process. As a result, individual part characterization is n...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1280
更新日期：2016-01-08 00:00:00
abstract：:A small library of 49 peptide-oligonucleotide conjugates were synthesized to explore the influence of various peptide side chains on the hybridization properties of the DNA. An invariant 8mer oligonucleotide was coupled to a peptide portion that contained a five residue variable region composed of the cationic amino a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.13.3136
更新日期：1998-07-01 00:00:00
abstract：:The P0 scaffold protein of the ribosomal stalk is mainly incorporated into pre-ribosomes in the cytoplasm where it replaces the assembly factor Mrt4. In analyzing the role of the P0 carboxyl terminal domain (CTD) during ribosomal stalk assembly, we found that its complete removal yields a protein that is functionally ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt637
更新日期：2013-10-01 00:00:00
abstract：:A C-->U mutation (rdn5) in the conserved sarcin/ricin domain of yeast 25S rRNA has been shown to cause translational suppression and paromomycin resistance. It also separates the killing from the misreading effect of this antibiotic. We confirm these findings and provide in vitro evidence that rdn5 causes a 3-fold inc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh860
更新日期：2004-10-11 00:00:00
abstract：:The complete nucleotide sequence of the Escherichia coli recB gene which encodes a subunit of the ATP-dependent DNase, Exonuclease V, has been determined. The proposed coding region for the RecB protein is 3543 nucleotides long and would encode a polypeptide of 1180 amino acids with a calculated molecular weight of 13...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.21.8573
更新日期：1986-11-11 00:00:00
abstract：:When designed to cleave a target RNA in trans, the hammerhead ribozyme contains two antisense flanks which form helix I and helix III by pairing with the complementary target RNA. The sequences forming helix II are contained on the ribozyme strand and represent a major structural component of the hammerhead structure....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.19.3951
更新日期：1994-09-25 00:00:00
abstract：:The location of proteins on the mitochondrial DNA (mtDNA) of Drosophila virilis was investigated by Me3 psoralen photoreaction of mitochondria isolated from embryos. After photoreaction the mtDNA was purified and the pattern of DNA cross-linking was determined by electron microscopy of the DNA under totally denaturing...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.4.1991
更新日期：1984-02-24 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp190
更新日期：2009-06-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz835
更新日期：2019-11-18 00:00:00
abstract：:Present results provide direct evidence of the nature of a conformational change in DNA when nucleosomes are formed from core histones and poly [d(A-T)]. First, we have found some features which have characteristic aspects of the A like conformation of DNA. Thus, an increased contribution due to a sugar conformation c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.19.4879
更新日期：1981-10-10 00:00:00
abstract：:Oligonucleotides synthesized in array format suffer from contamination by truncated species. We have developed a method to invert DNA molecules in situ after completed synthesis. Reactive functions at the 5'-ends of the oligonucleotides are permitted to react with functions on the support before the 3'-ends are releas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.24.4710
更新日期：1999-12-15 00:00:00
abstract：:Apolipoprotein B (apoB) is a major protein component of low density and very low density lipoproteins. Because of its large size and heterogeneity, molecular studies of apoB have been difficult, and its structure and regulation remain poorly understood. We now report the identification of human apoB cDNA clones by ant...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.19.6937
更新日期：1985-10-11 00:00:00
abstract：:DNA damage-induced cell cycle checkpoints serve as surveillance mechanisms to maintain genomic stability, and are regulated by ATM/ATR-mediated signaling pathways that are conserved from yeast to humans. Trypanosoma brucei, an early divergent microbial eukaryote, lacks key components of the conventional DNA damage-ind...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz476
更新日期：2019-09-05 00:00:00
abstract：:The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPre...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq318
更新日期：2010-07-01 00:00:00
abstract：:The eukaryotic ribosomal protein S26e (rpS26e) lacking eubacterial counterparts is a key component of the ribosomal binding site of mRNA region 5' of the codon positioned at the exit site. Here, we determined the rpS26e oligopeptide neighboring mRNA on the human 80S ribosome using mRNA analogues bearing perfluoropheny...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1212
更新日期：2012-04-01 00:00:00
abstract：:Muscleblind-like proteins (MBNLs) are regulators of RNA metabolism. During tissue differentiation the level of MBNLs increases, while their functional insufficiency plays a crucial role in myotonic dystrophy (DM). Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1158
更新日期：2017-02-28 00:00:00
abstract：:Nucleosomes released from oviduct nuclei during brief micrococcal nuclease digestions are enriched in transcribed sequences (bloom K.S. and Anderson, J.N. (1978) Cell, 15, 141-150). Such nucleosomes released into this 1Sf supernatant fraction are enriched in proteins HMG14, 17 and a third lower molecular weight protei...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.12.2761
更新日期：1981-06-25 00:00:00
abstract：:Precursor tRNAAsp molecules, containing a 26-base 5' leader, were treated with diethylpyrocarbonate, 50% hydrazine or anhydrous hydrazine/3M NaCl and then subjected to processing by RNase P RNAs from Escherichia coli or Bacillus subtilis. Fully processed tRNAs and material not successfully cleaved by the catalytic RNA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.4.885
更新日期：1991-02-25 00:00:00
abstract：:The expression of thymidine kinase in fungi, which normally lack this enzyme, will greatly aid the study of DNA metabolism and provide useful drug-sensitive phenotypes. The herpes simplex virus type-1 thymidine kinase gene ( tk ) was expressed in Neurospora crassa. tk was expressed as a fusion to N.crassa arg-2 regula...
journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：1997-06-15 00:00:00
abstract：:A new method of representing DNA sequences has been devised which is termed stave projection. Compared with other formats for showing the base sequences of DNA, this method greatly enhances the ease of visual analysis of the sequences of bases and it is also in a machine readable form. Using this method it is possible...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.1.509
更新日期：1986-01-10 00:00:00
abstract：:Messenger RNAs homologous to a cDNA clone (pTOM 13) derived from a ripe-tomato-specific cDNA library are expressed during tomato fruit ripening and after the wounding of leaf and green fruit material. Both responses involve the synthesis of the hormone ethylene. Accumulation of the pTOM 13--homologous RNA during ripen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.2.731
更新日期：1987-01-26 00:00:00
abstract：:Motif3D is a web-based protein structure viewer designed to allow sequence motifs, and in particular those contained in the fingerprints of the PRINTS database, to be visualised on three-dimensional (3D) structures. Additional functionality is provided for the rhodopsin-like G protein-coupled receptors, enabling finge...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg534
更新日期：2003-07-01 00:00:00
abstract：:Oligonucleotide-directed mutagenesis was used to introduce an A to C transversion at position 523 in the 16S ribosomal RNA gene of Escherichia coli rrnB operon cloned in plasmid pKK3535. E. coli cells transformed with the mutated plasmid were resistant to streptomycin. The mutated ribosomes isolated from these cells w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.20.9631
更新日期：1988-10-25 00:00:00
abstract：:The chemical reactivity of matched T and C bases to osmium tetroxide and hydroxylamine near mismatched and unmatched bases in a heteroduplex between two strands of DNA with multiple differences was examined. Data was available for matched bases one or two positions away from 24 mismatches. Reactive bases were found ne...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.11.4223
更新日期：1989-06-12 00:00:00
abstract：:Eukaryotic cells use numerous pathways to regulate RNA production, localization and stability. Several of these pathways are controlled by ribonucleases. The essential ribonuclease, Dis3, plays important roles in distinct RNA metabolic pathways. Despite much progress in understanding general characteristics of the Dis...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq295
更新日期：2010-09-01 00:00:00
abstract：:Chelation of divalent cations by 5 mM EDTA and subsequent removal by dialysis from a cytoplasmic HeLa cell extract leads to a complete loss of 5S rRNA transcription without affecting tRNA synthesis. Transcription complexes for 5S RNA can no longer be assembled in such a zinc-depleted extract and this ability can be fu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.23.8971
更新日期：1984-12-11 00:00:00
abstract：:In synthetic circuits, CRISPR-Cas systems have been used effectively for endpoint changes from an initial state to a final state, such as in logic gates. Here, we use deactivated Cas9 (dCas9) and deactivated Cas12a (dCas12a) to construct dynamic RNA ring oscillators that cycle continuously between states over time in ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa557
更新日期：2020-08-20 00:00:00
abstract：:A 34 base-pair (bp) fragment spanning sequences -154 to -120 of the promoter of the CHO1 gene (structural gene for phosphatidylserine synthase) from the yeast Saccharomyces cerevisiae has been shown to place transcription of a promoter-less Escherichia coli lacZ gene under control of the phospholipid precursors inosit...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.6.1411
更新日期：1992-03-25 00:00:00
