Abstract:
:It is well-known, but little understood, that the nucleotide sequences between phased A(4-6)-tracts (at 10-11 bp intervals) have only a slight effect on overall curvature. To explore this phenomenon, we have examined the gel-migration properties of sequences containing both A-tracts as well as G-tracts (i.e., sequences of the form G(n)C(m) or C(n)G(m), n + m > 4) in various relative positioning. We show that the composite bend of these sequences depends on their relative arrangement. When G-tracts are placed between two A-tracts, such that both tracts are repeated in phase to themselves (e.g., G(5)A(6)G(5)A(5)), or adjacent to the 3'-side of A-tracts (e.g., A(6)G(5)N(10)), they have minimal influence on the extent of bending of the composite sequence. When G-tracts are placed one helical repeat away from A-tracts (e.g., G(5)N(5)A(6)N(6)), or are adjacent only to the 5'-side of A-tracts (e.g., G(5)A(6)N(10)) their influence on the composite bend is larger. The differential behavior of AG- versus GA-tracts means that A-tracts influence their flanking sequences in a polar manner. Whereas they suppress, or make constant, the intrinsic bending characteristics of any sequence placed immediately 3' to them (and hence by definition any sequence placed between two phased A-tracts), sequences adjoining them on their 5'-side are free to modulate the overall curvature. We interpret these results as evidence for the dominant nature of the unique and nonuniform structure adopted by tracts of four adenines or more. The effects of A-tracts extend at least five base pairs into the adjoining 3' region. This is further evidence for the complexity of DNA structure and the inadequacy of simple nearest-neighbor models to explain all its manifestations.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Merling A,Sagaydakova N,Haran TEdoi
10.1021/bi020662wsubject
Has Abstractpub_date
2003-05-06 00:00:00pages
4978-84issue
17eissn
0006-2960issn
1520-4995journal_volume
42pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Plants employ a variety of light, oxygen, voltage (LOV) domain photoreceptors to regulate diverse aspects of growth and development. The Zeitlupe (ZTL), Flavin-Kelch-Fbox-1 (FKF1), and LOV-Kelch-Protein-2 (LKP2) proteins dictate measurement of the day length, flowering time, and regulation of the circadian clock by bl...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi401027n
更新日期:2013-10-08 00:00:00
abstract::Previous work has described the novel ability to modulate in vitro the activity of restriction endonuclease NaeI from Nocardia aerocoligenes by using cleavable DNA and spermidine [Conrad & Topal (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 9707-9711]. In this paper we report the results of a study of 49 type II restrictio...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00223a035
更新日期:1991-03-05 00:00:00
abstract::The structure of the copper site in oxidized and reduced Rhus vernicifera stellacyanin has been studied by X-ray absorption (XAFS) spectroscopy at different pH values. Data for the oxidized protein are consistent with the fourth ligand being an O- or N-donating ligand rather than a cysteine from the disulfide bridge. ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00001a026
更新日期:1995-01-10 00:00:00
abstract::Room temperature phosphorescence techniques were used to study the structural and dynamic features of the tryptophan residues in bovine alpha-crystallin. Upon excitation at 290 nm, the characteristic signature of tryptophan phosphorescence was observed with an emission maximum at 442 +/- 2 nm. The phosphorescence inte...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00439a027
更新日期:1989-06-27 00:00:00
abstract::The PEGylated hemoglobin (Hb) has been evaluated as a potential blood substitute. In an attempt to understand the autoxidation of the PEGylated Hb, we have studied the autoxidation of the PEGylated Hb site-specifically modified at Cys-93(beta) or at Val-1(beta). PEGylation of Hb at Cys-93(beta) perturbed the heme envi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi800906z
更新日期:2008-10-14 00:00:00
abstract::We have obtained a quantitative description of villin-nucleated actin polymerization in physiological salt by determining the concentrations of free villin (V), villin-actin monomer (VA), villin-actin dimer (VA2), and villin-actin oligomer (VAn). Over a range of actin-villin ratios from 0.1 to 20 we determined the con...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00383a019
更新日期:1987-05-05 00:00:00
abstract::The cellular site of formation, Galpha-coupling preference, and agonist regulation of mu-delta opioid receptor (OR) heterooligomers were studied. Bioluminescence resonance energy transfer (BRET) showed that mu-deltaOR heterooligomers, composed of preformed mu and delta homooligomers, interacted constitutively in the e...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi701436w
更新日期:2007-11-13 00:00:00
abstract::Human hemoglobin produced in the Escherichia coli coexpression system of Hernan et al. [(1992) Biochemistry 31, 8619-8628] has been transformed into a functionally homogeneous protein whose properties closely approximate those of normal hemoglobin A. Both of the alpha and beta chains of this hemoglobin contain a valin...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi981986g
更新日期:1999-01-19 00:00:00
abstract::The alpha-helix formed by the amino acid residues 9-19 of the B-chain of insulin is involved in the stabilization of its three-dimensional structure. We have shown that modification at positions B9, B10, B12, and B16 results in analogues possessing biological activities ranging from ca. 0.2% to ca. 500% relative to th...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00061a022
更新日期:1993-03-16 00:00:00
abstract::West Nile virus (WNV) is a mosquito-borne flavivirus with a rapidly expanding global distribution. Infection can cause severe neurological disease and fatality in humans. Efforts are ongoing to develop antiviral drugs that inhibit the WNV protease, a viral enzyme required for polyprotein processing. Unfortunately, lit...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi400782w
更新日期:2013-10-01 00:00:00
abstract::A new strategy to form stable and sequence-specific triple helical DNA structures at mixed purine/pyrimidine sequences using a combination of four C-glycosides (TRIPsides) has been described [Li et al. (2003) J. Am. Chem. Soc. 125, 2084]. The partial realization of the approach is demonstrated by incorporating two of ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi035648d
更新日期:2004-02-17 00:00:00
abstract::The DeltaG degrees (N)(-)(D) value obtained from extrapolation to zero denaturant concentration by the linear extrapolation method (LEM) is commonly interpreted to represent the Gibbs energy difference between native (N) and denatured (D) ensembles at the limit of zero denaturant concentration. For DeltaG degrees (N)(...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi001071d
更新日期:2000-12-12 00:00:00
abstract::The nucleotide binding site of the uncoupling protein (UCP) from brown adipose tissue was mapped by photoaffinity labeling with 2-azidoadenosine 5'-triphosphate (2-azido-ATP) and by affinity labeling with 3'-O-(5-fluoro-2,4-dinitrophenyl)adenosine 5'-triphosphate (FDNP-ATP). Both analogs bind with high affinity and sp...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00158a017
更新日期:1992-11-03 00:00:00
abstract::Calmodulin (CaM) is composed of two EF-hand domains tethered by a flexible linker. Upon Ca2+-binding, a fragment of CaM encompassing EF-hands 2 and 3 (CaM2/3; residues 46-113) folds into a structure remarkably similar to the N- and C-domains of CaM. In this study, we demonstrate that Ca2+-ligated CaM2/3 can also bind ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi700265j
更新日期:2007-07-24 00:00:00
abstract::The effects of various ginsenosides on calmodulin-dependent phosphodiesterase isozymes have been investigated. Ginsenosides were found to be potent inhibitors of bovine heart calmodulin-dependent phosphodiesterase and the 60-kDa isozyme of bovine brain calmodulin-dependent phosphodiesterase but not of the 63-kDa isozy...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00070a001
更新日期:1993-05-18 00:00:00
abstract::Monomeric sarcosine oxidase (MSOX) binds the L-proline zwitterion (pKa = 10.6). The reactive substrate anion is generated by ionization of the ES complex (pKa = 8.0). Tyr317 was mutated to Phe to determine whether this step might involve proton transfer to an active site base. The mutation does not eliminate the ioniz...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi051898d
更新日期:2005-12-27 00:00:00
abstract::We have synthesized a series of N-propylamino-substituted benzazepinones (NPSBs) as specific probes for the benzothiazepinone (BTZ) binding domain of muscle L-type calcium channels (LTCCs). NPSBs were identified which possess high affinity for the channel after purification. We synthesized a fluorescent NPSB, DMBODIPY...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00010a039
更新日期:1995-03-14 00:00:00
abstract::The repeating units of mouse, rat, and alpha-monkey satellites have been cloned. All three show properties that are characteristic of curved DNA: (i) their migration in polyacrylamide gels is slower than predicted from their sequences, and (ii) they appear as curved molecules when visualized by electron microscopy. Al...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00461a019
更新日期:1990-03-06 00:00:00
abstract::Introduction of specific structural probes into substrate binding sites of Escherichia coli glutamine synthetase is now possible. Various analogues of ATP substituted with an amino or sulfhydryl moiety at the 6- or 8-position of the purine ring have been found to substitute for ATP in the autoinactivation reaction of ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00349a020
更新日期:1986-01-14 00:00:00
abstract::The kinetic and equilibrium CO binding properties of hemoglobin (Hb) M Iwate (alpha2 87 His leads to Tyr beta2) have been investigated. The results show that the alpha(Met) beta2 (CO) tetramer of this protein has a low affinity for CO, as indicated by the stopped-flow and flash-photolysis kinetic, as well as the CO bi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00669a022
更新日期:1976-11-30 00:00:00
abstract::Carbonic anhydrase V (CA V) is a mitochondrial enzyme that catalyzes the hydration of CO2 to produce bicarbonate and a proton. The catalytic properties of wild-type murine CA V suggest the presence of a proton shuttle residue having pKa = 9.2, the role of which is to transfer a proton from zinc-bound water to solution...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9608018
更新日期:1996-09-10 00:00:00
abstract::In order to gain insight into the structure of human parathyroid hormone (hPTH), four fragments [hPTH(1-34), hPTH(18-48), hPTH(28-48), and hPTH(53-84)], which cover all regions of the intact hormone, have been investigated by CD and NMR spectroscopy in combination with distance geometry, and restrained molecular dynam...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00173a010
更新日期:1994-02-22 00:00:00
abstract::Hydroxyl radical induced formation of a DNA-protein cross-link involving thymine and tyrosine in nucleohistone is described. Hydroxyl radicals were generated in N2O-saturated aqueous solution by ionizing radiation. Samples of nucleohistone were hydrolyzed with HCl and trimethylsilylated. Analysis of irradiated samples...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00434a071
更新日期:1989-04-18 00:00:00
abstract::Activation of the zymogen form of a serine protease is associated with a conformational change that follows proteolysis at a specific site. Tissue-type plasminogen activator (t-PA) is homologous to mammalian serine proteases and contains an apparent activation cleavage site at arginine-275. To clarify the functional c...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00376a002
更新日期:1987-01-27 00:00:00
abstract::A heparin-induced conformational change is required to convert antithrombin from a slow to a fast inhibitor of factor Xa. It has been proposed [van Boeckel et al. (1994) Nat. Struct. Biol. 1, 423-425] that the reactive center residue P14 is inserted into beta-sheet A in native antithrombin and is displaced from the be...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9604643
更新日期:1996-07-02 00:00:00
abstract::Fluorescent derivatives of short oligonucleotides of defined sequence were prepared by the incorporation of 5-(propylamino)uridine via current phosphoramidite chemistry, followed by derivatization of the propylamine function with mansyl chloride. These oligomers, annealed to complementary oligomers, yielded short dupl...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00437a014
更新日期:1989-05-30 00:00:00
abstract::35S-labeled derivatives of the insecticides nodulisporic acid and ivermectin were synthesized and demonstrated to bind with high affinity to a population of receptors in Drosophila head membranes that were previously shown to be associated with a glutamate-gated chloride channel. Nodulisporic acid binding was modeled ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi015920o
更新日期:2002-05-21 00:00:00
abstract::Previously, we have demonstrated physical and functional interactions of the voltage-gated potassium channel Kv2.1 with the plasma membrane protein components of the exocytotic SNARE complex, syntaxin 1A, and the t-SNARE, syntaxin 1A/SNAP-25, complex. Importantly, the physical interaction of Kv2.1 with syntaxin was sh...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi800512p
更新日期:2008-08-12 00:00:00
abstract::The local environment of the transmembrane and C-terminal domain of M13 major coat protein was probed by site-directed ESR spin labeling when the protein was introduced into three membrane-mimicking systems, DOPC vesicles, sodium cholate micelles, and SDS micelles. For this purpose, we have inserted unique cysteine re...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi961770j
更新日期:1996-12-03 00:00:00
abstract::We have measured the temperature dependence of the oxygen-binding isotherms of human and bovine hemoglobin at pH 9.0 in 0.1 M borate buffer. In both hemoglobins the ionization of the Bohr protons is finished at this pH; therefore, their heat does not interfere with the measurements. Two sets of curves have been obtain...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00227a006
更新日期:1991-04-02 00:00:00