scholarly journals Kinetic and spectrophotometric studies on the renaturation of deoxyribonucleic acid

1968 ◽  
Vol 109 (4) ◽  
pp. 543-557 ◽  
Author(s):  
K. J. Thrower ◽  
A. R. Peacocke
Keyword(s):  
Ionic Strength ◽  
Rate Constant ◽  
Base Pairs ◽  
Phage Dna ◽  
Dna Strands ◽  
Entropy Of Activation ◽  
T7 Phage ◽  
Kinetics Of ◽  
Rate Controlling Step ◽  
Adenine Thymine

The kinetics of the renaturation of Escherichia coli DNA in 0·4–1·0m-sodium chloride at temperatures from 60° to 90° have been studied. The extent of renaturation was a maximum at 65° to 75° and increased with ionic strength, and the rate constant increased with both ionic strength and temperature. The energy and entropy of activation of renaturation were calculated to be 6–7kcal.mole−1 and −40cal.deg.−1mole−1 respectively. It has been shown that renaturation is a second-order process for 5hr. under most conditions. The results are consistent with a reaction in which the rate-controlling step is the diffusion together of two separated complementary DNA strands and the formation of a nucleus of base pairs between them. The kinetics of the renaturation of T7-phage DNA and Bordetella pertussis DNA have also been studied, and their rates of renaturation related quantitatively to the relative heterogeneity of the DNA samples. By analysis of the spectra of DNA at different stages during renaturation it was shown that initially the renatured DNA was rich in guanine–cytosine base pairs and non-random in base sequence, but that, as equilibrium was approached, the renatured DNA gradually resembled native DNA more closely. The rate constant for the renaturation of guanine–cytosine base pairs was slightly higher than for adenine–thymine base pairs.

scholarly journals The fidelity of replication of the three-base-pair set adenine/thymine, hypoxanthine/cytosine and 6-thiopurine/5-methyl-2-pyrimidinone with T7 DNA polymerase

2004 ◽  
Vol 381 (3) ◽  
pp. 709-717 ◽  
Author(s):  
Harry P. RAPPAPORT
Keyword(s):  
Dna Polymerase ◽  
Rate Constant ◽  
Base Pair ◽  
Apparent Rate Constant ◽  
Polymerase Activity ◽  
Exonuclease Activity ◽  
Base Pairs ◽  
Error Frequency ◽  
Steady State Kinetics ◽  
Adenine Thymine

With the goal of constructing a genetic alphabet consisting of a set of three base pairs, the fidelity of replication of the three base pairs TH (5-methyl-2-pyrimidinone)/HS (6-thiopurine; thiohypoxanthine), C/H (hypoxanthine) and T/A was evaluated using T7 DNA polymerase, a polymerase with a strong 3′→5′ exonuclease activity. An evaluation of the suitability of a new base pair for replication should include both the contribution of the fidelity of a polymerase activity and the contribution of proofreading by a 3′→5′ exonuclease activity. Using a steady-state kinetics method that included the contribution of the 3′→5′ exonuclease activity, the fidelity of replication was determined. The method determined the ratio of the apparent rate constant for the addition of a deoxynucleotide to the primer across from a template base by the polymerase activity and the rate constant for removal of the added deoxynucleotide from the primer by the 3′→5′ exonuclease activity. This ratio was designated the eni (efficiency of net incorporation). The eni of the base pair C/H was equal to or greater than the eni of T/A. The eni of the base pair TH/HS was 0.1 times that of A/T for TH in the template and 0.01 times that of A/T for HS in the template. The ratio of the eni of a mismatched deoxynucleotide to the eni of a matched deoxynucleotide was a measure of the error frequency. The error frequencies were as follows: thymine or TH opposite a template hypoxanthine, 2×10−6; HS opposite a template cytosine, <3×10−4. The remaining 24 mismatched combinations of bases gave no detectable net incorporation. Two mismatches, hypoxanthine opposite a template thymine or a template TH, showed trace incorporation in the presence of a standard dNTP complementary to the next template base. T7 DNA polymerase extended the primer beyond each of the matched base pairs of the set. The level of fidelity of replication of the three base pairs with T7 DNA polymerase suggests that they are adequate for a three-base-pair alphabet for DNA replication.

KINETICS OF THE OXIDATION OF URANIUM (IV) BY IRON (III) IN AQUEOUS SOLUTIONS OF PERCHLORIC ACID

1955 ◽  
Vol 33 (12) ◽  
pp. 1780-1791 ◽  
Author(s):  
R. H. Betts
Keyword(s):  
Electron Transfer ◽  
Ionic Strength ◽  
Aqueous Solutions ◽  
Perchloric Acid ◽  
Rate Constants ◽  
Kcal Mole ◽  
Kinetics Of Oxidation ◽  
Temperature Coefficients ◽  
Kinetics Of ◽  
Rate Controlling Step

The kinetics of oxidation of uranium (IV) by iron (III) in aqueous solutions of perchloric acid have been investigated at four temperatures between 3.1 °C. and 24.8 °C. The reaction was followed by measurement of the amount of ferrous ion formed. For the conditions (H+) = 0.1–1.0 M, ionic strength = 1.02, (FeIII) = 10−4–10−5 M, and (UIV) = 10−4–10−5 M, the observed rate law is d(Fe2+)/dt = −2d(UIV)/dt[Formula: see text]K1 and K2 are the first hydrolysis constants for Fe3+ and U4+, respectively, and K′ and K″ are pseudo rate constants. At 24.8 °C., K′ = 2.98 sec.−1, and K″ = 10.6 mole liter−1 sec−1. The corresponding temperature coefficients are ΔH′ = 22.5 kcal./mole and ΔH″ = 24.2 kcal./mole. The kinetics of the process are consistent with a mechanism which involves, as a rate-controlling step, electron transfer between hydrolyzed ions.

Kinetics of the reaction H + C2H6 → H2 + C2H5 in the temperature region of 1000 K

1984 ◽  
Vol 62 (1) ◽  
pp. 86-91 ◽  
Author(s):  
J.-R. Cao ◽  
M. H. Back
Keyword(s):  
Equilibrium Constant ◽  
Rate Constant ◽  
Temperature Region ◽  
Recent Measurement ◽  
Hydrogen Atoms ◽  
Elementary Reactions ◽  
Temperature Range ◽  
Hydrogen Molecules ◽  
Kinetics Of ◽  
Rate Controlling Step

A system for the measurement of rate constants for elementary reactions of hydrogen atoms in the temperature region of 1000 K is described. The concentration of hydrogen atoms is controlled by the equilibrium constant for dissociation of hydrogen molecules. The kinetics of the rate of conversion of ethane to ethylene in this system has been studied over the temperature range 876–1016 K. The results show that the rate-controlling step is[Formula: see text]and the value obtained for the rate constant is[Formula: see text](R = 1.987 cal mol−1 deg−1). This value is compared with values obtained from other methods over the temperature range 300–1400 K. Combination with a recent measurement of the rate constant for the reverse reaction yields an experimental value for the equilibrium constant for the reaction.

THE REACTION BETWEEN CYANATE AND HYPOCHLORITE

1956 ◽  
Vol 34 (4) ◽  
pp. 489-501 ◽  
Author(s):  
M. W. Lister
Keyword(s):  
Activation Energy ◽  
Ionic Strength ◽  
Rate Constant ◽  
Hypochlorous Acid ◽  
Effect Of Temperature ◽  
Slow Step ◽  
True Activation Energy ◽  
Rate Of Reaction ◽  
Different Temperatures ◽  
Kinetics Of

The reaction between sodium hypochlorite and potassium cyanate in the presence of sodium hydroxide has been examined. The main products are chloride, and carbonate ions and nitrogen; but, especially if much hypochlorite is present, some nitrate is formed as well. The rate of reaction is proportional to the cyanate and hypochlorite concentrations, but inversely proportional to the hydroxide concentration: the rate constant is 5.45 × 10−4 min.−1 at 65 °C, at an ionic strength of 2.2. The rate constant increases somewhat as the ionic strength rises from 1.7 to 3.5. The effect of temperature makes the apparent activation energy 25 kcal./gm-molecule. The kinetics of the reaction suggest that the slow step is really a reaction of hypochlorous acid and cyanate ions, and possible intermediate products of this reaction are suggested. Allowing for the different extent of hydrolysis of hypochlorite at different temperatures, the true activation energy is found to be 15 kcal./gm-mol., which is consistent with the observed rate of reaction.

Studies on Horseradish Peroxidase. VII. A Kinetic Study of the Oxidation of Iodide by Horseradish Peroxidase Compound II

1971 ◽  
Vol 49 (18) ◽  
pp. 3059-3063 ◽  
Author(s):  
R. Roman ◽  
H. B. Dunford ◽  
M. Evett
Keyword(s):  
Ionic Strength ◽  
Horseradish Peroxidase ◽  
Kinetic Study ◽  
Rate Constant ◽  
Ph Dependence ◽  
Order Rate Constant ◽  
Acid Dissociation ◽  
Ph Range ◽  
Compound Ii ◽  
Kinetics Of

The kinetics of the oxidation of iodide ion by horseradish peroxidase compound II have been studied as a function of pH at 25° and ionic strength of 0.11. The logarithm of the second-order rate constant decreases linearly from 2.3 × 105 to 0.1 M−1 s−1 with increasing pH over the pH range 2.7 to 9.0. The pH dependence of the reaction is explained in terms of an acid dissociation outside the pH range of the study.

The Kinetics of Reactions in and Near the Cytochrome b/f Complex of Chloroplast Thylakoids. I. Proton Deposition

1988 ◽  
Vol 15 (5) ◽  
pp. 695 ◽  
Author(s):  
AB Hope ◽  
J Liggins ◽  
DB Matthews
Keyword(s):  
Rate Constant ◽  
Bimolecular Reaction ◽  
Plastoquinone Pool ◽  
Rate Limiting Step ◽  
Fixed Concentration ◽  
Wide Range ◽  
Entropy Of Activation ◽  
Electron Donation ◽  
Rate Limiting ◽  
Kinetics Of

The kinetics of proton deposition in the intrathylakoid spaces of pea chloroplasts were measured under a wide range of conditions. With duroquinol added to reduce the plastoquinone pool, and 3-(3,4-dichlorophenyl)-1,1-dimethylurea added to inhibit photosystem II, but no ionophore present, the proton deposition, attributed to plastoquinol oxidation, was biphasic. About half the deposition had an apparent rate constant (k) of 150-200 s-1, the other half about 10 s-1. Valinomycin or nonactin (<0.1 �M) plus potassium ions made the deposition almost monophasic, with k = 140 s-1. When the state of reduction of the plastoquinone pool was varied by the addition of varied concentrations of duroquinol, in the presence of 1 �M nonactin, k for proton deposition varied from about 20 (0.01 mM duroquinol) up to a maximum of 140 s-1 (0.5 mM duroquinol). When temperature was varied between 4 and 23°C, with 1 �M nonactin, an Arrhenius plot of ln(k) for proton deposition was linear; the activation enthalpy was 67 kJ mol-1, the entropy of activation, 23 J K-1 mol-1. The data are analysed in terms of a bimolecular reaction between a varying concentration of plastoquinol and a fixed concentration of oxidised Rieske centre. The results are consistent with a rate constant, for the first electron donation by plastoquinol, of 28 s-1 (the rate-limiting step), followed by a relatively fast second electron donation to cytochrome b563 (low potential), followed by deposition of two protons. The speed of the second proton deposition is dependent on the membrane potential difference.

THE KINETICS OF THE FORMATION OF THE MONO–FLUORO COMPLEX OF IRON (III) IN AQUEOUS SOLUTION

1960 ◽  
Vol 38 (4) ◽  
pp. 567-575 ◽  
Author(s):  
D. Pouli ◽  
W. MacF. Smith
Keyword(s):  
Aqueous Solution ◽  
Ionic Strength ◽  
Aqueous Solutions ◽  
Temperature Interval ◽  
Kcal Mole ◽  
Entropy Of Activation ◽  
Fluoro Complex ◽  
Kinetics Of

The kinetics of the reactions involved in the formation of the mono–fluoro complex of iron (III) in aqueous solutions have been examined spectrophotometrically at ionic strength 0.5 and over the temperature interval 0.1 to 12.1 °C. The results are interpretable on the assumption that the following two reactions contribute significantly to the rate Fe+++ + F− = FeF++ and Fe+++ + HF = FeF++ + H+, the former having a heat of activation of 22.8 ± 2.5 kcal mole−1 and an entropy of activation of 35 ± 9 cal deg−1 mole−1, the latter having a heat of activation of 8.7 ± 0.7 kcal mole−1 and an entropy of activation of −24.5 ± 3 cal deg−1 mole−1.

Reductions by ferrocytochrome c peroxidase: 5. Kinetics of ferricyanide reduction

1995 ◽  
Vol 73 (7) ◽  
pp. 1181-1186 ◽  
Author(s):  
Eddy Cheung ◽  
Ann M. English
Keyword(s):  
Ionic Strength ◽  
Rate Constant ◽  
Heme Proteins ◽  
Amino Acid Content ◽  
Total Charge ◽  
Ferricyanide Reduction ◽  
Cross Reactions ◽  
Ferrocytochrome C ◽  
Strength Formula ◽  
Kinetics Of

The kinetics of reduction of ferricyanide by yeast ferrocytochrome c peroxidase (CPPII) were investigated as a function of ionic strength in phosphate buffers at pH 7.0 and 25 ± 1 °C. The observed bimolecular rate constant (k12) is 8.4 × 104 M−1 s−1 in 0.1 M phosphate. The dependence of the reaction rate on ionic strength indicates a change of −9 on the protein at pH 7.0, which is in good agreement with the total charge of −11 estimated for CCPII from its amino acid content. Substituting k12 at infinite ionic strength [Formula: see text] into the Marcus cross relation yields an electron self-exchange rate constant [Formula: see text] for the FeIII/FeII couple of CCP of 7.2 × 10−5 M−1 s−1. This value is over four orders of magnitude higher than that calculated for the FeIV/FeIII couple of CCP from literature data for cross-reactions with ferrocyanide at pH 7.0. Possible reasons for the large difference in the two CCP [Formula: see text] values are discussed. Literature data also allowed [Formula: see text] values for various other heme proteins to be determined from their cross-reactions with ferricyanide. The calculated rate constants vary by eight orders of magnitude, and the variation of [Formula: see text] with protein structure suggests that the redox reactivity of ferrous heme proteins towards ferricyanide is dependent on the spin state and coordination of iron, as well as on the accessibility of the heme. Keywords: cytochrome c peroxidase, ferricyanide, Marcus cross relation, electron self-exchange.

THE KINETICS OF THE CHELATION OF NICKEL (II) AND 1,10-PHENANTHROLINE

1964 ◽  
Vol 42 (4) ◽  
pp. 934-940 ◽  
Author(s):  
P. F. Barrett ◽  
W. MacF. Smith
Keyword(s):  
Ionic Strength ◽  
Rate Constant ◽  
Order Rate Constant ◽  
Second Order ◽  
Hydrogen Ion ◽  
Kinetic Behavior ◽  
Ion Concentrations ◽  
Order Rate ◽  
Kinetics Of ◽  
Limiting Values

The kinetics of the formation of the bidentate monocomplex of 1,10-phenanthroline and nickel (II) have been examined spectrophotometrically at ionic strength 0.5 over the range of temperatures 8 to 37 °C and over the range of hydrogen ion concentrations 0.01 to 0.30 molar. The kinetic behavior over the range of conditions is consistent with that found at 25 °C by Margerum, Bystroff, and Banks. The limiting values for the second-order rate constant for the reaction at high acidities have been assessed and imply associated values of ΔH≠and ΔS≠ of 9.5 kcal mol−1 and −5.3 e.u. respectively.

scholarly journals The kinetics of oxygen exchange between the sulfite ion and water

1970 ◽  
Vol 48 (13) ◽  
pp. 2035-2041 ◽  
Author(s):  
R. H. Betts ◽  
R. H. Voss
Keyword(s):  
Aqueous Solution ◽  
Ionic Strength ◽  
Rate Constant ◽  
Rate Constants ◽  
Time Rate ◽  
A Value ◽  
First Time ◽  
Kinetics Of ◽  
Sulfite Ion ◽  
Gross Rate

Oxygen of mass 18 was used as a stable tracer to measure the rate of exchange between the sulfite ion and water as a function of pH and total sulfite concentration. A value for the rate constant of hydration of SO2 in aqueous solution was determined. The gross rate constants k1 and k−1 for the overall reaction[Formula: see text]at 24.7 °C and ionic strength = 0.9 were evaluated from exchange results to be [Formula: see text]Also, for the first time, rate constants for the pyrosulfite equilibrium[Formula: see text]Were obtained[Formula: see text]at 24.7 °C and ionic strength = 0.9

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