当前位置： SCI文献检索 > BIOCHEMISTRY期刊下所有文献 > Imaging of kinked configurations of DNA molecules undergoing orthogonal field alternating gel electrophoresis by fluorescence microscopy.

Imaging of kinked configurations of DNA molecules undergoing orthogonal field alternating gel electrophoresis by fluorescence microscopy.

Abstract：

:The dynamics of individual DNA molecules undergoing orthogonal field alternating gel electrophoresis (OFAGE) have been studied by use of T2 DNA molecules labeled with a dye and visualized with a fluorescence microscope. The mechanism of reorientation used by a molecule to align itself in the direction of the new orthogonal field depends on the degree of extension of the chain immediately before the application of this field. The formation of kinks is promoted when time is allowed between the application of the two orthogonal fields so that the molecule attains a partially relaxed configuration. In this case, the chain appears bunched up in domains moving along the contour of the molecule. These regions are found to be the locations where the kinks are formed upon application of the second field perpendicular to the chain. The formation of kinks provides a significant retardation of the reorientation of the molecules, relative to molecules that do not form kinks, and appears to play an important role in the fractionation attained with OFAGE. A classification of various reorientation mechanisms observed in molecules that form kinks is presented.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Gurrieri S,Rizzarelli E,Beach D,Bustamante C

doi

10.1021/bi00465a036

subject

Has Abstract

pub_date

1990-04-03 00:00:00

pages

3396-401

issue

13

eissn

0006-2960

issn

1520-4995

journal_volume

29

pub_type

杂志文章

相关文献

BIOCHEMISTRY文献大全
  • γ-Synuclein: seeding of α-synuclein aggregation and transmission between cells.

    abstract：:Protein misfolding and aggregation is a ubiquitous phenomenon associated with a wide range of diseases. The synuclein family comprises three small naturally unfolded proteins implicated in neurodegenerative diseases and some forms of cancer. α-Synuclein is a soluble protein that forms toxic inclusions associated with ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi300478w

    authors： Surgucheva I,Sharov VS,Surguchov A

    更新日期：2012-06-12 00:00:00

  • Crystallographic structures of ribonuclease S variants with nonpolar substitution at position 13: packing and cavities.

    abstract：:Seven hydrophobic residues ranging in size from glycine to phenylalanine have been substituted for the wild-type methionine residue at position 13 in a 15-residue truncated version (S15) of S-peptide, the small component of ribonuclease S. Complexes of both S-15 and the seven variants with S-protein yielded isomorphou...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00164a005

    authors： Varadarajan R,Richards FM

    更新日期：1992-12-15 00:00:00

  • Glutaminyl cyclases display significant catalytic proficiency for glutamyl substrates.

    abstract：:N-Terminal glutaminyl and glutamyl residues of peptides and proteins tend to form pyroglutamic acid (pGlu) by intramolecular cylization. The rate constants for spontaneous cyclization of glutamine (10(-6) s(-1)) and glutamic acid (10(-9) s(-1)) in aqueous solution differ by approximately 3 orders of magnitude at pH 6....

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi9018835

    authors： Seifert F,Schulz K,Koch B,Manhart S,Demuth HU,Schilling S

    更新日期：2009-12-22 00:00:00

  • 111Cd NMR studies of the domain specificity of Ag+ and Cu+ binding to metallothionein.

    abstract：:Metal displacement reactions of Cd7MT with Ag+ or Cu+ and interprotein metal exchange reactions between Cd7MT and Ag12MT or Cu12MT were studied by 111Cd NMR. Titration of 111Cd7MT with Ag+ indicates that Ag+ binds preferentially to the beta-domain of the protein to form the metal hybrid species, (Cd4)alpha(Ag6)beta MT...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi961401n

    authors： Li H,Otvos JD

    更新日期：1996-11-05 00:00:00

  • Peptide cross-linking to calmodulin: attachment of [Tyr8]substance P.

    abstract：:Ultraviolet irradiation of calmodulin in the presence of calcium results in either the intramolecular cross-linking of Tyr99 and Tyr138 [Malencik, D.A., & Anderson, S.R. (1986) Biochemistry 25, 709] or, when [Tyr8]substance P is bound, the generation of peptide-calmodulin adducts. The latter consist of two chromatogra...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00403a016

    authors： Malencik DA,Anderson SR

    更新日期：1988-02-09 00:00:00

  • Incorporation of an Unnatural Amino Acid as a Domain-Specific Fluorescence Probe in a Two-Domain Protein.

    abstract：:The biophysical analysis of multidomain proteins often is difficult because of overlapping signals from the individual domains. Previously, the fluorescent unnatural amino acid p-cyanophenylalanine has been used to study the folding of small single-domain proteins. Here we extend its use to a two-domain protein to sel...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.6b00898

    authors： Ries LK,Schmid FX,Schmidpeter PA

    更新日期：2016-12-13 00:00:00

  • Rapid plasmenylethanolamine-selective fusion of membrane bilayers catalyzed by an isoform of glyceraldehyde-3-phosphate dehydrogenase: discrimination between glycolytic and fusogenic roles of individual isoforms.

    abstract：:Recently we demonstrated that the unique stereoelectronic relationships inherent in the structure of plasmenylethanolamine facilitate membrane fusion, and we postulated the existence of a membrane fusion protein which could exploit the propensity of plasmenylethanolamine molecular species to adapt an inverted hexagona...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00038a013

    authors： Glaser PE,Gross RW

    更新日期：1995-09-26 00:00:00

  • Mechanism-based inhibitors for the inactivation of the bacterial phosphotriesterase.

    abstract：:1-Bromovinyl (I), Z-2-bromovinyl (II), 1,2-dibromoethyl (III), and a series of 4-(halomethyl)-2-nitrophenyl (IVa-c) diethyl phosphate esters were examined as substrates and mechanism-based inhibitors for the bacterial phosphotriesterase. All of these compounds were found to act as substrates for the enzyme. Inhibitor ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi970680r

    authors： Hong SB,Mullins LS,Shim H,Raushel FM

    更新日期：1997-07-22 00:00:00

  • Effects of temperature and viscosity on R67 dihydrofolate reductase catalysis.

    abstract：:R67 dihydrofolate reductase (DHFR) is a novel homotetrameric protein that possesses 222 symmetry and a single, voluminous active site pore. This symmetry poses numerous limitations on catalysis; for example, two dihydrofolate (DHF) molecules or two NADPH molecules, or one substrate plus one cofactor can bind. Only the...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi052504l

    authors： Chopra S,Lynch R,Kim SH,Jackson M,Howell EE

    更新日期：2006-05-30 00:00:00

  • Product dependence of deuterium isotope effects in enzyme-catalyzed reactions.

    abstract：:Theory for enzyme-catalyzed reactions is developed for the dependence on product concentration of deuterium isotope effects on V and V/K. Generally, a product that decreases the off-rate for a second product to zero causes the isotope effect on V/K to decrease to DKeq and that on V to decrease to a value between 1 and...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00058a013

    authors： Cook PF,Yoon MY,Hara S,McClure GD Jr

    更新日期：1993-02-23 00:00:00

  • Analyzing the Folding and Binding Steps of an Intrinsically Disordered Protein by Protein Engineering.

    abstract：:Intrinsically disordered proteins (IDPs) are functionally active despite lacking a well-defined three-dimensional structure. Such proteins often undergo a disorder-to-order transition, or induced folding, when binding to their specific physiological partner. Because of cooperativity, the folding and binding steps typi...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.7b00350

    authors： Bonetti D,Troilo F,Toto A,Brunori M,Longhi S,Gianni S

    更新日期：2017-07-25 00:00:00

  • Electrostatic Constituents of the Interaction of Cardiolipin with Site A of Cytochrome c.

    abstract：:Cytochrome c binds to cardiolipin (CL) on the inner mitochondrial membrane during the initial stages of apoptosis where it oxidizes CL, promoting its release into the cytoplasm where it initiates apoptosis. Previous work has identified interaction sites on cytochrome c involved in the cytochrome c-CL interaction. The ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.8b00704

    authors： Elmer-Dixon MM,Bowler BE

    更新日期：2018-10-02 00:00:00

  • Timing of electron and proton transfer in the ba(3) cytochrome c oxidase from Thermus thermophilus.

    abstract：:Heme-copper oxidases are membrane-bound proteins that catalyze the reduction of O(2) to H(2)O, a highly exergonic reaction. Part of the free energy of this reaction is used for pumping of protons across the membrane. The ba(3) oxidase from Thermus thermophilus presumably uses a single proton pathway for the transfer o...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi300132t

    authors： von Ballmoos C,Lachmann P,Gennis RB,Ädelroth P,Brzezinski P

    更新日期：2012-06-05 00:00:00

  • Relevance of partially structured states in the non-classical secretion of acidic fibroblast growth factor.

    abstract：:Acidic fibroblast growth factor (aFGF) is a signal peptide-less protein that is secreted into the extracellular compartment as part of a multiprotein release complex, consisting of aFGF, S100A13 (a calcium binding protein), and a 40 kDa (p40) form of synaptotagmin (Syt1), a protein that participates in the docking of ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi7002586

    authors： Rajalingam D,Graziani I,Prudovsky I,Yu C,Kumar TK

    更新日期：2007-08-14 00:00:00

  • Role of the PufX protein in photosynthetic growth of Rhodobacter sphaeroides. 2. PufX is required for efficient ubiquinone/ubiquinol exchange between the reaction center QB site and the cytochrome bc1 complex.

    abstract：:The PufX membrane protein is essential for photosynthetic growth of Rhodobacter sphaeroides because it is required for multiple-turnover electron transfer under anaerobic conditions [see accompanying article; Barz, W. P., Francia, F., Venturoli, G., Melandri, B. A., Verméglio, A., & Oesterhelt, D. (1995) Biochemistry ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00046a033

    authors： Barz WP,Verméglio A,Francia F,Venturoli G,Melandri BA,Oesterhelt D

    更新日期：1995-11-21 00:00:00

  • Mannitol-specific carrier protein from the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system can be extracted as a dimer from the membrane.

    abstract：:The association state of the mannitol-specific enzyme II (EIIMtl) has been studied both in the purified form and embedded in the cytoplasmic membrane. Membrane fragments obtained from mannitol-grown Escherichia coli catalyze the phosphoenolpyruvate- (PEP) dependent phosphorylation of both glucose and mannitol; thus th...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00319a003

    authors： Roossien FF,Robillard GT

    更新日期：1984-11-20 00:00:00

  • The linker between SH2 and kinase domains positively regulates catalysis of the Tec family kinases.

    abstract：:Tec family nonreceptor tyrosine kinases are key immunological enzymes that control processes that range from T and B cell development to reorganization of the actin cytoskeleton. The full-length Tec kinases have been resistant to crystallization. This lack of structural data and the paucity of in vitro biochemical dat...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi602512e

    authors： Joseph RE,Min L,Andreotti AH

    更新日期：2007-05-08 00:00:00

  • Lipid-free structure and stability of apolipoprotein A-I: probing the central region by mutation.

    abstract：:To probe the structure and stability of the central region of lipid-free apolipoprotein (apo) A-I (residues 123-165), we studied the effects of four mutations made in this region on the conformation, stability, dimyristoylphosphatidylcholine (DMPC) binding kinetics, and size of discoidal reconstituted high-density lip...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi025807d

    authors： Gorshkova IN,Liu T,Zannis VI,Atkinson D

    更新日期：2002-08-20 00:00:00

  • Oxy intermediates of homoprotocatechuate 2,3-dioxygenase: facile electron transfer between substrates.

    abstract：:Substrates homoprotocatechuate (HPCA) and O(2) bind to the Fe(II) of homoprotocatechuate 2,3-dioxygenase (FeHPCD) in adjacent coordination sites. Transfer of an electron(s) from HPCA to O(2) via the iron is proposed to activate the substrates for reaction with each other to initiate aromatic ring cleavage. Here, rapid...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi201436n

    authors： Mbughuni MM,Chakrabarti M,Hayden JA,Meier KK,Dalluge JJ,Hendrich MP,Münck E,Lipscomb JD

    更新日期：2011-11-29 00:00:00

  • A fluorescent mutant of the NM domain of the yeast prion Sup35 provides insight into fibril formation and stability.

    abstract：:The Sup35 protein of Saccharomyces cerevisiae forms a prion that generates the [PSI(+)] phenotype. Its NM region governs prion status, forming self-seeding amyloid fibers in vivo and in vitro. A tryptophan mutant of Sup35 (NM(F117W)) was used to probe its aggregation. Four indicators of aggregation, Trp 117 maximum em...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi9000276

    authors： Palhano FL,Rocha CB,Bernardino A,Weissmuller G,Masuda CA,Montero-Lomelí M,Gomes AM,Chien P,Fernandes PM,Foguel D

    更新日期：2009-07-28 00:00:00

  • Structure and function in rhodopsin: effects of disulfide cross-links in the cytoplasmic face of rhodopsin on transducin activation and phosphorylation by rhodopsin kinase.

    abstract：:Six rhodopsin mutants containing disulfide cross-links between different cytoplasmic regions were prepared: disulfide bond 1, between Cys65 (interhelical loop I-II) and Cys316 (end of helix VII); disulfide bond 2, between Cys246 (end of helix VI) and Cys312 (end of helix VII); disulfide bond 3, between Cys139 (end of ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi9912443

    authors： Cai K,Klein-Seetharaman J,Hwa J,Hubbell WL,Khorana HG

    更新日期：1999-09-28 00:00:00

  • Single-turnover kinetics of helicase-catalyzed DNA unwinding monitored continuously by fluorescence energy transfer.

    abstract：:We describe a fluorescence assay that can be used to monitor helicase-catalyzed unwinding of duplex DNA continuously in real time. The assay is based on the observation that fluorescence resonance energy transfer (FRET) occurs between donor (fluorescein) and acceptor (hexachlorofluorescein) fluorophores that are in cl...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00251a044

    authors： Bjornson KP,Amaratunga M,Moore KJ,Lohman TM

    更新日期：1994-11-29 00:00:00

  • Influence of the calcium-induced gel phase on the behavior of small molecules in phosphatidylserine and phosphatidylserine-phosphatidylcholine multilamellar vesicles.

    abstract：:The behavior of fluorescent and spin-label probes is examined in several fluid and gel phospholipid phases, with particular focus on the Ca2+-induced gel phase in phosphatidylserine (PS). These probes have behavior characteristic of the type of probe and of the type of lipid environment. Anthroyloxy- and doxyl-labeled...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00380a039

    authors： Florine KI,Feigenson GW

    更新日期：1987-03-24 00:00:00

  • Solution structure of a designed spirocyclic helical ligand binding at a two-base bulge site in DNA.

    abstract：:The solution structure of the complex formed between an oligodeoxynucleotide containing a two-base bulge (5'-CCATCGTCTACCTTTGGTAGGATGG) and SCA-alpha2, a designed spirocyclic helical molecule, has been elucidated. SCA-alpha2, a close mimic of the metabolite, NCSi-gb, of the DNA bulge-specific enediyne antibiotic neoca...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi602599d

    authors： Zhang N,Lin Y,Xiao Z,Jones GB,Goldberg IH

    更新日期：2007-04-24 00:00:00

  • Domain organization and functional analysis of type IIS restriction endonuclease Eco31I.

    abstract：:Type IIS restriction endonuclease Eco31I harbors a single HNH active site and cleaves both DNA strands close to its recognition sequence, 5'-GGTCTC(1/5). A two-domain organization of Eco31I was determined by limited proteolysis. Analysis of proteolytic fragments revealed that the N-terminal domain of Eco31I is respons...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi800660u

    authors： Jakubauskas A,Sasnauskas G,Giedriene J,Janulaitis A

    更新日期：2008-08-19 00:00:00

  • Erythrocyte band 3 protein: evidence for multiple membrane-crossing segments in the 17 000-dalton chymotryptic fragment.

    abstract：:We have investigated the topology of the band 3 protein of the human erythrocyte membrane by a combination of chemical labeling and proteolytic cleavage. The N-terminal third of the membrane-bound domain of band 3 is a 17 000-dalton chymotryptic fragment that is known to traverse the membrane an odd number of times. A...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00321a024

    authors： Jennings ML,Nicknish JS

    更新日期：1984-12-18 00:00:00

  • Aspartate receptors of Escherichia coli and Salmonella typhimurium bind ligand with negative and half-of-the-sites cooperativity.

    abstract：:The aspartate receptors of Escherichia coli and Salmonella typhimurium which mediate chemotactic responsiveness to aspartate have 79% amino acid sequence identity but exhibited apparently quite different aspartate binding plots. The Scatchard plot of the Salmonella receptor was concave upward whereas the E. coli recep...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00169a002

    authors： Biemann HP,Koshland DE Jr

    更新日期：1994-01-25 00:00:00

  • Medium-Throughput Screen of Microbially Produced Serotonin via a G-Protein-Coupled Receptor-Based Sensor.

    abstract：:Chemical biosensors, for which chemical detection triggers a fluorescent signal, have the potential to accelerate the screening of noncolorimetric chemicals produced by microbes, enabling the high-throughput engineering of enzymes and metabolic pathways. Here, we engineer a G-protein-coupled receptor (GPCR)-based sens...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.7b00605

    authors： Ehrenworth AM,Claiborne T,Peralta-Yahya P

    更新日期：2017-10-17 00:00:00

  • Relationship between folding and function in a sequence-specific miniature DNA-binding protein.

    abstract：:Previously, we have described a miniature protein-based approach to the design of molecules that bind DNA or protein surfaces with high affinity and specificity. In this approach, the small, well-folded protein avian pancreatic polypeptide acts as a scaffold to present and stabilize an alpha-helical or PPII-helical re...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi050121h

    authors： Yang L,Schepartz A

    更新日期：2005-05-24 00:00:00

  • Calcium regulation of calmodulin binding to and dissociation from the myo1c regulatory domain.

    abstract：:Myo1c is an unconventional myosin involved in cell signaling and membrane dynamics. Calcium binding to the regulatory-domain-associated calmodulin affects myo1c motor properties, but the kinetic details of this regulation are not fully understood. We performed actin gliding assays, ATPase measurements, fluorescence sp...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi700894h

    authors： Manceva S,Lin T,Pham H,Lewis JH,Goldman YE,Ostap EM

    更新日期：2007-10-23 00:00:00