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20.411 Aktuelle Fachpublikationen zum Thema Addition

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Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe

01.02.2015 | Yuan Ding; Xiaojun Zhang; Kenneth W. Tham; Peter Z. Qin, Nucleic Acids Research, 2015

Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as ‘DNA shape’, critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA ...


Single-molecule analysis uncovers the difference between the kinetics of DNA decatenation by bacterial topoisomerases I and III

01.02.2015 | Ksenia Terekhova; John F. Marko; Alfonso Mondragón, Nucleic Acids Research, 2015

Escherichia coli topoisomerases I and III can decatenate double-stranded DNA (dsDNA) molecules containing single-stranded DNA regions or nicks as well as relax negatively supercoiled DNA. Although the proteins share a mechanism of action and have similar structures, they participate in different ...


Monomeric nature of dengue virus NS3 helicase and thermodynamic analysis of the interaction with single-stranded RNA

01.02.2015 | Leopoldo G. Gebhard; J. Jeremías Incicco; Clara Smal; Mariana Gallo; Andrea V. Gamarnik; Sergio B. Kaufman, Nucleic Acids Research, 2015

Dengue virus nonstructural protein 3 (NS3) is a multifunctional protein formed by a superfamily-2 RNA helicase linked to a protease domain. In this work, we report results from in vitro experiments designed to determine the oligomeric state of dengue virus NS3 helicase (NS3h) and to characterize ...


Tls1 regulates splicing of shelterin components to control telomeric heterochromatin assembly and telomere length

01.02.2015 | Jiyong Wang; Xavier Tadeo; Haitong Hou; Stuart Andrews; James J. Moresco; John R. Yates III; Peter L. Nagy; Songtao Jia, Nucleic Acids Research, 2015

Heterochromatin preferentially forms at repetitive DNA elements through RNAi-mediated targeting of histone-modifying enzymes. It was proposed that splicing factors interact with the RNAi machinery or regulate the splicing of repeat transcripts to directly participate in heterochromatin assembly. ...


Invincible DNA tethers: covalent DNA anchoring for enhanced temporal and force stability in magnetic tweezers experiments

01.02.2015 | Richard Janissen; Bojk A. Berghuis; David Dulin; Max Wink; Theo van Laar; Nynke H. Dekker, Nucleic Acids Research, 2015

Magnetic tweezers are a powerful single-molecule technique that allows real-time quantitative investigation of biomolecular processes under applied force. High pulling forces exceeding tens of picoNewtons may be required, e.g. to probe the force range of proteins that actively transcribe or ...


What makes the lac-pathway switch: identifying the fluctuations that trigger phenotype switching in gene regulatory systems

01.02.2015 | Prasanna M. Bhogale; Robin A. Sorg; Jan-Willem Veening; Johannes Berg, Nucleic Acids Research, 2015

Multistable gene regulatory systems sustain different levels of gene expression under identical external conditions. Such multistability is used to encode phenotypic states in processes including nutrient uptake and persistence in bacteria, fate selection in viral infection, cell-cycle control ...


Silkworm HP1a transcriptionally enhances highly expressed euchromatic genes via association with their transcription start sites

01.02.2015 | Keisuke Shoji; Kahori Hara; Munetaka Kawamoto; Takashi Kiuchi; Shinpei Kawaoka; Sumio Sugano; Toru Shimada; Yutaka S ..., Nucleic Acids Research, 2015

Heterochromatin protein 1 (HP1) is an evolutionarily conserved protein across different eukaryotic species and is crucial for heterochromatin establishment and maintenance. The silkworm, Bombyx mori, encodes two HP1 proteins, BmHP1a and BmHP1b. In order to investigate the role of BmHP1a in ...


Two ZNF509 (ZBTB49) isoforms induce cell-cycle arrest by activating transcription of p21/CDKN1A and RB upon exposure to genotoxic stress

01.02.2015 | Bu-Nam Jeon; Min-Kyeong Kim; Jae-Hyeon Yoon; Min-Young Kim; Haemin An; Hee-Jin Noh; Won-Il Choi; Dong-In Koh; Man-Wo ..., Nucleic Acids Research, 2015

ZNF509 is unique among POK family proteins in that four isoforms are generated by alternative splicing. Short ZNF509 (ZNF509S1, -S2 and -S3) isoforms contain one or two out of the seven zinc-fingers contained in long ZNF509 (ZNF509L). Here, we investigated the functions of ZNF509 isoforms in ...


AP endonucleases process 5-methylcytosine excision intermediates during active DNA demethylation in Arabidopsis

01.02.2015 | Jiyoon Lee; Hosung Jang; Hosub Shin; Woo Lee Choi; Young Geun Mok; Jin Hoe Huh, Nucleic Acids Research, 2015

DNA methylation is a primary epigenetic modification regulating gene expression and chromatin structure in many eukaryotes. Plants have a unique DNA demethylation system in that 5-methylcytosine (5mC) is directly removed by DNA demethylases, such as DME/ROS1 family proteins, but little is known ...


Selective recognition of parallel and anti-parallel thrombin-binding aptamer G-quadruplexes by different fluorescent dyes

01.02.2015 | Dan Zhao; Xiongwei Dong; Nan Jiang; Dan Zhang; Changlin Liu, Nucleic Acids Research, 2015

G-quadruplexes (G4) have been found increasing potential in applications, such as molecular therapeutics, diagnostics and sensing. Both Thioflavin T (ThT) and N-Methyl mesoporphyrin IX (NMM) become fluorescent in the presence of most G4, but thrombin-binding aptamer (TBA) has been reported as the ...


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