Abstract:
:Stability increments of terminal unpaired nucleotides (dangling ends) and terminal base pairs on the core helixes AUGCAU and UGCGCA are reported. Enthalpy, entropy, and free energy changes of helix formation were measured spectrophotometrically for 18 oligoribonucleotides containing the core sequences. The results indicate 3' dangling purines add more stability than 3' dangling pyrimidines. In most cases, the additional stability from a 3' dangling end on an AU base pair is less than that on a GC base pair [Freier, S.M., Burger, B.J., Alkema, D., Neilson, T., & Turner, D.H. (1985) Biochemistry 22, 6198-6206]. The sequence dependence provides a test for the importance of dangling ends for various RNA interactions. Correlations are suggested with codon context effects and with the three-dimensional structure of yeast phenylalanine transfer RNA. In the latter case, all terminal unpaired nucleotides having stability increments more favorable than -1 kcal/mol are stacked on the adjacent base pair. All terminal unpaired nucleotides having stability increments less favorable than -0.3 kcal/mol are not stacked on the adjacent base pair. In several cases, this lack of stacking is associated with a turn in the sugar-phosphate backbone. This suggests stability increments measured on oligoribonucleotides may be useful for predicting tertiary structure in large RNA molecules. Comparison of the stability increments for terminal dangling ends and base pairs, and of terminal GC and AU base pairs, indicates the free energy increment associated with forming a hydrogen bond can be about -1 kcal/mol of hydrogen bond.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Sugimoto N,Kierzek R,Turner DHdoi
10.1021/bi00388a058subject
Has Abstractpub_date
1987-07-14 00:00:00pages
4554-8issue
14eissn
0006-2960issn
1520-4995journal_volume
26pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Glutamate racemase, MurI, catalyzes the interconversion of glutamate enantiomers in a cofactor-independent fashion and provides bacteria with a source of D-Glu for use in peptidoglycan biosynthesis. The enzyme uses a "two-base" mechanism involving a deprotonation of the substrate at the alpha-position to form an anion...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi002703z
更新日期:2001-05-29 00:00:00
abstract::Band 3, the anion transport protein of human erythrocyte membranes, can be transferred from cells to liposomes and from liposomes back to cell membranes, retaining function and native orientation. After incubation with cells, sonicated phosphatidylcholine vesicles bind a transmembrane protein that comigrates with band...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00295a011
更新日期:1983-12-20 00:00:00
abstract::The conformation of two fragments derived from anti-poly(D-alanyl) antibodies, the divalent fragment (Fab')2 and the monovalent fragment Fab', was studied by small-angle X-ray scattering before and after interaction with the tetra-D-alanine amide hapten. More than 90% of the combining sites were occupied by the hapten...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00677a035
更新日期:1975-03-25 00:00:00
abstract::Heme A, an obligatory cofactor in eukaryotic cytochrome c oxidase, is produced from heme B (protoheme) via two enzymatic reactions catalyzed by heme O synthase and heme A synthase. Heme O synthase is responsible for the addition of a farnesyl moiety, while heme A synthase catalyzes the oxidation of a methyl substituen...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0203536
更新日期:2002-09-10 00:00:00
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 ortho...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00465a036
更新日期:1990-04-03 00:00:00
abstract::The ileal apical and liver basolateral bile acid transporters catalyze the Na+-dependent uptake of these amphipathic molecules in the intestine and liver. They contain nine predicted helical hydrophobic sequences (H1-H9) between the exoplasmic N-glycosylated N terminus and the cytoplasmic C terminus. Previous in vitro...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi051291x
更新日期:2005-10-25 00:00:00
abstract::3-Deoxy-d-manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the condensation of arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) to form KDO8P, a key precursor in the biosynthesis of the endotoxin of Gram-negative bacteria. Earlier studies have established that the condensation occurs with a syn addit...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi901341h
更新日期:2009-12-15 00:00:00
abstract::The lipid A disaccharide of the Escherichia coli envelope is synthesized from the two fatty acylated glucosamine derivatives UDP-N2,O3-bis[(R)-3-hydroxytetradecanoyl]-alpha-D- glucosamine (UDP-2,3-diacyl-GlcN) and N2,O3-bis[(R)-3-hydroxytetradecanoyl]-alpha-D-glucosamine 1-phosphate (2,3-diacyl-GlcN-1-P) [Ray, B. L., ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00406a017
更新日期:1988-03-22 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::The trifunctional dinuclear platinum compounds 1,2/c,c [[cis-PtCl(NH(3))(2)]mu-H(2)N(CH(2))(6)NH(2)[cis-PtCl(2)(NH(3))]](+) and 1,2/t,c [[trans-PtCl(NH(3))(2)]mu-H(2)N(CH(2))(6)NH(2)[cis-PtCl(2)(NH(3))]](+) contain a monofunctional platinum coordination sphere linked to a cis-[PtCl(2)(amine)(2)] moiety. The compounds ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi030243e
更新日期:2004-06-22 00:00:00
abstract::TAR DNA-binding protein 43 (TDP-43) has been identified as the major constituent of the proteinaceous inclusions that are characteristic of most forms of amyotrophic lateral sclerosis (ALS) and ubiquitin positive frontotemporal lobar degeneration (FTLD). Wild type TDP-43 inclusions are a pathological hallmark of >95% ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.9b00592
更新日期:2019-10-01 00:00:00
abstract::An assay was developed to study the spontaneous transfer and transbilayer movement (flip-flop) of lipid analogs labeled with the fluorescent fatty acid, 5-(5,7-dimethyl BODIPY)-1-pentanoic acid (C5-DMB-) in large unilamellar lipid vesicles comprised of 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC). The assay is base...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi970145r
更新日期:1997-07-22 00:00:00
abstract::The relative activities of 313 mutants of the gene V protein of bacteriophage f1, assayed in vivo, have been used to evaluate two approaches to predicting the effects of single amino acid substitutions on the function of a protein. First, we tested methods that only depend on the properties of the wild-type and substi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00239a022
更新日期:1991-06-25 00:00:00
abstract::Base excision repair is a major pathway for the removal of simple lesions in DNA including base damage and base loss (abasic site). Base excision repair requires the coordinated action of several repair and ancillary proteins, the impairment of which can lead to genetic instability. Using a protein-DNA cross-linking a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi050085m
更新日期:2005-08-09 00:00:00
abstract::Dihydrofolate reductase (DHFR) is often used as a model system to study the relation between protein dynamics and catalysis. We have studied a number of variants of the cold-adapted DHFR from Moritella profunda (MpDHFR), in which the catalytically important M20 and FG loops have been altered, and present a comparison ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi500508z
更新日期:2014-07-29 00:00:00
abstract::The spontaneous hydrolyses of lactic acid O-phenyl phosphate (I) and, to a lesser extent, 3-hydroxybutyric acid O-phenyl phosphate (II) have been investigated and compared with similar intramolecular and bimolecular reactions. Compared to bimolecular nucleophilic reactions, the reactivity of II is similar to other sys...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00682a025
更新日期:1975-06-03 00:00:00
abstract::The effect of anions on the stability of different functional conformations of Hb is examined through the determination of the dependence of O(2) affinity on water activity (a(w)). The control of a(w) is effected by varying the sucrose osmolal concentration in the bathing solution according to the "osmotic stress" met...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9905361
更新日期:1999-09-07 00:00:00
abstract::We have prepared the following cadmium-113-substituted derivatives of bovine superoxide dismutase and recorded the nuclear magnetic resonance (NMR) spectrum of the cadmium: 2Cd(II), in which Cd(II) is presumed to bind to the Zn(II) site and the copper site is unoccupied, and 2Cd(II)--2Cu(I), which is analogous to the ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00544a031
更新日期:1980-02-05 00:00:00
abstract::Two peptides designed for drug delivery were generated by the combination of a signal peptide with a nuclear localization sequence and are shown to facilitate the cellular internalization of small molecules which are covalently linked to these peptides. In order to understand the mechanism of internalization, the conf...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9708491
更新日期:1997-09-16 00:00:00
abstract::Nucleic acid aptamers are rapidly gaining prominence as diagnostic tools, targeting reagents, and potential therapeutics. To extend the use of aptamers into the biochemical analysis of protein interactions on the surface of live cells, we converted an enzymatically generated RNA aptamer into a photo-cross-linkable aff...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi8004208
更新日期:2008-11-18 00:00:00
abstract::Glu58 is known to participate in phosphodiester transesterification catalyzed by the enzyme RNase T1. For Glu58 RNase T1, an altered mechanism has been proposed in which His40 replaces Glu58 as the base catalyst [Steyaert, J., Hallenga, K., Wyns, L., & Stanssens, P. (1990) Biochemistry 29, 9064-9072]. Glu58Ala Rnase T...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00173a006
更新日期:1994-02-22 00:00:00
abstract::In this study, we prepared several shortened and full-length insulin analogues with substitutions at position B26. We compared the binding affinities of the analogues for rat adipose membranes with their ability to lower the plasma glucose level in nondiabetic Wistar rats in vivo after subcutaneous administration, and...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi702086w
更新日期:2008-05-27 00:00:00
abstract::To reduce ribonucleotides to deoxyribonucleotides, the manganese-bound form of class Ib ribonucleotide reductase (RNR) must be activated via a pathway that involves redox protein(s). The reduced flavoprotein NrdI is an important protein in this pathway, as it reduces dioxygen to superoxide. Superoxide then reacts with...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.6b00699
更新日期:2016-09-13 00:00:00
abstract::The reduction of substrates catalyzed by nitrogenase utilizes an electron transfer (ET) chain comprised of three metalloclusters distributed between the two component proteins, designated as the Fe protein and the MoFe protein. The flow of electrons through these three metalloclusters involves ET from the [4Fe-4S] clu...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi201003a
更新日期:2011-11-01 00:00:00
abstract::The qualitative and quantitative features of mutagenesis by two DNA adducts of carcinogenic alkylating agents, O6-methylguanine (m6G) and O4-methylthymine (m4T), were examined in vivo. The deoxyhexanucleotides 5'-GCTAGC-3' and 5'-GCTAGC-3' were synthesized, where the underlined bases are the positions of m4T or m6G, r...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00242a031
更新日期:1991-07-16 00:00:00
abstract::Three electrochromic difference spectra induced by the deposition of (1) a negative charge on the primary quinone acceptor, Q(A), (2) a positive charge on (or near) Tyr161 of the D1 subunit (Y(Z)), and (3) a positive charge on the manganese cluster were determined at room temperature in photosystem II (PSII) core part...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9513057
更新日期:1996-03-05 00:00:00
abstract::Despite the high degree of sequence similarity in their basic-helix-loop-helix (BHLH) domains, MASH-1 and MyoD are involved in different biological processes. In order to define possible differences between the DNA binding specificities of these two proteins, we investigated the DNA binding properties of MASH-1 by cir...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00035a008
更新日期:1995-09-05 00:00:00
abstract::In this study, we investigated the role of ubiquitination in the disposition of the inactivated O6-methylguanine-DNA methyltransferase (MGMT) protein in human (HT-29 and CEM) and murine (ts85) tumor cells. Using a combination of immunoprecipitation and immunoblotting techniques with antibodies against ubiquitin and MG...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9518205
更新日期:1996-01-30 00:00:00
abstract::SHP-1, a protein tyrosine phosphatase containing two tandem SH2 domains, is autoinhibited at rest by its N-terminal SH2 (N-SH2) domain. Relief from autoinhibition and a subsequent 10-60-fold increase in V(max) have been observed upon N-SH2 domain engagement by a specific phosphotyrosyl ligand or upon deletion of the S...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9611873
更新日期:1997-03-11 00:00:00
abstract::The equilibrium binding of influenza virus hemagglutinin to derivatives of its cell-surface ligand, sialic acid, was measured by nuclear magnetic resonance (NMR) spectroscopy. Binding was quantified by observing perturbations of sialic acid resonances in the presence of protein. The major perturbation observed was a c...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00447a018
更新日期:1989-10-17 00:00:00