Effects of pressure on the helix-coil transitions of the poly A-poly U system

Studies were made of the influence of hydrostatic pressure on the helix–coil transitions of poly (A + U) and poly (A + 2U). The results were analyzed by a thermodynamic treatment which emphasized the cooperative aspect of the transitions. The helix-to-coil volume changes were found to be small and negative indicating pressure stabilization of the coil form. The significance of the results with respect to other denaturation measurements was discussed.     

Heats of thermally induced helix-coil transitions of DNA in aqueous solution

Thermal denaturation of calf thymus DNA at both alkaline and neutral pH values was studied by differential scanning calorimetry. It was shown that the dependence of the enthalpy of transition on pH and salt concentration could be accounted for on the basis of a heat capacity change of +40 cal deg^?1(base pair)^?1. In the pH range between 10.3 and 11.3, a release of 0.6 proton per base pair was calculated from the pH dependence of the melting temperature. The heat effect associated with the release of this proton was calculated to be 5 kcal mole^?1.     

An IR-investigation of the helix-coil conversion of poly U

In the presence of two or polyvalent cations, e. g., Mg²⁺, protonated ethylenediamine, protonated spermidine, and protonated spermine, poly U forms an ordered structure in aqueous solution. At elevated temperatures, the secondary structure is lost by a cooperative process. The melting temperature T_m rises with the size of the cations. Using IR-spectroscopy, we could show that the secondary structure of poly U is stabilized by hydrogen bonds. Both carbonyl groups of the uracil are involved in the hydrogen bonding. This experimental result enables us to choose the right arrangement for UU base pairing.     

Effects of deuterium on the thermal stability of the poly A-poly U helix

The effect of deuterium on the thermal stability of the polynecleotide double helix formed by the homopolymers polyadenylie acid (poly A)and polyuridylic acid (poly U)has been invertigated by measuring the best capacity as a function of temperature in an automatic scanning adiabatic calorimeter. Hydrogen-bounded and deuterium-bonded helical conformations of the polynecleotides used have been melted in H₂O and D₂O₂ respectively, as solvent. Within the limits of experimental error, there is no dfference in the measured enthallpy change accompanying the helix-random coil transition. The enthalpy change ΔH is 6.6 Kcal/MBP ub any case. The half-conversion temperatures T_m differ by two degrees. T_m for poly (AU) in H₂O is 45.8°C, T_m for poly (AU) in D₂is 47.7.°C.     

Local effects of partial adenine-N1-oxidation on poly A-poly U and poly A-2 poly U helix conformations

We prepared helices with noncomplementary bases by N1-oxidation of poly A, followed by reaction with poly U. Mixing curves indicate that doubly and triply helical structures form, with only the unmodified adenines involved in base pair formation. Circular dichroism spectra were examined particularly at the absorbance maximum of the adenine N1-oxide (A*). In the single strand poly (A,A*), there is a relatively strong pair of positive and negative CD bands from the A*. These are greatly reduced in the double helix, and abolished in the triple helix. We conclude that A* stacks in a conventional manner with A in the single strand, but is rotated out of the double and triple helix. In the double helix the A* probably maintains a preferred orientation with respect to the helix, but rotates randomly in the triple helix.     

Influence of poly A-poly U on early events in the immune response in vitro

Adjuvant action of artificial homopolyribonucleotides and nucleic acid digests was studied in mouse spleen-cell cultures, stimulated with sheep red cells by the technique of Mishell and Dutton. Assays of antibody-forming cells were performed according to the Jerne and Nordin technique. Doublestranded poly A-poly U, and RNA digests had adjuvant activity over a wide dose range (0.01–100 μg/ml). DNA digests, single stranded polynucleotides (poly A, poly U, poly C) and mixtures of ribonucleosides and ribonucleotides had little or no enhancing effect at comparable doses. From our study of the kinetics of increase of plaque-forming cells in cultures treated with poly A-poly U, in conjunction with in vivo studies of others, we concluded that adjuvant action, during induction, indirectly increased the number of bone marrow-derived cells that responded to antigenic stimulation by increasing the effectiveness of the thymus-derived cells in the culture.     

Study of the hydratation of the double-helical poly A-poly U complex by IR-spectroscopy and piezogravimetry methods

IR-spectra of a double-helical poly A-poly U complex and coiled poly U were studied at various r.h. in a 900-3800 cm-1 region. By the method of piezomicrobalance hydration isotherms for these polynucleotides were obtained. It is concluded that, as in the DNA case, simultaneous hydration of nucleic bases the backbone of polynucleotides occurs at lower r.h., and that the poly A-poly U hydration level is higher than poly A and poly U ones separately. Drastic changes in spectral parameters of poly A poly U uracil and adenine in-ring and out-of-ring absorption bands observed in 44-76% r.h. region were interpreted as a transition to helical conformation of the complex. Calculation of resonance frequencies for these normal vibrations in the dipole-dipole approximation agrees with the experimental data.     

Raman studies of nucleic acids. VII. Poly A-poly U and poly G-poly C

Laser-excited Raman spectra of the double-helical complexes poly A·poly U and poly G·poly C are reported for ²H₂O and H₂O solutions. The spectra are discussed in relation to their use as quantitative reference spectra for determining the dependence of the Raman scattering of RNA on secondary structure. The Raman line at 815 cm^?1, due to the phosphodiester group, exhibits the same intrinsic intensity in spectra of poly A·poly U and poly G·poly C and is thus dependent only upon the amount of ordering of the helix and not on the kinds of nucleotides involved. The hypochromic Raman lines in spectra of poly A·poly U are identified and their intensity changes are determined quantitatively over the temperature range 32–85°C. Comparison of the spectra in the 1500–1750 cm^?1 region reveals that the Raman lines from carbonyl group vibrations of uracil are about sevenfold more intense than those of guanine and cytosine for both paired and unpaired states and will thus dominate the spectra of RNA. The Raman frequencies in this region are also compared with previously reported infrared frequencies and give evidence of being strongly perturbed by base-stacking interactions in the helices.     

Abrogation of the tumor promoting effect of allogeneic blood transfusion by polyadenylic-polyuridylic acid (poly A-poly U)

Summary Studies from several centers have shown an immunosuppressive effect of surgical procedures, whilst others have shown blood transfusion in association with cancer surgery to have an adverse effect on ultimate prognosis. We have previously demonstrated enhanced growth of tumor metastases, in rats following allogeneic blood transfusion and surgery. Polyadenylic-polyuridylic acid (poly A-poly U) has been reported to stimulate immune responses. In this report, we have investigated the effectiveness of poly A-poly U as an adjuvant to blood transfusion and surgical procedures in BN rats bearing artificial lung metastases. Significantly reduced tumor growth was observed, following poly A-poly U adjuvant treatment. These results lead to serious contemplation of the use of this drug as adjuvant therapy in blood transfused and surgically treated patients.     

From helix-coil transitions to protein folding

An evolution of procedures to simulate protein structure and folding pathways is described. From an initial focus on the helix-coil transition and on hydrogen-bonding and hydrophobic interactions, our original attempts to determine protein structure and folding pathways were based on an experimental approach. Experiments on the oxidative folding of reduced bovine pancreatic ribonuclease A (RNase A) led to a mechanism by which the molecule folded to the native structure by a minimum of four different pathways. The experiments with RNase A were followed by development of a molecular mechanics approach, first, making use of global optimization procedures and then with molecular dynamics (MD), evolving from an all-atom to a united-residue model. This hierarchical MD approach facilitated probing of the folding trajectory to longer time scales than with all-atom MD, and hence led to the determination of complete folding trajectories, thus far for a protein containing as many as 75 amino acid residues. With increasing refinement of the computational procedures, the computed results are coming closer to experimental observations, providing an understanding as to how physics directs the folding process.     

The helix-coil transitions of poly (dA)-poly (dT) and poly (dA-dT)-poly (dA-dT)

Helix–coil transition curves are calculated for poly (dA) poly(dT) and poly (dA-dT) poly (dA-dT) using the integral equation approach of Goel and Montroll.⁵ The transitions are described by the loop entropy model with the exponent of the loop entropy factor, k, remaining an arbitrary constant. The theoretical calculations are compared with experimental transition curves of the two polymers. Results indicate that the stacking energies for these two polymers differ by about 1 kcal/mole of base pairs. Also, a fit between theory and experiment was not possible for k > 1.70.     

Molecular field theory of hysteresis in helix-coil transitions of polynucleotides

A molecular field theory, taking into account long-range electrostatic forces is used to study helix–coil transitions of polynucleotides. The theory predicts the existence of hysteresis when the electrostatic interaction parameter is large compared to the thermal energy. The theory is applied to the acid–base titration of poly(A)·2 poly(U).     

Comparison of several calculations of helix-coil transitions in heterogeneous polymers

Random number methods are used to calculate helix—coil transition curves for the model of a heterogeneous polypeptide of random sequence. These curves are compared with several other calculations. The random number computations confirm the exact calculation of Lehman; among the several approximate calculations examined only that of Fixman and Zeroka agrees closely with results of the random number method over the whole range of conditions considered. Calculations are also reported of the average length of helix and coil sections in a heterogeneous molecule of random sequence which is undergoing the helix-coil transition.     

Possible role of helix-coil transitions in the microscopic mechanism of muscle contraction.

Local helix-coil transitions in the coiled coil portion of myosin have long been implicated as a possible origin of tension generation in muscle. From a statistical mechanical theory of conformational transitions in coiled coils, the free energy required to form a randomly coiled bubble in the hinge region of myosin of the type conjectured by Harrington (Harrington, W. F., 1979, Proc. Natl. Acad. Sci. USA, 76:5066-5070) is estimated to be approximately 25 kcal/mol. Unfortunately this is far more than the free energy available from ATP hydrolysis if the crossbridges operate independently. Thus, in solution such bubbles are predicted to be absent, and the theory requires that the rod portion of myosin be a hingeless, continuously deforming rod. While such bubble formation in vivo cannot be entirely ruled out, it appears to be unlikely. We further conjecture that in solution the swivel located between myosin subfragments 1 and 2 (S-2 and S-1) is due to a locally random conformation of the chains caused by the presence of a proline residue at the point that physically separates the coiled coil from the globular portion of myosin. On attachment of S-1 to actin in the strong binding state, the configurational entropy of the random coil in the swivel region is greatly reduced relative to the case where the ends are free. This produces a spontaneous coil-to-helix transition in the swivel region that causes rotation of S-1 and the translation of actin. Thus, the model predicts that the actin filaments are pushed rather than pulled past the thick filaments by the crossbridges. The specific mechanism of force generation is examined in detail, and a simple statistical mechanical realization of the model is proposed. We find that the model gives a substantial number of qualitative and at times quantitative predictions in accord with experiment, and is particularly appealing in that it provides a simple means of free energy transduction--the well known fact that topological constraints shift the equilibrium between helical and random coil states.     

Enthalpy of helix-coil transitions from heats of solution. I. Polyglutamates

The heat of solution of a series of three polyglutamates as a function of solvent composition was measured. The abrupt increase in heat of solution at the solvent composition of the helix–coil transition (as evidenced by optical rotation data) allows the estimation of the transition enthalpy change. The difference of side chain in the three polyglutamates has no appreciable effect on the transition enthalpy, although it affects the helix stability, as judged from the solvent composition at the transition points. These facts are discussed on the basis of existing models of the transition.     

Competing B-Z and helix-coil conformational transitions in supercoiled plasmid DNA.

The formation of melted regions from A + T-rich sequences and left-handed Z-DNA by alternating purine-pyrimidine sequences will both be facilitated by negative supercoiling, and thus if the sequences are present within the same plasmid molecule they will compete for the free energy of supercoiling. We have studied a series of plasmids that contain either (CG)8 or (TG)12 sequences in either G + C or A + T-rich contexts, by means of two-dimensional gel electrophoresis and chemical modification. We observe both B-Z and helix-coil transitions in all plasmids at elevated temperatures and low ionic strength. The plasmids fall into a number of different classes, in terms of the conformational behavior. As the superhelix density is increased, pCG8/vec ((CG)8 in G + C-rich context) undergoes an initial B-Z transition, followed by melting transitions in sequences remote from the (CG)8 sequence. The two transitions are coupled through the topology of the molecule but are otherwise independent. When the (CG)8 sequence was placed in an A + T-rich context (pCG8/col), the helix-coil transition was perturbed by the presence of the Z-DNA segment. Replacement of the (CG)8 tracts by (TG)12 sequences resulted in a further level of interaction between the transitions. Statistical mechanical modeling of the transitions suggested that at intermediate levels of negative supercoiling the Z-DNA formed by the (TG)12 sequence has a lowered probability due to the helix-coil transition in the A + T-rich sequences. These studies illustrate the complexities of competing conformational equilibria in supercoiled DNA molecules.     

Enthalpy changes in the helix-coil transition of poly(gamma-benzyl L-glutamate)

The helix-coil transition temperature T_c of poly(γ-benzyl L -glutamate) in binary solvent mixtures of dichloroacetic acid and 1,4-dichlorobutane, 1-chlorooctane, or 1-chlorododecane have been measured. A treatment is presented with which the transition enthalpy can be calculated from the observed dependence of T_c on solvent composition. Results are compared with previously obtained calorimetric data. The underlying assumptions of the calculation are discussed.