Renaturation of bacteriophage phiX174 DNA-RNA hybrid: RNA length effect and nucleation rate constant

A one to one RNA-DNA hybrid was synthesized using bacteriophage φX174 DNA as a template for the Escherichia coli RNA polymerase system. The renaturation rate for the hybrid was found to vary as the square root of the molecular weight of the RNA. The RNA molecular weights were determined using a standardized dimethylsulfoxide, cesium sulfate equilibrium density gradient. The optimum nucleation rate constant for the renaturation of the hybrid in 0.4 m-sodium chloride was found to be 1.3 × 10⁵, as compared with to 1.7 × 10⁵ for DNA renaturation.     

Tandem pentuplication of a DNA segment in a derivative of bacteriophage P2: its use in the study of the mechanism of DNA annealing.

From a tandem duplication mutant of phage P2, triplication, quadruplication and pentuplication forms were derived. They were recognized by decreased virion heat stability resulting from the increase in DNA content, and were confirmed by electron microscope heteroduplex mapping. These forms of partially repeated DNA are quite stable in P2 because of the low level of recombination typical of this phage. Under conditions normally employed for full DNA renaturation, these high order repeat chromosomes gave often incomplete renaturation over the repeated segments. Based on current models for DNA renaturation, several predictions were made and tested. The results, although not quantitatively exhaustive, indicated that base pairing proceeding from a nucleation site was sufficiently slow to allow a second nucleation to occur with a fair probability over a length of a few thousand base pairs.     

Interaction of lysine-rich histone and DNA in chromatin structure.

The heat denaturation and renaturation curves of rat liver and ascites hepatoma (AH 108A) chromatins were measured. In these renaturation curves, there are small sigmoidal regions. These sigmoidal regions remained in redenaturation curves and were largely stable to DNAase I digestion. When the chromatins were treated stepwise with NaClO4 and lysine-rich histones were removed, the sigmoidal regions in the renaturation curves disappeared. These results suggested that the sigmoidal regions reflected the interaction of DNA and lysine-rich histones.     

Denaturation and renaturation of Penicillium chrysogenum mycophage double-stranded ribonucleic acid in tetraalkylammonium salt solutions

The base composition dependence of double-stranded ribonucleic acid (RNA) melting was studied by observing the structure and widths of melting transitions for Penicillium chrysogenum mycophage RNA as well as differences in melting temperatures of two RNAs of different base composition. Double-stranded RNA melting is independent of base compositions in 3.5 M Et4NCl and 4.6 M Me4NCl, where the melting temperatures are 25 and 92 degrees C, respectively. Double-stranded RNA renaturation rate constants are reported in Et4NCl solutions. The nucleation rate constant is about 10 times lower than that for double-stranded deoxyribonucleic acid. Analyses of renaturation kinetics results lead to the conclusion that each of the three similar but separable RNA segments of Penicillium chrysogenum mycophage is unique.     

A study of the reversibility of helix-coil transition in DNA.

The reversibility of DNA melting has been thoroughly investigated at different ionic strengths. We concentrated on those stages of the process that do not involve a complete separation of the strands of the double helix. The differential melting curves of pBR 322 DNA and a fragment of T7 phage DNA in a buffer containing 0.02M Na+ have been shown to differ substantially from the differential curves of renaturation. Electron-microscopic mapping of pBR 322 DNA at different degrees of unwinding (by a previously elaborated technique) has shown that the irreversibility of melting under real experimental conditions is connected with the stage of forming new helical regions during renaturation. In a buffer containing 0.2M Na+ the melting curves of the DNAs used (pBR322, a fragment of T7 phage DNA, a fragment of phage Lambda DNA, a fragment of phiX174 phage DNA) coincide with the renaturation curves, i.e. the process is equilibrium. We have carried out a semi-quantitative analysis of the emergence of irreversibility in the melting of a double helix. The problem of comparing theoretical and experimental melting curves is discussed.     

Kinetics of sickle hemoglobin polymerization. III. Nucleation rates determined from stochastic fluctuations in polymerization progress curves

The polymerization kinetics of sickle cell hemoglobin are found to exhibit stochastic variations when observed in very small volumes (approximately 10(-10) cm3). The distribution of progress curves has been measured at several temperatures for a 4.50 mM-hemoglobin S sample using a laser-photolysis, light-scattering technique. The progress curves at a given temperature are superimposable when translated along the time axis, showing that the variability of the kinetic progress curves results primarily from fluctuations in the time at which polymerization is initiated. The shapes of the initial part of the progress curves are well-fitted using the functional form I(t) = Io + As exp (Bt), derived from a dual nucleation model. When the distribution of the measured tenth times is broad, the rate of homogeneous nucleation can be obtained by fitting the exponential tail of the distribution. As the distribution sharpen, the rate of homogeneous nucleation can be estimated by modelling the width of the distribution function using a simple Monte-Carlo simulation of the polymerization kinetics. Using the rates of homogeneous nucleation obtained from the distributions, the rates of heterogeneous nucleation and polymer growth can be obtained from the experimental parameters As and B. The resulting nucleation rates are roughly 1000 times greater than those obtained from an analysis of bulk kinetic data. The results provide strong support for the dual-nucleation mechanism and show that the distribution of progress curves provides a powerful independent method for measuring the rate of homogeneous nucleation and thereby obtaining values for the other principal rates of the mechanism.     

A Mesoscale Model of DNA and Its Renaturation

A mesoscale model of DNA is presented (3SPN.1), extending the scheme previously developed by our group. Each nucleotide is mapped onto three interaction sites. Solvent is accounted for implicitly through a medium-effective dielectric constant and electrostatic interactions are treated at the level of Debye-Hückel theory. The force field includes a weak, solvent-induced attraction, which helps mediate the renaturation of DNA. Model parameterization is accomplished through replica exchange molecular dynamics simulations of short oligonucleotide sequences over a range of composition and chain length. The model describes the melting temperature of DNA as a function of composition as well as ionic strength, and is consistent with heat capacity profiles from experiments. The dependence of persistence length on ionic strength is also captured by the force field. The proposed model is used to examine the renaturation of DNA. It is found that a typical renaturation event occurs through a nucleation step, whereby an interplay between repulsive electrostatic interactions and colloidal-like attractions allows the system to undergo a series of rearrangements before complete molecular reassociation occurs.     

Cooperative effect of artificial chaperones and guanidinium chloride on lysozyme renaturation at high concentrations

It has been recognized that the artificial chaperone system, cetyltrimethylammonium bromide and beta-cyclodextrin, is effective for enhancing protein renaturation. In this work, we studied the effect of the artificial chaperone system and guanidinium chloride (GdmCl) on the oxidative renaturation of lysozyme at 0.21-1.05 mg/mL, and a kinetic model based on the competition between protein folding and aggregation was employed to express the renaturation process. The refolding rate constant increased, while the aggregation rate constant decreased, with increasing concentration of the artificial chaperones. With increasing GdmCl concentration (0.28-2 M), both rate constants decreased, but there existed a specific GdmCl concentration that maximized the ratio of the two rate constants and thus the renaturation yield. The results obviously indicated the cooperative effect of GdmCl and the artificial chaperones on enhancing protein renaturation.     

Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water.

Thermal unfolding curves have been measured for a series of short alanine-based peptides that contain repeating sequences and varying chain lengths. Standard helix-coil theory successfully fits the observed transition curves, even for these short peptides. The results provide values for sigma, the helix nucleation constant, delta H0, the enthalpy change on helix formation, and for s (0 degree C), the average helix propagation parameter at 0 degree C. The enthalpy change agrees with the value determined calorimetrically. The success of helix-coil theory in describing the unfolding transitions of short peptides in water indicates that helical propensities, or s values, can be determined from substitution experiments in short alanine-based peptides.     

Independence of length and temperature effects on the rate of helix formation between complementary ribopolymers

The rate of double helix formation by single stranded Poly A plus Poly U, Poly I plus Poly C, Poly G plus Poly C, and T2 DNA has been investigated as a function of both the length of the reacting strands and temperature. The length dependence of the rate is found to be independent of temperature. All of the reactions studied show a rate approximately proportional to the square root of the length of the shorter of the complementary strands. At or about 30°C below the melting temperature the ribopolymers react with about the same rate. This rate is four to five times slower than DNA renaturation rates. The effect of temperature on ribopolymer reaction rates is interpreted in terms of a steady-state model for helix propagation.     

Promotion of DNA renaturation by a non-DNA factor in crown call tumor DNA preparation.

A 5400-fold excess of tobacco crown gall tumor DNA increased the renaturation rate of $\text{Agrobacterium tumefaciens}$ DNA, whereas, the same excess of healthy plant DNA had no effect on the rate or kinetics of renaturation. Since deoxyribonuclease treatment of the tumor DNA did not remove its ability to accelerate renaturation, the tumor tissue contains a non-DNA factor that increases the rate of renaturation of $\text{A. tumefaciens}$ DNA.     

Renaturation kinetics and thermal stability of DNA in aqueous solutions of formamide and urea.

This paper reports the results of a systematic study of the effects of formamide and urea on the thermal stability and renaturation kinetics of DNA. Increasing concentrations of urea in the range 0 to 8 molar lower the Tm by 2.25 degrees C per molar, and decreases the renaturation rate by approximately 8 percent per molar. Increasing concentrations of formamide in the range from 0 to 50 percent lowers the Tm by 0.60 degrees C per percent formamide for sodium chloride concentrations ranging from 0.035M to 0.88M. At higher salt concentrations the dependence of Tm on percent formamide was found to be slightly greater. Increasing formamide concentration decreases the renaturation rate linearly by 1.1% per percent formamide such that the optimal rate in 50% formamide is 0.45 the optimal rate in an identical solution with no formamide. The effects of urea and formamide on the renaturation rates of DNA are explained by consideration of the viscosities of the solutions at the renaturation temperatures.     

Kinetics of protein subunit interactions: simulation of a polymerization overshoot

Theoretical calculations of the kinetics of a polymerization reaction have been carried out for a scheme in which there is a nucleation step that is slow relative to subsequent propagation steps. A transient maximum (overshoot) in molecular weight can be expected in such reversibly self-associating systems when polymerization is initiated suddenly. The extent of overshoot decreases with increasing initial concentration of true equilibrium is strongly dependent on the rate of nucleus formation and the rate of depolymerization when the absolute values of both are small relative to the rate of propagation.     

Multiple parameter kinetic studies of the oxidative folding of reduced lysozyme

We have compared the oxidative renaturation of reduced hen egg white lysozyme promoted by Cu(II) + O2 with that promoted by a glutathione redox buffer. The progress curves for protein fluorescence, circular dicroism, thiol oxidation, hydrodynamic volume, and enzymic activity were determined for both regeneration systems. All of these processes were more rapid in the glutathione regeneration than in the copper-catalyzed. Comparison of the two systems was carried out by normalizing the progress curves with a coordinate system where "time" is replaced by "extent of protein thiol oxidation." While similar progress curves were obtained for circular dichroism, the two systems produced distinctly different progress curves for enzymic activity, fluorescence, and gel permeation chromatographic reflection of protein hydrodynamic volume. We infer that all these differences result from differences in relative amounts and/or kind of reaction intermediates. Thus, there are substantial differences between the renaturation mechanisms of the glutathione- and the copper-promoted systems.     

Nucleation and growth of ice in deeply undercooled erythrocytes

Previous studies of the mechanism of freezing of erythrocytes in the absence of intracellular ice have been extended to define the catalytic sites responsible for promoting nucleation. The following aspects have been investigated: (1) the freeze propagation between undercooled erythrocytes, (2) the nucleation of ice in undercooled erythrocyte ghosts, and (3) the freezing behavior of undercooled hemoglobin solutions. The main findings are: (1) no cross-nucleation occurs between individual cells packed within the same emulsified water droplet; (2) the differential scanning calorimetric power-time curves of intact cells and ghosts are identical, indicating that hemoglobin does not affect ice nucleation; (3) the nucleation temperature of ice in an aqueous solution of hemoglobin (isolated from the cells) is substantially lower than that for the same solution when contained in the intact cell; (4) the threefold freeze concentration which accompanies the freezing of a 25% hemoglobin solution does not cause denaturation of the protein.     

Thermal stability and renaturation of DNA in dimethyl sulfoxide solutions: Acceleration of the renaturation rate

The thermal stability and renaturation kinetics of DNA have been studied as a function of dimethyl sulfoxide (DMSO) concentration. Increasing the concentration of DMSO lowers the melting temperature of DNA but results in an increased second-order renaturation rate. For example, in a DNA solution containing 0.20M NaCl, 0.01M Tris (pH 8.0), and 0.001M EDTA, the addition of 40% DMSO lowers the melting temperature of the DNA by 27°C and approximately doubles the optimal renaturation rate. The effect of DMSO on the renaturation rate is shown to be at least partially due to its effect on the solution dielectric constant and to be consistent with the polyelectrolyte counterion condensation theory of Manning [(1976) Biopolymers 15 , 1333–1343].     

Folding of staphylococcal nuclease: kinetic studies of two processes in acid renaturation

The folding of acidified staphylococcal nuclease, upon neutralization, was studied in a stopped-flow spectrofluorometer by measuring the increase in tryptophanyl fluorescence during renaturation. At 25 °C and 0.1 ionic strength, the fluorescence change may be described by two first-order rate processes with half-times of 55 and 350 msec. No significant change in either rate was effected on varying the initial pH from 3.2 to 3.8 (corresponding to 0 to 50% levels of folding) or the initial ionic strength from 0.001 to 0.1. In contrast, the over-all rate of folding is dependent upon temperature. The half-time of the slower rate process decreases from 600 msec at 13 °C to 150 msec at 38 °C; the half-time of the faster rate process does not change significantly over this temperature range. These results suggest that the two processes may correspond to a sequence involving nucleation of ordered structure followed by the formation of hydrophobic interactions. Possible structural correlates of these processes are discussed with respect to the crystallographic model of this protein.     

The effect of thymine dimers on DNA:DNA hybridization

DNA from bacteriophage T7 was irradiated at long ultraviolet wavelengths in the presence of silver ions. Such treatment leads to selective production of thymine: thymine dimers in DNA. The DNA was melted and the renaturation rate was determined as a function of thymine dimer content and renaturation temperature. Under “normal” hybridization conditions little change in the renaturation rate was observed even when 30% of the thymine was dimerized. This result is consistent with the view that up to a 15% change in the primary sequence of DNA dose not appreciably change the renaturation rate.     

Effects of microscopic and macroscopic viscosity on the rate of renaturation of DNA

The effect of solvent viscosity on DNA renaturation rates has been investigated as a function of temperature for a number of solvent systems. The results are all consistent with a microscopic viscosity limitation of the rate determining step. Rates of renaturation in perchlorate and quaternary ammonium salt solutions are also discussed. Increasing the macroscopic viscosity with dissolved neutral or anionic polymers increases, rather than decreases, renaturation rates due to the excluded volume of the dissolved polymers.     

Kinetic model of lysozyme renaturation with the molecular chaperone GroEL

From the renaturation kinetics of denatured/reduced lysozyme assisted by the molecular chaperone GroEL, a simplified kinetic model was established based on the competition between protein folding and aggregation. In the presence of GroEL and ATP, the aggregate formation was a second order reaction. With 2 mM ATP, a renaturation yield of 90% at a high renaturation rate was obtained when the molar ratio of GroEL to lysozyme was 1:1.