Nucleotides In Solution Research Articles

Cross-linking study on skeletal muscle actin: properties of suberimidate-treated actin.

Cross-linking experiments were performed on muscle skeletal actin, using imidoesters of various chain lengths. Chemical analyses on all products except one (derived from succinimidate) show evidence of the presence of intramolecular cross-links in the molecule. The detailed properties of suberimidate-treated actin (SA) are as follows: SA contains nearly 1 mol of intramolecular cross-link per mol of actin and less than 15% of intermolecularly cross-linked products. Even at a low salt concentration, SA is polymeric, exchanges slowly its bound nucleotide with free nucleotides in solution, and shows an F-actin-type CD spectrum. Electron micrographs of SA reveal that SA exists actually as fibrous polymers in solutions of low ionic strength, although the fibers seem to be less rigid than those at high salt concentration. The F-form of SA at a high salt concentration is indistinguishable from intact F-actin. SA can bind heavy meromyosin and activate the ATPase of heavy meromyosin as observed for intact F-actin. Tropomyosin binds SA only at a high salt concentration. These results show that SA possesses the properties of F-actin even in media of low salt concentration, which are favorable for depolymerization of F-actin. Thus, we may infer that the conformation of SA is frozen in the F-state of actin by the introduction of intramolecular cross-links in the protein.

Fluorescent nucleotides: Application in a fluorescence immune assay

A fluorescence immune assay designed to measure anti-nucleotide antibody activity is described based on the synthesis of a fluorescent nucleotide probe possessing a low fluorescence quantum yield when free in aqueous solution (neutral pH). The fluorophore, AmNS (1-naphthylamine-5-sulfonic acid), was covalently conjugated to various phosphate derivatives of nucleotides through carbodiimide activation to form the fluorescent probe. The quantum yield (Φ) of the fluorescent nucleotide in solution (neutral pH) was ~ 0.025 based on an excitation maximum of 320 nm and an emission maximum of 460 nm. Anti-nucleotide antibodies elicited in rabbits and mice served as standard immunological reagents in development of the fluorescence assay. Upon binding of an AmNS-nucleotide conjugate with homologous anti-nucleotide antibodies, the fluorescence quantum yield of the conjugate was significantly enhanced (12–35 x). Fluorescence enhancement was not obtained upon incubation of the fluorescent probe with normal Ig, non-immune rabbit sera and murine ascites fluid, or bovine and rabbit serum albumin. Nucleotide inhibition reactions were quantitatively measured in the fluorescence assay. Nucleotide binding results obtained with the fluorescence assay were correlated with a modified radioimmune Farr assay.

The relationship between proton–proton NMR coupling constants and substituent electronegativities. II—conformational analysis of the sugar ring in nucleosides and nucleotides in solution using a generalized Karplus equation

AbstractThe relationship between vicinal NMR proton–proton coupling constants and the pseudorotational properties of the sugar ring in nucleosides and nucleotides is reinvestigated. Compared with our earlier study several important improvements are introduced: first, a new empirical generalization of the classical Karplus equation is utilized, which allows an accurate correction for the effects of electronegativity and orientation of substituents on 3J(HH); second, empirical correlations between the parameters governing the conformation of β‐D‐furanosides (taken from an analysis of 178 crystal structures) were used to define proton–proton torsion angles as a function of the pseudorotation parameters P and Φm; and, third an iterative least‐squares computer program was devised to obtain the best fit of the conformational parameters to the experimental coupling constants. NMR data for the sugar ring in the following compounds were taken from the literature and analysed: 3′,5′‐cyclic nucleotides, a base‐stacked ribonucleotide, 2′‐anhydroarabinonucleosides, α‐D‐2′,2‐O‐cyclouridine, 2′‐ and 3′‐aminosubstituted ribonucleosides, 2′‐ and 3′‐deoxyribonucleosides. The present results confirm that the conformational properties found in the solid state are, on the whole, preserved in solution.

ChemInform Abstract: BACKBONE CONFORMATIONAL PROPERTIES OF NUCLEOTIDES IN SOLUTION DETERMINED BY PROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY

Chemischer InformationsdienstVolume 10, Issue 41 Natural Products ChemInform Abstract: BACKBONE CONFORMATIONAL PROPERTIES OF NUCLEOTIDES IN SOLUTION DETERMINED BY PROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY D. B. DAVIES, D. B. DAVIESSearch for more papers by this author D. B. DAVIES, D. B. DAVIESSearch for more papers by this author First published: October 9, 1979 https://doi.org/10.1002/chin.197941331Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article. Volume10, Issue41October 9, 1979 RelatedInformation

Backbone conformational properties of nucleotides in solution determined by 1H nuclear magnetic resonance spectroscopy

The backbone conformational properties of adjacent O(5′)–C(5′) and C(5′)–C(4′) bonds of nucleotides in aqueous solution have been investigated from available n.m.r. results for monomers, dimers, trimers, and polynucleotides. Results for monoribonucleotides show that the backbone conformation depends, primarily, on the glycosidic bond conformation and, to a lesser extent, on the sugar ring conformation of the monomer. On the other hand, the backbone conformational properties of oligoribonucleotides (dimer and trimer) depend, primarily, on the sugar ring conformation (i.e. base-stacking on the Altona model) and, to a much lesser extent, on the glycosidic bond conformation. The implications of this nucleotide conformational model for polymer results are discussed.

Pyrimidine Nucleosides in Solution

Proton magnetic resonance (PMR) spectra of 45 nucleoside and nucleotide derivatives of uracil, thymine, cytosine, 5‐methylcytosine, and other substituted pyrimidines in water or dimethyl sulfoxide solutions have been analysed in order to correlate structure variations with molecular conformations and to gain insight into the nature of intramolecular forces which are responsible for the ‘rigidity’ of the molecules. Irrespective of the structure of pyrimidine base and the absolute chemical shift values (δ) the C(6)‐H and, to a lesser degree, the C(5)‐H and C(5)‐CH3 resonances are shifted downfield by very similar amounts (Δδ) in the regular nucleosides or in the presence of charged or polar C‐4′ substituents. In detail, the following conformation‐determining effects are seen.1. Ribose vs 2‐deoxyribose substitution of a pyrimidine makes little difference for the chemical environment of base hydrogens but an intact pentofuranose ring (4′‐O) and the exocyclic 5′‐OH group are essential for a nucleoside to assume a specific conformation.2. Profound shielding or deshielding of H‐6 by exocyclic nitrate, halogen, hydroxyl, phosphate, and carboxylate substituents indicates preference for the anti and gauche, gauche conformation ranges in all compounds except in the case of C‐6 substitution.3. Halogen atoms and the hydroxyl group (Δδ∼ 0.30–0.40 ppm) interact with pyrimidine bases by induced polarisation of the C(5)=C(6) double bond, phosphate anions (Δδ∼ 0.50 ppm) interact by the electrostatic attraction mechanism previously described, and in nucleoside 5′‐carboxylates (Δδ > 0.90 ppm) a hydrogen bond between −COO− and H‐6 is formed.4. The deshielding effects caused by a 5′‐OH group and monoanionic 5′‐phosphate are similar (Δδ∼ 0.35–0.45 ppm), supporting the view that intramolecular rigidity of nucleosides and the nucleotide unit is not fundamentally different.This systematic survey, together with our previous studies of adenosine derivatives, provides a rationale for why the majority of both pyrimidine and purine nucleosides and nucleotides in solution exhibit closely comparable conformations, which in turn explain the group specificity of certain key enzymes in nucleic acid metabolism.

Tightly bound nucleotides of the energy-transducing ATPase, and their role in oxidative phosphorylation. II. The beef heart mitochondrial system

1. Beef heart mitochondrial ATPase, in both the membrane-bound and isolated form, contains tightly bound ATP and ADP. Each mol of ATPase contains about 2.2 mol ATP and 1.3 mol ADP. 2. In the absence of ATPase activity, these nucleotides exchange only slowly with nucleotides in solution. The exchange rate is increased during coupled ATPase activity, but not when the ATPase is uncoupled. 3. Oligomycin and dicyclohexylcarbodiimide inhibit exchange of the bound nucleotides, as does the ATPase inhibitor protein, although in each case some residual exchange occurs. Aurovertin, although inhibiting phosphorylation, does not inhibit the exchange. This is discussed in terms of the reversibility of these inhibitors. 4. The stimulation of exchange seen during coupled ATPase activity requires energisation of the ATPase molecule. Using the exchange reaction as a probe of energisation, it is deduced that energy can be transferred between different ATPase molecules. 5. It is proposed that coupled ATPase activity and phosphorylation in submitochondrial particles involve the tight nucleotide binding sites and the (weak) ATPase site, while uncoupled ATPase activity involves only the weak site.

An improved T1 relaxation time determination of the syn-anti equilibrium of nucleotides in solution

An improved T1 relaxation time determination of the syn-anti equilibrium of nucleotides in solution

Studies of energy transport in heart cells. Mitochondrial isoenzyme of creatine phosphokinase: kinetic properties and regulatory action of Mg2+ ions.

1. The kinetic properties of mitochondrial creatine phosphokinase (Km for all substrates and maximal rates of the forward and reverse reaction) have been studied. Since (a) Km value for MgADP- (0.05 mM) and creatine phosphate (0.5 mM) are significantly lower than Km for MgATP2- (0.7 mM) and creatine (5.0 mM) and (b) maximal rate of the reverse reaction (creatine phosphate + ADP leads to ATP + creatine) equal to 3.5 mumol times min-1 times mg-1 is essentially higher than maximal rate of the forward reaction (0.8 mumol times min-1 times mg-1), ATP synthesis from ADP and creatine phosphate is kinetically preferable over the forward reaction. 2. A possible regulatory role of Mg2+ ions in the creatine phosphokinase reaction has been tested. It has been shown that in the presence of all substrates and products of the reaction the ratio of the rates of forward and reverse reactions can be effectively regulated by the concentration of Mg2+ ions. At limited Mg2+ concentrations creatine phosphate is preferably synthesized while at high Mg2+ concentrations (more ATP in the reaction medium) ATP synthesis takes place. 3. The kinetic (mathematical) model of the mitochondrial creatine phosphokinase reaction has been developed. This model accounts for the existence of a variety of molecular forms of adenine nucleotides in solution and the formation of their complexes with magnesium. It is based on the assumption that the mitochondrial creatine phosphokinase reactions mechanism is analogous to that for soluble isoenzymes. 4. The dependence of the overall rate of the creatine phosphokinase reaction on the concentration of total Mg2+ ions calculated from the kinetic model quantitatively correlates with the experimentally determined dependence through a wide range of substrates (ATP, ADP, creatine and creatine phosphate) concentration. The analysis of the kinetic model demonstrates that the observed regulatory effect of Mg2+ on the overall reaction rate can be expained by (a) the sigmoidal variation in the concentration of the MgADP- complex resulting from the competition between ATP AND ADP for Mg2+ and (b) the high affinity of the enzyme to MgADP-. 5. The results predicted by the model for the behavior of mitochondrial creatine phosphokinase under conditions of oxidative phosphorylation point to an intimate functional interaction of mitochondrial creatine phosphokinase and ATP-ADP translocase.

Optical rotatory dispersion and circular dichroism of silver(I):Polyribonucleotide complexes

AbstractOptical rotatory dispersion (ORD) and circular dichroism (CD) spectra of single‐ and multistranded polyribonucleotides undergo extensive changes on binding of the silver ion. These changes are consistent with the proposition that Ag(I) binds to the heterocyclic bases and not to the phosphate groups of polynucleotides. ORD and CD of silver complexes of poly(A)·poly(U) and double‐helical rice dwarf viral RNA display negative Cotton effects when there is more than one Ag(I) per two nucleotide residues in solution. These observations suggest a significant distortion of the double‐helical conformation as a result of Ag(I) binding. Silver(I) binding sites of pyrimidine polynucleotides are apparently saturated when there is one Ag(I) per two nucleotide residues and those of purine polynucleotides at one Ag(I) per nucleotide in solution. These data are consistent with the supposition that some Ag(I) binding sites exist on the pyrimidine ring and additional sites on the imidazole ring of polynucleotides. The sedimentation coefficient of poly(A) increases by severalfold when one Ag(I) is present per nucleotide residue. Silver(I) may introduce intra‐ and interstrand cross‐links (through bidentate chelates) in single‐stranded polynucleotides, resulting in structures with high sedimentation coefficients. Among the polynucleotides studied, poly(U) was an exception. Silver(I) did not affect the optical properties (absorbance, ORD, and CD) of poly(U) at neutral pH.

ChemInform Abstract: A NUCLEAR MAGNETIC RESONANCE STUDY OF NUCLEOSIDE CONFORMATION IN SOLUTION, THE EFFECT OF STRUCTURE AND CONFORMATION ON THE MAGNETIC NONEQUIVALENCE OF THE 5′‐METHYLENE HYDROGENS

AbstractDie NMR‐Daten von 42 Verbindungen (z.T.

A Nuclear Magnetic Resonance Study of Nucleoside Conformation in Solution. The Effect of Structure and Conformation on the Magnetic Nonequivalence of the 5′-Methylene Hydrogens

The relative chemical shift between the 5′-methylene hydrogens of a number of purine and pyrimidine nucleosides and nucleotides in solution are presented. For structurally related pyrimidine nucleosides in aqueous solution a good correlation between this relative shift and the sum of the 4′–5′ hydrogen–hydrogen vicinal coupling constants is noted. For this series of related molecules arguments are presented that the variation in the magnetic nonequivalence of this pair of hydrogens is a consequence of conformational changes about the C4′—C5′ bond. Deviations from the correlation plot are observed for purine derivatives, nucleoside monophosphates etc. and discussed in terms of the effect of the specific chemical modification upon the nucleoside conformation and upon the intrinsic chemical shift nonequivalence of the 5′-methylene hydrogens.

Determination of the preferred conformations constrained along the C-4'-C-5' and C-5'-O-5' bonds of beta-5'-nucleotides in solution. Four-bond 31P-1H coupling.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of the preferred conformations constrained along the C-4'-C-5' and C-5'-0-5' bonds of .beta.-5'-nucleotides in solution. Four-bond phosphorus-31-proton couplingRamaswamy H. Sarma, Richard J. Mynott, Donald J. Wood, and Frank E. HruskaCite this: J. Am. Chem. Soc. 1973, 95, 19, 6457–6459Publication Date (Print):September 1, 1973Publication History Published online1 May 2002Published inissue 1 September 1973https://doi.org/10.1021/ja00800a055RIGHTS & PERMISSIONSArticle Views69Altmetric-Citations72LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (368 KB) Get e-Alerts Get e-Alerts

Correction: A Structure of Pyridine Nucleotides in Solution

Correction: A Structure of Pyridine Nucleotides in Solution

A structure of pyridine nucleotides in solution

A structure of pyridine nucleotides in solution

Kinetic complexity of RNA molecules

A procedure has been developed for calculating the base sequence complexity of polyribonucleotides using RNA-DNA hybridization on membrane filters. Optimal rate temperature ( T opt) in hybridization media containing 6 × SSC (SSC is 0.15 m-NaCl, 0.015 m-sodium citrate) (pH 7.2), 50% formamide or 1.15 m-sodium acetate (pH 5), 60% formamide were determined for a variety of RNA species. The T opt in formamide were found to be unexpectedly high for all RNA species investigated. It is suggested that the high T opt are caused by increased stability of RNA-DNA hybrids in these incubation mixtures. It is demonstrated that RNA-DNA reactions with homogeneous RNA species present in excess are most easily characterized by C r t 1 2 where C r is the molar concentration of RNA nucleotides in solution and t 1 2 is the time taken to reach the 50% saturation value. Within certain limits C r t 1 2 is independent of the amount of DNA on filter disks and the degree of fragmentation of the RNA. C r t 1 2 increases linearly with the base sequence complexity of RNA molecules. Using complementary RNA derived from a balanced synthetic RNA-ΦX DNA hybrid we show that the slope of the straight linear standard curve which links C r t 1 2 to base sequence complexity is 9.3 × 10 −9 moles.sec/l. dalton for 6 × SSC, 50% formamide. In 1.15 m-sodium acetate (pH 5), 60% formamide, the slope is 2.3 × 10 −8 moles.sec/l. daltons. Applications of the kinetic standard curve for evaluation of purity and concentration of isolated messenger RNA's are discussed. We show that transfer RNA of both Escherichia coli and Xenopus laevis is made up from 30 to 40 basic nucleotide sequences distinguishable by RNA-DNA hybridization. In Xenopus there are some 6500 cistrons for tRNA and so each tRNA sequence is, on average, 160-fold reiterated. 5 s RNA of Xenopus, coded by some 9000 cistrons, and ribosomal RNA of Bacillus subtilis, rabbit and Xenopus coded by 8, 250 and 610 cistrons, respectively, each contain a single family of nucleotide sequences and are therefore highly conserved in these species.

A structure of pyridine nucleotides in solution.

Re-examination of the structure of pyridine coenzymes in solution by use of the 220-MHz high-frequency nuclear magnetic resonance spectrometer indicates that there is primarily one folded structure that is in rapid equilibrium with an open form. Reduced DPN(+) and reduced analogs of DPN(+) exist predominantly with the B side of the dihydropyridine ring folded against the adenine moiety. (The oxidized coenzymes appear to exist in the same folded structure.) Furthermore, the ribose protons undergo very little conformational change upon reduction of the pyridine ring; this observation strongly suggests a considerable similarity between the folded forms of the oxidized and reduced coenzymes. A model of the folded structure is presented.

Conformation and conformational changes of reduced diphosphospyridine nucleotide in solution.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConformation and conformational changes of reduced diphosphopyridine nucleotide in solutionDallas G. Cross and Harvey F. FisherCite this: Biochemistry 1969, 8, 3, 1147–1155Publication Date (Print):March 1, 1969Publication History Published online1 May 2002Published inissue 1 March 1969https://doi.org/10.1021/bi00831a048RIGHTS & PERMISSIONSArticle Views49Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (891 KB) Get e-Alerts Get e-Alerts