Kinetic study of DNA condensation by cationic peptides used in nonviral gene therapy: analogy of DNA condensation to protein folding.

Abstract:

:Synthetic nonviral vector systems are attractive because of their apparent simplicity of preparation and use. However, there are many barriers to success at the moment, including the formulation of uniform and reproducible particles of transfection competent, condensed nucleic acids such as plasmid DNA (pDNA). For this reason, we have been studying the kinetics of cationic peptide-mediated pDNA condensation and the reverse process following peptide dissociation by stopped-flow techniques under conditions commonly used to prepare synthetic nonviral vector systems. We observe that the process of pDNA condensation and the reverse process of pDNA expansion appear to be equivalent to protein folding and unfolding, respectively. We also observe chaotic behavior at low peptide/pDNA ratios that becomes more uniform at higher ratios suggesting that with suboptimal ratios, pDNA is condensing in a multitude of conformations, each representing different stages of hydrophobic collapse in the search for the thermodynamically most stable (i.e., the fully condensed pDNA molecule). At higher ratios, peptide/pDNA complexes formed appear to be increasingly irreversible consistent with the formation of kinetically and/or thermodynamically stable, condensed pDNA molecules. Such stable states could create problems for the successful transcription of pDNA post delivery to cells.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Tecle M,Preuss M,Miller AD

doi

10.1021/bi034325e

subject

Has Abstract

pub_date

2003-09-09 00:00:00

pages

10343-7

issue

35

eissn

0006-2960

issn

1520-4995

journal_volume

42

pub_type

杂志文章
  • Spectroscopic Investigation of Cysteamine Dioxygenase.

    abstract::Thiol dioxygenases are mononuclear non-heme FeII-dependent metalloenzymes that initiate the oxidative catabolism of thiol-containing substrates to their respective sulfinates. Cysteine dioxygenase (CDO), the best characterized mammalian thiol dioxygenase, contains a three-histidine (3-His) coordination environment rat...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.0c00267

    authors: Fernandez RL,Dillon SL,Stipanuk MH,Fox BG,Brunold TC

    更新日期:2020-07-07 00:00:00

  • "Nonclassical" secretion of annexin A2 to the lumenal side of the enterocyte brush border membrane.

    abstract::Annexin A2 is a member of the annexin family of Ca(2+)-dependent lipid binding proteins and believed to be engaged in membrane transport processes in a number of cell types. In small intestinal enterocytes, we localized annexin A2 to the brush border region, where it was found mainly on the lumenal side of the microvi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0355239

    authors: Danielsen EM,van Deurs B,Hansen GH

    更新日期:2003-12-16 00:00:00

  • Kinetics of hepatic cytochrome P-450 reduction: correlation with spin state of the ferric heme.

    abstract::The reduction kinetics of cytochrome P-450 are known to be biphasic, with a rapid initial phase and a slower subsequent phase, both of which appear linear in semilogarithmic plots. The present report demonstrates that these biphasic reduction kinetics can be described in terms of a preequilibrium between high- and low...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00535a034

    authors: Backes WL,Sligar SG,Schenkman JB

    更新日期:1982-03-16 00:00:00

  • Escherichia coli phosphoenolpyruvate dependent phosphotransferase system. Copurification of HPr and alpha 1-6 glucan.

    abstract::A rapid, high-yield procedure has been developed for the purification of HPr from the Escherichia coli phosphoenolpyruvate dependent phosphotransferase system. During this procedure, the protein copurifies with a 2500-dalton homopolysaccharide which we have identified as alpha 1-6 glucan. The results of steady-state k...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00581a013

    authors: Dooijewaard G,Roossien FF,Robillard GT

    更新日期:1979-07-10 00:00:00

  • Lipid mobility and order in bovine rod outer segment disk membranes. A spin-label study of lipid-protein interactions.

    abstract::Lipid-protein interactions in bovine rod outer segment disk membranes have been studied by using a series of eight stearic acid spin-label probes which were labeled at different carbon atom positions in the chain. In randomly oriented membrane dispersions, the electron spin resonance (ESR) spectra of the C-8, C-9, C-1...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00375a005

    authors: Pates RD,Marsh D

    更新日期:1987-01-13 00:00:00

  • Purification and characterization of a novel growth factor from human breast cancer cells.

    abstract::We have purified and characterized a novel 30-kDa glycoprotein (gp30) with TGF alpha-like properties secreted from the estrogen receptor negative breast cancer cell line MDA-MB-231. This factor was immunoprecipitated by an anti-TGF alpha polyclonal antibody and also had TGF alpha-like biological activity, as assayed b...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00147a018

    authors: Lupu R,Wellstein A,Sheridan J,Ennis BW,Zugmaier G,Katz D,Lippman ME,Dickson RB

    更新日期:1992-08-18 00:00:00

  • Gene structure of cytochrome P-450(M-1) specifically expressed in male rat liver.

    abstract::Cytochrome P-450(M-1) [P-450(M-1)] is specifically expressed in adult male rat liver [Yoshioka, H., Morohashi, K., Sogawa, K., Miyata, T., Kawajiri, K., Hirose, T., Inayama, S., Fujii-Kuriyama, Y., & Omura, T. (1987) J. Biol. Chem. 262, 1706-1711]. Isolation and analysis of the gene for P-450(M-1) revealed that the co...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00399a039

    authors: Morishima N,Yoshioka H,Higashi Y,Sogawa K,Fujii-Kuriyama Y

    更新日期:1987-12-15 00:00:00

  • Ligand-specific binding and activation of the human adenosine A(2B) receptor.

    abstract::Adenosine A(2B) receptors, which play a role in inflammation and cancer, are of considerable interest as novel drug targets. To gain deeper insights into ligand binding and receptor activation, we exchanged amino acids predicted to be close to the binding pocket. The alanine mutants were stably expressed in CHO cells ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi3012065

    authors: Thimm D,Schiedel AC,Sherbiny FF,Hinz S,Hochheiser K,Bertarelli DC,Maass A,Müller CE

    更新日期:2013-01-29 00:00:00

  • tRNA discrimination at the binding step by a class II aminoacyl-tRNA synthetase.

    abstract::Aminoacyl-tRNA synthetases preserve the fidelity of decoding genetic information by accurately joining amino acids to their cognate transfer RNAs. Here, tRNA discrimination at the level of binding by Escherichia coli histidyl-tRNA synthetase is addressed by filter binding, analytical ultracentrifugation, and iodine fo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi991182g

    authors: Bovee ML,Yan W,Sproat BS,Francklyn CS

    更新日期:1999-10-12 00:00:00

  • Differential modulation of P-glycoprotein transport by protein kinase inhibition.

    abstract::Previous studies of P-glycoprotein have demonstrated that its function can be modulated by phosphorylation. In the present study, inhibition of protein kinase C with calphostin C or stauroporine or prolonged treatment with the phorbol ester TPA decreased phosphorylation of P-glycoprotein, and impaired transport of vin...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00086a022

    authors: Bates SE,Lee JS,Dickstein B,Spolyar M,Fojo AT

    更新日期:1993-09-07 00:00:00

  • Effect of flap modifications on human FEN1 cleavage.

    abstract::The flap endonuclease, FEN1, plays a critical role in DNA replication and repair. Human FEN1 exhibits both a 5' to 3' exonucleolytic and a structure-specific endonucleolytic activity. On primer-template substrates containing an unannealed 5'-tail, or flap structure, FEN1 employs a unique mechanism to cleave at the poi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi991321u

    authors: Bornarth CJ,Ranalli TA,Henricksen LA,Wahl AF,Bambara RA

    更新日期:1999-10-05 00:00:00

  • Control of the integral membrane proton pump, bacteriorhodopsin, by purple membrane lipids of Halobacterium halobium.

    abstract::Brief exposure of purple membrane (PM) to dilute Triton X-100 eliminates the actinic light effect on the relative amounts of fast M (Mf) and slow M (Ms) intermediates and alters the character and kinetics of the photocycle, without destroying the native BR trimers (Mukhopadhyay et al., 1994). Particular membrane lipid...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi960738m

    authors: Mukhopadhyay AK,Dracheva S,Bose S,Hendler RW

    更新日期:1996-07-16 00:00:00

  • Contribution of intra- and intermolecular hydrogen bonds to the conformational stability of human lysozyme(,).

    abstract::In globular proteins, there are intermolecular hydrogen bonds between protein and water molecules, and between water molecules, which are bound with the proteins, in addition to intramolecular hydrogen bonds. To estimate the contribution of these hydrogen bonds to the conformational stability of a protein, the thermod...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9910169

    authors: Takano K,Yamagata Y,Funahashi J,Hioki Y,Kuramitsu S,Yutani K

    更新日期:1999-09-28 00:00:00

  • Measuring the strength of side-chain hydrogen bonds in peptide helices: the Gln.Asp (i, i + 4) interaction.

    abstract::Whether hydrogen bonds between side chains are energetically significant in proteins and peptides has been controversial. A method is given here for measuring these interactions in peptide helices by comparing the helix contents of peptides with 1, 2, or 3 interactions. Results are given for the glutamine--aspartate (...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00041a001

    authors: Huyghues-Despointes BM,Klingler TM,Baldwin RL

    更新日期:1995-10-17 00:00:00

  • Characterization of hemopexin and its interaction with heme by differential scanning calorimetry and circular dichroism.

    abstract::Hemopexin is a plasma glycoprotein that has two structural domains (I and II) and binds and transports heme particularly to liver cells. Differential scanning calorimetry (DSC) studies show that hemopexin is largely stabilized by heme, which binds exclusively to domain I. The melting temperature (Tm) of heme-hemopexin...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00079a018

    authors: Wu ML,Morgan WT

    更新日期:1993-07-20 00:00:00

  • Novel mechanistic class of fatty acid amide hydrolase inhibitors with remarkable selectivity.

    abstract::Fatty acid amide hydrolase (FAAH) is an integral membrane enzyme that degrades the fatty acid amide family of signaling lipids, including the endocannabinoid anandamide. Genetic or pharmacological inactivation of FAAH leads to analgesic, anti-inflammatory, anxiolytic, and antidepressant phenotypes in rodents without s...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi701378g

    authors: Ahn K,Johnson DS,Fitzgerald LR,Liimatta M,Arendse A,Stevenson T,Lund ET,Nugent RA,Nomanbhoy TK,Alexander JP,Cravatt BF

    更新日期:2007-11-13 00:00:00

  • Allosteric models for multimeric proteins: oxygen-linked effector binding in hemocyanin.

    abstract::In many crustaceans, changing concentrations of several low molecular weight compounds modulates hemocyanin oxygen binding, resulting in lower or higher oxygen affinities of the pigment. The nonphysiological effector caffeine and the physiological modulator urate, the latter accumulating in the hemolymph of the lobste...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi050507s

    authors: Menze MA,Hellmann N,Decker H,Grieshaber MK

    更新日期:2005-08-02 00:00:00

  • The carboxy terminus of sodium and potassium ion transporting ATPase is located on the cytoplasmic surface of the membrane.

    abstract::The positions, with respect to the plasma membrane, of lysine 905, contained in the peptide QRKIVE, and of lysine 1012, contained in the carboxy-terminal peptide, RPGGWVEKETYY, of ovine Na+/K(+)-transporting ATPase have been reported to be cytoplasmic and extracytoplasmic, respectively [Bayer, R. (1990) Biochemistry 2...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00062a012

    authors: Thibault D

    更新日期:1993-03-23 00:00:00

  • Site specific combinations of stabilizing and destabilizing amino acid replacements in yeast cytochrome c: in vivo and in vitro effects.

    abstract::Oligonucleotide-directed mutagenesis in vivo was used to create destabilizing site specific changes at position 6 in iso-1-cytochrome c in Saccharomyces cerevisiae. These changes were made in combination with the stabilizing N52I substitution. The resulting proteins showed that a variety of forces and interactions are...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00021a023

    authors: Linske-O'Connell LI,Sherman F,McLendon G

    更新日期:1995-05-30 00:00:00

  • Mutational analysis reveals a single binding interface between RhoA and its effector, PRK1.

    abstract::Protein kinase C-related kinases (PRKs) are serine/threonine kinases that are members of the protein kinase C superfamily and can be activated by binding to members of the Rho family of small G proteins via a Rho binding motif known as an HR1 domain. The PRKs contain three tandem HR1 domains at their N-termini. The st...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi200039u

    authors: Hutchinson CL,Lowe PN,McLaughlin SH,Mott HR,Owen D

    更新日期:2011-04-12 00:00:00

  • Molecular basis of reduced albumin synthesis in Morris hepatoma 7777.

    abstract::The level of albumin mRNA in the normal Buffalo rat liver and Morris hepatoma 7777 was compared by molecular hybridization with albumin complementary DNA (cDNA) and translational assays. Albumin mRNA was found to be 10% of the total rat liver poly(A)-containing RNA population but reduced approximately fourfold in the ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00608a028

    authors: Tse TP,Morris HP,Taylor JM

    更新日期:1978-07-25 00:00:00

  • Conformation and reactivity changes induced by N-methylkirromycin (aurodox) in elongation factor Tu.

    abstract::Kirromycin and related antibiotics inhibit protein synthesis in bacteria by acting on elongation factor Tu (EF-Tu). We have studied the effects of N-methylkirromycin (aurodox) on some molecular properties of this protein. The binding of the antibiotic causes a dramatic variation in the protein fluorescence emission sp...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00443a046

    authors: Balestrieri C,Giovane A,Quagliuolo L,Servillo L,Chinali G

    更新日期:1989-08-22 00:00:00

  • A monoclonal antibody against brain calmodulin-dependent protein kinase type II detects putative conformational changes induced by Ca2+-calmodulin.

    abstract::A mouse monoclonal IgG1 antibody has been generated against the soluble form of the calmodulin-dependent protein kinase type II. This antibody recognizes both the soluble and cytoskeletal forms of the enzyme, requiring Ca2+ (EC50 = 20 microM) for the interaction. Other divalent cations such as Zn2+, Mn2+, Cd2+, Co2+, ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00417a060

    authors: LeVine H 3rd,Su JL,Sahyoun NE

    更新日期:1988-08-23 00:00:00

  • Threonine 41 in beta-catenin serves as a key phosphorylation relay residue in beta-catenin degradation.

    abstract::Beta-catenin phosphorylation at serine 45 (Ser45), threonine 41 (Thr41), Ser37, and Ser33 is critical for beta-catenin degradation, and regulation of beta-catenin phosphorylation is a central part of the canonical Wnt signaling pathway. Beta-catenin mutations at Ser45, Thr41, Ser37, and Ser33 perturb beta-catenin degr...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0601149

    authors: Wu G,He X

    更新日期:2006-04-25 00:00:00

  • X-ray and EPR Characterization of the Auxiliary Fe-S Clusters in the Radical SAM Enzyme PqqE.

    abstract::The Radical SAM (RS) enzyme PqqE catalyzes the first step in the biosynthesis of the bacterial cofactor pyrroloquinoline quinone, forming a new carbon-carbon bond between two side chains within the ribosomally synthesized peptide substrate PqqA. In addition to the active site RS 4Fe-4S cluster, PqqE is predicted to ha...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b01097

    authors: Barr I,Stich TA,Gizzi AS,Grove TL,Bonanno JB,Latham JA,Chung T,Wilmot CM,Britt RD,Almo SC,Klinman JP

    更新日期:2018-02-27 00:00:00

  • Specific inhibition of expression of a human collagen gene (COL1A1) with modified antisense oligonucleotides. The most effective target sites are clustered in double-stranded regions of the predicted secondary structure for the mRNA.

    abstract::A series of antisense oligonucleotides (ASOs) were synthesized and tested to define the best target sites within an RNA transcript of collagen for effective inhibition of expression. The test system consisted of mouse NIH 3T3 fibroblasts that were stably transfected with a human minigene for procollagen I so that the ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00202a024

    authors: Laptev AV,Lu Z,Colige A,Prockop DJ

    更新日期:1994-09-13 00:00:00

  • Kinetics of the subtransition of asymmetrically substituted phosphatidylcholines.

    abstract::The thermodynamics and kinetics of the subtransition L epsilon----P beta of sonicated unilamellar vesicles of 1-myristoyl-2-stearoylphosphatidylcholine (1M-2S-PC) and of 1-stearoyl-2-myristoylphosphatidylcholine (1S-2M-PC) were studied by equilibrium cooling curves and temperature-jump relaxation spectrometry with an ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00313a009

    authors: Tümmler B,Herrmann U,Maass G,Eibl H

    更新日期:1984-08-28 00:00:00

  • 13C NMR studies of methylene and methine carbons of substrate bound to a 280,000-dalton protein, porphobilinogen synthase.

    abstract::13C NMR has been used to observe the equilibrium complex of [5,5-2H,5-13C]-5-aminolevulinate [( 5,5-2H,5-13C]ALA) bound to porphobilinogen (PBG) synthase (5-aminolevulinate dehydratase), a 280,000-dalton protein. [5,5-2H,5-13C]ALA (chemical shift 46.9 ppm in D2O) was prepared from [5-13C]ALA through enolization in deu...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00412a039

    authors: Jaffe EK,Markham GD

    更新日期:1988-06-14 00:00:00

  • We FRET so You Don't Have To: New Models of the Lipoprotein Lipase Dimer.

    abstract::Lipoprotein lipase (LPL) is a dimeric enzyme that is responsible for clearing triglyceride-rich lipoproteins from the blood. Although LPL plays a key role in cardiovascular health, an experimentally derived three-dimensional structure has not been determined. Such a structure would aid in understanding mutations in LP...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b01009

    authors: Hayne CK,Yumerefendi H,Cao L,Gauer JW,Lafferty MJ,Kuhlman B,Erie DA,Neher SB

    更新日期:2018-01-16 00:00:00

  • Inhibition of rabbit globin mRNA translation by sequence-specific oligodeoxyribonucleotides.

    abstract::Oligodeoxyribonucleotides 8-12 nucleotides in length whose sequences are complementary to the 5' end, the initiation codon regions, or the coding regions of rabbit globin mRNA were tested for their ability to inhibit translation in a rabbit reticulocyte lysate and in a wheat germ extract. The oligomers interact specif...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00343a015

    authors: Blake KR,Murakami A,Miller PS

    更新日期:1985-10-22 00:00:00