Fluorescence resonance energy transfer studies of U-shaped DNA molecules.

Abstract:

:Fluorescence resonance energy transfer studies allow to determine global shape properties of nucleic acids and nucleoprotein complexes. In many DNA-protein complexes, the DNA is more or less bent and the degree of bending can be obtained by FRET. For example, the DNA in complex with the integration host factor (IHF) is kinked by approximately 160 degrees building a U-shaped structure. The two DNA helix ends come close to one another in space in a distance range easily measurable by FRET. The global DNA structure of this complex can be mimicked by introducing two regions with unpaired bases ('bulges') into the DNA each producing a sharp kink of approximately 80 degrees. These U-shaped DNA constructs were used to measure the electrostatic interaction of the two nearly parallel negatively charged DNA helix arms. The electrostatic repulsion between the helix arms, and as a consequence their distance, decreases with growing salt concentration of mono- or divalent cations. This experimental approach also allows the sensitive study of the local structure of DNA sequences positioned between the two bulges.

journal_name

J Biotechnol

journal_title

Journal of biotechnology

authors

Lorenz M,Hillisch A,Diekmann S

doi

10.1016/s1389-0352(01)00038-1

subject

Has Abstract

pub_date

2002-01-01 00:00:00

pages

197-209

issue

3

eissn

0168-1656

issn

1873-4863

pii

S1389-0352(01)00038-1

journal_volume

82

pub_type

杂志文章
  • Using liquid crystals for the label-free detection of catalase at aqueous-LC interfaces.

    abstract::In this study, we developed a simple label-free method for the detection of catalase (CAT) using liquid crystals (LCs). The optical appearance of LCs changed from bright to dark when hydrogen peroxide was in contact with the dodecanal-doped nematic LC, 4-cyano-4'-pentylbiphenyl (5CB). Since hydrogen peroxide can oxidi...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2011.11.010

    authors: Hu QZ,Jang CH

    更新日期:2012-01-01 00:00:00

  • Increased gene expression and inflammatory cell infiltration caused by electroporation are both important for improving the efficacy of DNA vaccines.

    abstract::One potential reason for the enhancement of immune responses to DNA vaccines following electroporation is increased gene expression. However, the inflammatory response and accompanying cellular infiltration stimulated by electroporation may also be essential for enhancing immune responses to DNA vaccines. These parame...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2004.01.015

    authors: Babiuk S,Baca-Estrada ME,Foldvari M,Middleton DM,Rabussay D,Widera G,Babiuk LA

    更新日期:2004-05-13 00:00:00

  • Impact of transport processes in the osmotic response of Corynebacterium glutamicum.

    abstract::Osmoregulation, the adaptation of cells to changes in the external osmolarity, is an important aspect of the bacterial stress response, in particular for a soil bacterium like Corynebacterium glutamicum. Consequently, this organism is equipped with several redundant systems for coping with both hyper- and hypoosmotic ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0168-1656(03)00164-0

    authors: Morbach S,Krämer R

    更新日期:2003-09-04 00:00:00

  • Solid-phase cloning to create sublibraries suitable for DNA sequencing.

    abstract::A solid-phase method is described to create subclones, suitable for DNA sequencing, from lambda or cosmid libraries. The purified target DNA is sonicated and two linkers, with one oligonucleotide biotinylated in the 5'-end, are ligated to the ends of the fragments produced by sonication. After size separation, the fra...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/0168-1656(94)90038-8

    authors: Hultman T,Uhlén M

    更新日期:1994-06-30 00:00:00

  • Towards the in vivo production of tocotrienol compounds: engineering of a plasmid-free Escherichia coli strain for the heterologous synthesis of 2-methyl-6-geranylgeranyl-benzoquinol.

    abstract::The vitamin E family consists of 4 tocopherol and 4 tocotrienol compounds. During recent years, tocotrienols have gained increased interest due to their biological activities that are beyond the vitamin E activity. Here we report the engineering of plasmid-free Escherichia coli strains for an efficient synthesis of 2-...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2012.08.010

    authors: Ghanegaonkar S,Conrad J,Beifuss U,Sprenger GA,Albermann C

    更新日期:2012-12-15 00:00:00

  • D-xylose detection in Escherichia coli by a xylose binding protein-dependent response.

    abstract::A gene circuit for the controlled expression of a marker gene and for the assay of xylose concentration in Escherichia coli has been designed and tested. The xylF coding sequence for the xylose binding protein (XBP) was cloned in pT7T318U downstream from the promoter for xylanase A from B. subtilis (Pbsu), together wi...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2013.10.019

    authors: Ribeiro LF,Bressan F,Furtado GP,Meireles F,Ward RJ

    更新日期:2013-12-01 00:00:00

  • High-level expression of porcine muscle adenylate kinase in Escherichia coli: effects of the copy number of the gene and the translational initiation signals.

    abstract::Porcine muscle adenylate kinase (ADK) was overproduced in Escherichia coli using the expression plasmid with double A-T-G codon at the translational starting site and the Shine-Dalgarno (SD) sequence 10 bp apart from the first A-T-G. We used the expression vectors pKK223-3 and pMK2. pMK2 is about 10-20 times larger in...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/0168-1656(94)90176-7

    authors: Hibino T,Misawa S,Wakiyama M,Maeda S,Yazaki K,Kumagai I,Ooi T,Miura K

    更新日期:1994-02-14 00:00:00

  • Preparation of a reversible soluble-insoluble β-d-Glucosidase with perfect stability and activity.

    abstract::Rebuilding enzymes with high activities, stability and reusability has been constantly pursued for application of enzymaticcatalysis in wide field. Rebuilding enzymes by chemical approaches, including immobilization and chemicalmodification, represents a simple but effective route. Here, a class of highly stable and a...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2018.12.014

    authors: Li L,Li H,Yan B,Yu S

    更新日期:2019-02-10 00:00:00

  • Extracellular transglycosylase and glyceraldehyde-3-phosphate dehydrogenase attributed to the anti-staphylococcal activity of Lactobacillus plantarum USM8613.

    abstract::Increasing levels of antibiotic resistance in pathogens, including Staphylococcus aureus, remains a serious problem for public health, leading to the need for better alternative antimicrobial strategies. The antimicrobial proteins produced by Lactobacillus plantarum USM8613 attributed to its anti-staphylococcal activi...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2019.05.006

    authors: Ong JS,Taylor TD,Wong CB,Khoo BY,Sasidharan S,Choi SB,Ohno H,Liong MT

    更新日期:2019-07-20 00:00:00

  • Metabolic flux analysis of Escherichia coli K12 grown on 13C-labeled acetate and glucose using GC-MS and powerful flux calculation method.

    abstract::A new algorithm was developed for the estimation of the metabolic flux distribution based on GC-MS data of proteinogenic amino acids. By using a sensitive GC-MS protocol as well as by combining the global search algorithm such as the genetic algorithm with the local search algorithm such as the Levenberg-Marquardt alg...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(02)00316-4

    authors: Zhao J,Shimizu K

    更新日期:2003-03-06 00:00:00

  • Optimization of a high-cell-density polyethylenimine transfection method for rapid protein production in CHO-EBNA1 cells.

    abstract::For pre-clinical evaluation of biotherapeutic candidates, protein production by transient gene expression (TGE) in Chinese Hamster Ovary (CHO) cells offers important advantages, including the capability of rapidly and cost-effectively generating recombinant proteins that are highly similar to those produced in stable ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2018.06.307

    authors: Stuible M,Burlacu A,Perret S,Brochu D,Paul-Roc B,Baardsnes J,Loignon M,Grazzini E,Durocher Y

    更新日期:2018-09-10 00:00:00

  • Identification and analysis of the chivosazol biosynthetic gene cluster from the myxobacterial model strain Sorangium cellulosum So ce56.

    abstract::Myxobacteria belonging to the genus Sorangium are known to produce a variety of biologically active secondary metabolites. Chivosazol is a macrocyclic antibiotic active against yeast, filamentous fungi and especially against mammalian cells. The compound specifically destroys the actin skeleton of eucaryotic cells and...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2005.10.011

    authors: Perlova O,Gerth K,Kaiser O,Hans A,Müller R

    更新日期:2006-01-24 00:00:00

  • Effects of metabolic pathway gene copy numbers on the biosynthesis of (2S)-naringenin in Saccharomyces cerevisiae.

    abstract::Flavonoids have notable biological activities and have been widely used in the medicinal and chemical industries. However, single-copy integration of heterologous pathway genes limits the production of flavonoids. In this work, we designed and constructed single-step integration of multiple flavonoid (2S)-naringenin b...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2020.11.009

    authors: Li H,Gao S,Zhang S,Zeng W,Zhou J

    更新日期:2021-01-10 00:00:00

  • A game with many players: control of gdh transcription in Corynebacterium glutamicum.

    abstract::Glutamate dehydrogenase is a central enzyme connecting nitrogen and carbon metabolism via its precursors ammonium and oxoglutarate and its product glutamate. In Corynebacterium glutamicum glutamate dehydrogenase is especially important, since it is a key enzyme for the biotechnological production of the flavour enhanc...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2009.04.007

    authors: Hänssler E,Müller T,Palumbo K,Patek M,Brocker M,Krämer R,Burkovski A

    更新日期:2009-06-15 00:00:00

  • Cellulase production by Penicillium funiculosum and its application in the hydrolysis of sugar cane bagasse for second generation ethanol production by fed batch operation.

    abstract::This study aimed to produce a cellulase blend and to evaluate its application in a simultaneous saccharification and fermentation (SSF) process for second generation ethanol production from sugar cane bagasse. The sugar cane bagasse was subjected to pretreatments (diluted acid and alkaline), as for disorganizing the l...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2012.10.014

    authors: Maeda RN,Barcelos CA,Santa Anna LM,Pereira N Jr

    更新日期:2013-01-10 00:00:00

  • Complete genome sequence of Streptomyces fulvissimus.

    abstract::The complete genome sequence of Streptomyces fulvissimus (DSM 40593), consisting of a linear chromosome with a size of 7.9Mbp, is reported. Preliminary data indicates that the chromosome of S. fulvissimus contains 32 putative gene clusters involved in the biosynthesis of secondary metabolites, two of them showing very...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2013.08.013

    authors: Myronovskyi M,Tokovenko B,Manderscheid N,Petzke L,Luzhetskyy A

    更新日期:2013-10-10 00:00:00

  • In vitro molecular evolution of AL NEIBMs improved immunoglobulin (Ig) binding and antibody detection.

    abstract::AL (SpA A domain-PpL B3 domain), LD5 (PpL B3 domain-SpA D domain-PpL B3 domain-SpA D domain-PpL B3 domain, L-D-L-D-L) and LD3 (PpL B3 domain-SpA D domain-PpL B3 domain, L-D-L) are novel evolved Ig binding molecules (NEIBMs) derived from the in vitro molecular evolution of combinatorial phage libraries displaying rando...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2014.05.014

    authors: He T,Ding YY,Feng JJ,Chen QL,Zhu HM,Peng H,Rui B,Li XY,Cao MM,Pan W

    更新日期:2014-08-20 00:00:00

  • Continuous cultivation start-up control--an experimental investigation.

    abstract::A control strategy to avoid development of synchronous growth in carbohydrate limited Saccharomyces cerevisiae cultivations is proposed and experimentally investigated. The basic idea is to control the metabolic flux through the pathways by manipulating the substrate feed rate to keep the ethanol concentration at a lo...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(97)01662-3

    authors: Møller H,Jørgensen SB

    更新日期:1997-02-28 00:00:00

  • Complete genome sequence of Rufibacter tibetensis strain 1351, a radiation-resistant bacterium from Tibet plateau.

    abstract::Rufibacter tibetensis strain 1351, isolated from the soil of the Tibet plateau of China, belongs to the family of Cytophagaceae. It is a red-pigmented, gram-negative, strictly aerobic and rod-shaped bacterium and shows resistance to UV radiation. Here, we report its complete genome sequence, which can help us find the...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2015.10.015

    authors: Zhang Y,Yu C,Zhou M,Tang J,Li X,Wang Z,Li Z,Yao J,Li P,Zheng G,Chen X,Dai J

    更新日期:2015-12-20 00:00:00

  • Bacterial ghosts: non-living candidate vaccines.

    abstract::Expression of cloned PhiX174 gene E in bacteria results in lysis of bacteria. It is unique among phage lysis systems as it introduces a transmembrane tunnel structure through the cell envelope complex of Gram-negative bacteria. The resulting bacterial ghosts have intact envelope structures devoid of cytoplasmic conten...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/0168-1656(95)00123-9

    authors: Szostak MP,Hensel A,Eko FO,Klein R,Auer T,Mader H,Haslberger A,Bunka S,Wanner G,Lubitz W

    更新日期:1996-01-26 00:00:00

  • Piezophilic adaptation: a genomic point of view.

    abstract::Two-thirds of Earth's surface is covered by oceans, yet the study of this massive integrated living system is still in its infancy. Various environmental variables, such as high salinity, low and changeable nutrient availability and depth-correlated gradients of light, temperature, nutrients and pressure shape the div...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jbiotec.2006.03.038

    authors: Simonato F,Campanaro S,Lauro FM,Vezzi A,D'Angelo M,Vitulo N,Valle G,Bartlett DH

    更新日期:2006-10-20 00:00:00

  • Macroporous monolithic gels, cryogels, with immobilized phages from phage-display library as a new platform for fast development of affinity adsorbent capable of target capture from crude feeds.

    abstract::Selected phage clones expressing a peptide with high binding affinity for recombinant human lactoferrin or von Willebrand factor (vWF) were covalently coupled to macroporous poly(dimethylacrylamide) monolithic column. Large pore size (10-100 microm) of macroporous poly(dimethylacrylamide) makes it possible to couple l...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2007.06.021

    authors: Noppe W,Plieva FM,Vanhoorelbeke K,Deckmyn H,Tuncel M,Tuncel A,Galaev IY,Mattiasson B

    更新日期:2007-09-15 00:00:00

  • Screening for improved isoprenoid biosynthesis in microorganisms.

    abstract::The production of isoprenoids in recombinant microbes for flavor & fragrance, pharmaceutical, agricultural or fuel applications is a booming research field. Isoprenoid extraction from natural resources and chemical synthesis is frequently neither ecological nor commercially profitable. However, recombinant microbes al...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jbiotec.2016.03.051

    authors: Emmerstorfer-Augustin A,Moser S,Pichler H

    更新日期:2016-10-10 00:00:00

  • Synthesis and release of the bacterial compatible solute 5-hydroxyectoine in Hansenula polymorpha.

    abstract::Ectoine and 5-hydroxyectoine belong to the family of compatible solutes which are known to mainly contribute to the adaptation of the cell to osmotic stress by mediation of a constant turgor. In addition the cell's essential functions are maintained under stress conditions like high salinity, heat or aridity stress. H...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2013.02.005

    authors: Eilert E,Kranz A,Hollenberg CP,Piontek M,Suckow M

    更新日期:2013-08-20 00:00:00

  • Complete genome sequence of Pandoraea thiooxydans DSM 25325(T), a thiosulfate-oxidizing bacterium.

    abstract::Pandoraea thiooxydans DSM 25325(T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of a sesame plant. Here, we present the first complete genome of P. thiooxydans DSM 25325(T). Several genes involved in thiosulfate oxidation and biodegradation of aromatic compounds were identified. ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2015.11.009

    authors: Yong D,Ee R,Lim YL,Yu CY,Ang GY,How KY,Tee KK,Yin WF,Chan KG

    更新日期:2016-01-10 00:00:00

  • Identification of the bacterial superoxide dismutase (SodM) as plant-inducible elicitor of an oxidative burst reaction in tobacco cell suspension cultures.

    abstract::Three of the most abundant proteins (OmpW, MopB and SodM) of the extracellular proteome of Xanthomonas campestris pv. campestris were analysed in a luminol-based oxidative burst assay to identify novel pathogen-associated molecular patterns (PAMP). Tobacco cell suspension cultures were used as a model system to monito...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2006.02.022

    authors: Watt SA,Tellström V,Patschkowski T,Niehaus K

    更新日期:2006-10-20 00:00:00

  • Setting up and modelling of overflowing fed-batch cultures of Bacillus subtilis for the production and continuous removal of lipopeptides.

    abstract::This work is related to the set-up of overflowing exponential fed-batch cultures (O-EFBC) derived from carbon limited EFBC dedicated to the production of mycosubtilin, an antifungal lipopeptide belonging to the iturin family. O-EFBC permits the continuous removal of the product from the bioreactor achieving a complete...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2007.05.025

    authors: Guez JS,Chenikher S,Cassar JP,Jacques P

    更新日期:2007-08-01 00:00:00

  • Magnetic field intensified bi-enzyme system with in situ cofactor regeneration supported by magnetic nanoparticles.

    abstract::Efficient dynamic interactions among cofactor, enzymes and substrate molecules are of primary importance for multi-step enzymatic reactions with in situ cofactor regeneration. Here we showed for the first time that the above dynamic interactions could be significantly intensified by exerting an external alternating ma...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2013.05.016

    authors: Zheng M,Su Z,Ji X,Ma G,Wang P,Zhang S

    更新日期:2013-10-20 00:00:00

  • Genome-wide analysis of the L-methionine biosynthetic pathway in Corynebacterium glutamicum by targeted gene deletion and homologous complementation.

    abstract::The genome sequence of Corynebacterium glutamicum, a gram-positive soil bacterium widely used as an amino acid producer, was analyzed by a similarity-based approach to elucidate the pathway for the biosynthesis of L-methionine. The functions of candidate ORFs were derived by gene deletion and, if necessary, by homolog...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(03)00158-5

    authors: Rückert C,Pühler A,Kalinowski J

    更新日期:2003-09-04 00:00:00

  • Draft genome sequence of Herbinix hemicellulosilytica T3/55 T, a new thermophilic cellulose degrading bacterium isolated from a thermophilic biogas reactor.

    abstract::A novel bacterial species was isolated from an industrial-scale biogas plant. The isolate Herbinix hemicellulosilytica T3/55(T) is able to degrade crystalline cellulose. Comparative 16S rRNA gene sequencing demonstrated that the isolate is closely related to environmental samples forming a hitherto unknown sub-cluster...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2015.07.022

    authors: Koeck DE,Maus I,Wibberg D,Winkler A,Zverlov VV,Liebl W,Pühler A,Schwarz WH,Schlüter A

    更新日期:2015-11-20 00:00:00