Showing papers in "Biopolymers in 1969"

Viscosity and sedimentation study of sonicated DNA–proflavine complexes†

Abstract: The intrinsic viscosity of sonicated calf thymus DNA (molecular weight 4–5 × 105) increases and the sedimentation constant decreases, with increasing binding of proflavine at 0. 2 ionic strength and at 25°C. The measurements correspond to a linear increase in length of the almost rodlike DNA molecules with the amount of proflavine bound; independent calculations from viscosity and sedimentation measurements yield almost identical results. Over the range of r (moles of proflavine bound per moles of nucleotides) equal to zero to r = 0.13, the length increases by about 20%. This extension is compatible with the intercalation hypothesis proposed by Lerman. Density increments at various values of r, at constant chemical potential of diffusible solutes, were determined. It was also found that, in addition to the known isosbestic point of DNA-proflavine complexes at 455.5 mμ, an additional isosbestic point exists at 225.5 mμ; this proved extremely useful for the evaluation of binding studies.

Stereochemistry of nucleic acids and their constituents.† IV. Allowed and preferred conformations of nucleosides, nucleoside mono-, di-, tri-, tetraphosphates, nucleic acids and polynucleotides‡

Abstract: A uniform notation and convention is suggested to describe the torsional angles in nucleic acids and their derivatives. The torsional angle χ, relating the stereochemistry of the base with respect to the sugar, shows more variation for the β-purine glycosides than for the β-pyrimidine glycosides. This variation is attributed to the fact that the β-purine derivatives may form intramolecular O(5′)-H…N(3) hydrogen bonding. The χ values for the α-purine and α-pyrimidine glycosides show preference for the –syn-clinal (or anti) conformation. The mode of puckering of the sugar also influences the χ value. The various possible conformations for the furanose ring are described by the torsional angles τ0 τ1, τ2, τ3, τ4, about the five ring bonds. From an analysis of the torsional angles (ω, ϕ, ψ, ψ′, ϕ′, ω′) about the sugar phosphate bonds in the x-ray structures of the known nucleosides, nucleotides, phosphodiesters, nucleic acids, and related compounds, and from a consideration of molecular models, it is found that the possible conformations for the backbone of helical nucleic acids is strikingly limited. Most importantly, the preferred conformation of the nucleotide unit in poly nucleotides and nucleic acids turns out to be the same as that found for the nucleotide in the crystal structure. It is observed that base “stacking” is a consequence of the restricted backbone conformation. The torsional angles are illustrated in the form of conformational “wheels”. Interrelation between the torsion angles about successive pairs of sugar-phosphate bonds are presented in the form of conformational maps: ω,ϕ; ϕ,ψ; ψ.ψ′; ψ′,ϕ′; ϕ′,ω′; ω′,ω. The ω′,ω map shows the perferred conformations about the inter-nucleotide bonds of right- and left-handed helices and the possible conformations of phosphodiesters. The preferred conformation of the pyrophosphate and triphosphate is that in which the phosphate oxygens display a staggered arrangement when viewed along the P–P axis. A plausible structure and conformation for the ATPM2− backbound complex is presented. This structure differs from that proposed by SzentGyorgi in that the metal (only transition metals are considered here) is not bound to the NH2 nitrogen of adenine, but rather is simultaneously bound to N(7) of the ring and three phosphates (α, β, γ), or N(7) of the ring and two phosphates (β, γ). The remaining metal coordination may be satisfied by solvent–metal or enzyme–metal bonds.

Time-dependent fluorescence depolarization and Brownian rotational diffusion coefficients of macromolecules

Abstract: Using a distribution function formalism, we have derived relations between the time-dependent fluorescence polarization anistropy r(t) = [I‖(t) − I⟂(t)]/[I‖(t) + 2I⟂(t)] and the Brownian rotational diffusion coefficients of macromolecules It is shown that in the most general case of a completely asymmetric body, five exponentials appear in r(t) Reduction to previously obtained simpler expressions are presented and discussed Experiments were performed to measure r(t) for the complex of 1-anilino-8-naphthalene sulfonate (ANS) and apomyoglobin The results revealed a spherical geometry, with a radius of 208 A Similar experiments were performed on the ANS–apohorse radish peroxidase complex The results were inconclusive towards the geometry of the complex, but when assumed to be spherical, the radius was estimated to be 296 A, consistent with the larger molecular weight of horse radish peroxidase

Determination of DNA base compositions from melting profiles in dilute buffers.

Abstract: Equations were determined for the dependency of the melting temperature (Tm) of DNA upon the logarithm of the sodium ion concentration, for four DNA samples of widely different base compositions (θGC). The slopes of these Tm versus log M equations wore found to decrease with increasing θG Cof the samples. An empirical equation relating Tm, log M (Na+) and θG C was derived, which also accounts for differences in Tm versus log M slopes. Data from the literature for some synthetic polynucleotides and for the crab(Cancer pagarus) satellite poly AT are discussed in relation to the above finding. The changes in Tm versus log M slopes with θG C are interpreted in terms of changes in the thermodynamic parameters ΔS and ΔH with base composition.

Concerning the kinetics of polypeptide synthesis on polyribosomes

Abstract: The kinetics of biosynthesis of polypeptides on polyribosomes is analyzed in accordance with a simple mathematical model. Each ribosome is assumed to block L adjacent. (m-RNA) template sites but to move a distance of one, and only one, template site (nucleotide triplet) upon the addition of each monomer unit to the growing polypeptide chain bound to it. Solutions are sought, for the probability, nj(t), that a template possesses, at time t, a polypeptide chain that has reached degree of polymerization j. Several classes of steady-state solutions are obtained via machine computation. These correspond to various choices of relative rates of initiation, polymerization along templates, and termination (release of completed chains from templates). Experimental data available from radioactive pulse labeling experiments are discussed. The data obtained by Dintzis, and by Winslow and Ingram, in studies of the synthesis of the α chain of rabbit hemoglobin and human hemoglobin, respectively, are consistent with steady-state solutions obtained from the current theoretical calculations when the rates of initiation and termination are of comparable magnitude and rate-determining. In this case, a (relatively) small number of chains are polymerized at a (relatively) fast rate each near the beginning of the template, and there exists a transition to a situation near the end of the template in which a (relatively) large number of chains are polymerized at a (relatively) slow rate each. For this solution the situation near the end of the template is entirely analogous to a traffic jam in automobile traffic.

Circular dichroism of the “random” polypeptide chain

Abstract: The circular dichroism (CD) spectrum of an unordered polypeptide chain does not correspond, as has been assumed heretofore, to that of a charged chain such as poly-L-glutamic acid or poly-L-lysine. The latter have been shown to have locally ordered structures with characteristic CD spectra. We have now obtained CD spectra of the unordered forms of the above synthetic, polypeptides, as well as of two fibrous proteins (collagen and feather keratin) and a globular protein (myoglobin). These spectra are all similar to that of unordered polyproline, having a negative band in the vicinity of 2000 mμ and no additional bands at longer wavelengths. The lack of structural uniqueness of the unordered polypeptide chain is emphasized by these studies.

Circular dichroism of polynucleotides: A simple theory

Abstract: A particularly simple theory of circular dichroism is described and applied to the polynucleotides. It works surprisingly well and predicts the conservative spectrum of DNA and the more intense nonconservative spectrum of RNA. The anomalously low intensity of the CD of the nucleic acids is shown to be a natural consequence of the cancellation of the rotational strengths of the many CD bands. The theory's many successes and predictions as well as its weaknesses are discussed.

Structure of beta-chitin or parallel chain systems of poly-beta-(1-4)-N-acetyl-D-glucosamine

Abstract: The structure of β-chitin has been reexamined in an X-ray diffraction study of the highly crystalline material available from pogonophore tubes. Oriented specimens were prepared by suspending the dispersed deproteinized tube in a fibrin clot which was then stretched into an oriented fiber. The X-ray diffraction patterns of pogonophore β-chitin were explained by proposing that this material consists of a mixture of two structural phases which have been named β-chitins A and B. This view was confirmed by the preparation of specimens which gave only the diffraction pattern of the A phase by treating the tubes with diaphanol. Both A and B phases gave rise to a series of hydrate structures. The lowest hydrate of β-chitin A has been studied in detail and shown to consist of an anhydrous system of parallel chitin chains. For this form, the unit cell was monoclinic with dimensions a = 4.85 A, b = 10.38 A (fiber axis), c = 9.26 A, and β = 97.5°, and space group P21. Reasonable agreement was obtained between the observed X-ray intensities and those calculated for such a structure. Examination of the β-chitin of Loligo pen and diatom spines showed that these materials also consist of these A and B phases.

Hydrogen-Tritium Exchange of the Random Chain Polypeptide

Abstract: The Hydrogen–tritium exchange character of poly-D,L-alanine was studied in detail as a model for the hydrogen exchange behavior of the unhindered, polymeric peptide group. The random chain nature of poly-D,L-alanine was evident in the uniformity of exchange rate of all its hydrogens and in the similarity between this rate and that of random chain poly-D,L-lysine and other known, unhindered secondary amide groups. An equilibrium isotope effect favoring the binding of tritium over protium to the extent of 21% was measured. Specific acid and base catalysis of the exchange and the absence of detectable general catalysis were demonstrated. Apparent energy of activation is 17 kcal/mole for deprotonation, largely due to dependence of Kw on temperature, and 15 kcal/mole for protonation, which correlates with the extreme apparent pK. The hydrogen –tritium exchange half-time rate; of poly-D,L-alamine at any pH and temperature (T: °C) is given by the equation:

Determination of stability of the DNA double helix in an aqueous medium

Abstract: The possibility of determining the free energy of stabilization ΔG0 of native DNA structure with the help of calorimetric data on heats ΔH of transition from the native to denaturated state is considered. Results of microcalorimetric measurements of heats of denaturation of T2 phage DNA at, different values of pH and ionic strength of solution are given. Values of free energy of stabilization of the DNA native structure ΔG0 under various conditions have been obtained. It is shown that under conditions close to physiological ΔG0 approaches 1200 cal/mole per base pair.

Matching of single‐strand breaks to form double‐strand breaks in DNA

Abstract: Single-strand breaks (ssb) in opposite strands of DNA can be sufficiently near that a double-strand break (dsb) results. A theory is presented by which the maximum number h of base pairs which cannot prevent double-strand breakage can be determined from the rates of production of ssb and dsb. The assumptions required to derive the necessary equations as well as the range of validity of the equations are discussed in detail. In the experiments ssb and dsb were produced by x-irradiation in buffers which do not eliminate indirect effects and were measured by analytical ultracentrifugation. Values of h have been determined in low and high ionic strength and in low ionic strength over a range of temperatures. The values, 2.64 and 15.8, were obtained for high and low ionic strength, respectively.

Etude, par spectroscopie infra-rouge, de la conformation de quelques composés peptidiques modèles

Abstract: Some experimental data are given on the infrared spectra between 3300 and 3500 cm−1 of dilute solutions in carbon tetrachloride of three types of model compounds: CH3−CONH-CH(R1)-CONH(R2), (I); CH3-CON(CH3)-CH(R1)-CONH(R2), (II) and CH3-CONH-CH(R1)-CON(R2)2, (III). In studying the N-H stretching bands, it was found that there are two types of intramolecular hydrogen bonds in these molecules; these result in two different cyclized conformations, C5 and C7, which contain respectively, five and seven atoms in the ring. By using model substances I, II, and III, in which the nitrogen atoms are unequally substituted, it is possible to identify the N-H stretching bands which are to be ascribed to the N-H oscillators included in the two different chelated conformations. It is found also that the stretching frequency of a free N-H oscillator depends upon the substituent on the nitrogen atom. Thus, it is possible to observe, with some of the model compounds I, four different absorption bands located at 3340, 3420, 3440, and 3460 cm−1. The first two are ascribed to the N-H oscillators included in the Hbonds which lock the C7 and C5 conformations; the last two correspond to free N-H which differ with the substituent on the nitrogen atom.

Stereochemistry of nucleic acids and polynucleotides. IV. Conformational energy of base-sugar units

Abstract: In this paper, the preferred conformations of the bases with respect to the sugar in various base-sugar units are worked out using criteria of potential energy. The van der Waals type of intercations between nonbonded atoms is represented by a 6-12 function and the electrostatic interactions have been calculated in the monopole approximation using Coulomb's law. The torsional contributions to the total energy have been neglected. It is found that in general the pyrimidines have preferred anti contributions (as described by Donohue and Trueblood) and purines have both syn and anti and conformations. Certain differences between differently puckered riboses in regard to the above general tendency are discussed. The conclusions, in general, conform with the results obtained by us earlier with the use of hard-sphere potential and are also supported by observations on conformations of nucleotides and nucleotides in crystal structure.

Effect of pressure on the temperature‐dependent association of β‐casein

Abstract: The effect of pressure on the temperature-dependent association of β-casein was studied by the method of light scattering. Between 1 and 1500 kg/cm2, β-casein is reversibly depolymerized, indicating an increase in partial specific volume of the protein with association. Possible mechanisms for association are discussed. At still higher pressures reversible reassociation is observed, which is ascribed to conformational changes in the β-casein molecule.

Persistence length of DNA

Abstract: In the wormlike chain (Kratky-Porod) model of DNA the stiffness of the chain is determined by the persistence length, a. The persistence length may be evaluated from light-scattering measurements of the molecular weight and the mean-square radius if the samples are not polydisperse or if the polydispersity can be quantitatively determined. The persistence length can also be evaluated with the aid of hydro dynamic theory from measurements of intrinsic viscosity and sedimentation coefficient. Data taken from the literature and from other studies by the authors are examined by these methods. The light-scattering method yields a value of a of 900 ± 200 A the hydrodynamic data yield 600 ± 100 A. These values are considerably larger than those obtained by most previous authors.

Optical properties of polypeptides in the β‐conformation

Abstract: The rotational strengths and oscillator strengths of the nπ* band and ππ* exciton bands have been calculated for antiparallel and parallel β-structures of varying length and width. The results are compared with experiment and with previous theoretical treatments of β-structures. The generally good agreement of calculations on the antiparallel β-structure with experimental results on poly-L-lysine and poly-L-serine indicates that these systems are indeed in the antiparallel conformation. It is found that the exciton component strongest in absorption shifts to longer wavelengths as the width of an antiparallel structure increases, and it is suggested that the position of the ππ* absorption band may be a useful criterion of sheet width. The results also reconcile the linear dichroism measurements of Rosenheck and Sommer on poly-L-lysine films with an anti-parallel structure. Calculations on parallel β-structures indicate that the CD spectra of this form will be rather similar to that of the antiparallel form. However, the major absorption band in the antiparallel form is associated with a small positive CD band, while in the parallel form it coincides with a large negative CD band. Finally, it is pointed out that the large positive CD bands predicted for single-stranded parallel and antiparallel β-structures at about 200 mμ render unlikely the suggestion that random-coil polypeptides contain a substantial fraction of extended chain.

Intrinsic viscosity of native and single-stranded T7 DNA and its relationship to sedimentation coefficient.

Abstract: The intrinsic viscosity and sedimentation coefficient of native and single-stranded T7 DNA have been determined at 25⁰C as a function of ionic strength in neutral and alkaline NaCl. The relationship between [η] and S⁰(20,w), is well represented by the Mandelkern-Flory equation over the entire range of conditions between 0.0013 and 1M Na+. An apparent discrepancy between the two methods at moderate to high ionic strengths is probably due to a change in V with ionic strength. It appears that [η] is a more sensitive and reliable measure of molecular expansion for native DNA,but S⁰(20,w) is a better index of conformational change in single strands, since [η] becomes too small to measure conveniently at high ionic strengths. At moderate to high ionic strengths, denaturation leads to a decrease in [η], although unfolded single strands retain considerable viscosity. At sufficiently low ionic strength, the intrinsic viscosity of the single strands becomes higher than that of native DNA, and the effective volume of a single strand approaches that of the native molecule.

Optical activity of single stranded polydeoxyadenylic and polyriboadenylic acids; dependence of adenine chromophore cotton effects on polymer conformation

Abstract: Circular dichroism (CD) curves are reported for poly dA, (pdA)6, (pdA)2, poly A, ApAp, ApA, AMP, dApA, pdApA, A-2′-O-methyl pA, and A-2′-O-methyl pAp. Analysis of these curves indicated the presence of single CD bands at 228–230 mμ and at 278–280 mμ in oligomers longer than dinucleotides. In the case of dinucleotides and mononucleotides (from the literature, in addition to those studied here), the 230 mμ CD of band appears but the 280 mμ CD band does not. We assign the 230 mμ band to a very weak π–π* transition at this wavelength. From theoretical considerations, we show that the 280 mμ band is not an exciton component of the strong π–π* transition at 260 mμ in adenine. We conclude that the 280 mμ CD band must be assigned to a distinct absorption, not previously reported, which we suggest arises from an n–π* transition. The fact that the n–π* CD band at 280 mμ is not seen in mononucleotides or dinucleotides is ascribed to solvation of the adenine ring by water, which shifts the band to shorter wavelengths. Therefore, only interior residues of oligomers have the 280 mμ band, and the optical activity of a polymer cannot be computed from that of a dinucleotide, by using a nearest-neighbor approximation. The existence of this end effect hag been tested, by taking it into account in computing the rotational strengths of the 278 mμ n–π* transition for several oligomers; it is pointed out that a more sensitive test of this end effect would require CD data for the oligo dA series of 3 to 5 residues. We speculate about the structural and optical differences between poly dA and poly A, and point out the need for a theoretical treatment of n–π* Cotton effects in polynucleotides.

Single crystals of poly(L-glutamic acid)†

Abstract: Lamellar single crystals of alkaline earth salts of poly(L-glutamic acid) have been grown by precipitation from dilute aqueous solution and studied by optical and electron microscopy and by x-ray and electron diffraction. The calcium, strontium and barium salts were crystallized in the β form above room temperature and could be converted to crystals of β-poly(L-glutamic acid) by washing in dilute hydrochloric acid. The magnesium salt, on the other hand, was crystallized in the α form at or below room temperature but could not be converted into crystals of α-poly(L-glutamic acid) by washing in hydrochloric acid. The crystalline lamellae are very thin (thicknesses range from 25 to 60 A in β crystals and are about 100 A in α crystals) and the polypeptide chains are oriented normal to the planes of the lamellae. It is clear from the disparity between crystal thickness and molecular length that the molecules crystallize by folding at the upper and lower surfaces of the crystals. Conformations of the molecules at these folds are discussed briefly.

Fluorescence polarization study of DNA--proflavine complexes.

Abstract: The binding of proflavine to DNA has been studied by measuring the polarization and intensity of emission of DNA–dye complexes. Such measurements also permit the determination of the fluorescence of the bound dye as a function of the degree of binding. Techniques of emission spectroscopy permit the study of complexing at high phosphate to dye ratios, and we have examined complexes formed at up to 12,300:1 phosphates to dye. At high phosphate to dye ratios, we find that equilibrium plots of the binding data show only one type of binding. Reports in the literature of multiple binding constants are shown to be due to the incorrect assumption that the fluorescence of the bound dye is independent of the amount bound. The emission properties can be qualitatively accounted for by assuming that nearest-neighbor interaction between bound dyes quenches the fluorescence. We report that, within experimental error, the binding constant is insensitive to the base content of the DNA. The DNA-dye complexes show a temperature dependent depolarization, the cause of which is, as yet, unknown. Heat denaturation of the DNA–dye complex may be followed on a Perrin plot.

Far‐infrared spectra of poly(‐α‐amino acids) with basic alkyl group side chains

Abstract: Far-infrared spectra in the region from 700 to 60 cm−1 have been measured for the α-helix structures of poly(L-α-amino-n-butyric acid), poly-L-norvaline, poly-L-norleucine, and poly-L-leucine and for the β-form structures of poly(L-α-amino-n-butyric acid), poly-L-valine, poly(DL-amino-n-butyric acid), poly-DL-norvaline, and poly-DL-norleucine. The changes of the spectra on N-deuteration have been measured in the region between 700 and 400 cm−1. It is concluded that, the α-helix has characteristic bauds near 690, 650, 610, 380, 150, and 100 cm−1, and that the β-form has characteristic bands near 700, 240, and 120 cm−1. The main-chain vibrations in the region from 600 to 200 cm−1 are strongly coupled with the side-chain deformation vibrations.

Studies of the optical properties of the proflavine–DNA complex

Abstract: We report studies of the optical properties of the proflavine–DNA complex, using absorbance and circular dichroism spectroscopy. From comparison of the absorption spectra of proflavine complexed with calf thymus and T2 DNA, we conclude that stacking of the dyes external to the double helix is comparatively much weaker with T2 DXA, probably because of its glucosylation. Several sources are found for the circular dichroism induced in proflavine when it is complexed with DNA. There is a relatively weak circular dichroism induced when the dye is infinitely dilute on the DNA lattice; this presumably arises from the environmental asymmetry of the binding site. Stronger circular dichroism effects are induced by interaction of intercalated and stacked dyes; studies with T2 DNA, for which stacking seems to be blocked, permit a tentative resolution of effects due to the two modes of binding. One recurring theme of these studies is the observation that the optical properties are quite dependent on environment. The most dramatic example is a strong variation with salt concentration of the amplitude of the circular dichroism induced in the isolated (intercalated) monomer by the surrounding DNA. This suggests that the structure of the intercalated complex is quite sensitive to external conditions.

Differential elution of histones from gel-trapped nuclei.

Abstract: A method has been developed for characterizing at, submicrogram levels the heterogeneity of histones from purified nuclei. The histones are eluted with a smooth concentration gradient from nuclei trapped in polyacrylamide–gel threads and are collected in a micro fraction collector suitable for volumes in the 10–100 μl range. The gradient and fraction collection systems are governed by cam driven syringes. Samples obtained are subjected to electrophoresis in a starch-gel system and the gels are stained with a highly sensitive stain specific for guanidinium groups. Seven major and a similar number of minor components are demonstrated in the histones. The method of differential elution of trapped macromolecules is suitable for use with systems other than nuclei and histones.

Fluorescence of proflavine--DNA complexes: heterogeneity of binding sites.

Abstract: Measurements of the relative quantum yield of fluorescence of proflavine bound to DNA as a function of the number of bound dyes per nucleotide and the ionic strength allow the determination of the binding constants and respective number of the two types of sites previously postulated. It is demonstrated that 2–3% of the base pairs form sites where the dye is strongly bound and fluoresces normally while in the other set of sites the binding constant is 3–4 times weaker and the fluorescence completely quenched. Comparison with complexes of Pro with double stranded polynucleotides poly (A + U), poly (I + C), poly(G + C), confirm that the strong binding sites correspond to A-T-rich regions of the DNA while the quenched sites seem to require the presence of a neighboring guanine. The role of charge transfer in quenching of fluorescence and mutagnic action is considered. An original method for the determination of free dye and bound dye, based upon the use of an external quencher is described in the Appendix.

On the complex formation of acridine dyes with DNA. VII. Dependence of the binding on the dye structure.

Abstract: The binding constants for the complex formation of more than twenty ring nitrogen-and amino-substituted acridine derivatives with calf thymas DNA were measured by a fluorescence method. DNA quenches the fluorescence of the aminoacridine dyes so long as both amino hydrogens are not substituted. These dyes show an enhancement of their fluorescence intensity in the presence of DNA. Typical representatives of both are proflavine and acridine orange derivatives, respectively. A discussion of steric and electronic influences of various substituents attached to the ring nitrogen and amino groups on the binding led to the concept of different conformations for intercalated acridines without amino groups and the aminoacridines. The electrostatic binding site of the former seems to be the positively charged ring nitrogen, while the binding sites in the aminoacridines are so located that the amino groups are directed towards the negatively charged DNA phosphates.

Determination of the base pairing content of ribonucleic acids by infrared spectroscopy

Abstract: A method is described for determining the fractions of adenine-uracil and guanine-cytosine base pairs of partly double-helical ribonucleic acids in aqueous solution. The method is based upon the ability to distinguish between paired and unpaired bases by means of infrared spectroscopy of their deuterium oxide solutions in the 1500–1800 cm−1 frequency region of the infrared spectrum. An application of the method to yeast ribosomal RNA is described. At 30°C, ribosomal RNA is 64± 6% paired (35% GC, 29% AU). The method can be applied to determine the fractions of Watson-Crick base pairs at a given temperature in any RNA containing the four common bases in known ratios.

Salt effects on the denaturation of DNA

Abstract: When DNA's of differing GC:AT base ratios, e.g. synthetic poly dAT, T4 DNA,calf thymus DNA, E. coli DNA, and M. lysodeikticus DNA, are heat-denatured at neutral pH in increasing concentrations of N(a)(2)SO(4) or C(s)(2)SO(4) as supporting electrolytes,the variation of melting temperature with average base composition, dT(m)/dX(G)(C), changes from 45°C (in 0.002M Na) to ll°C (in 4.5M Na) and from 42°C (in 0.002M Cs) to 3°C(in 4.5M Cs). The decrease of dT(m)/dX(G)(C) is a monotonic function of decreasing water activity in the salt solutions. We interpret this decreased composition dependence of the thermal stability of the various DNA's as being due to a destabilization of the GC base pairs relative to the AT base pairs by the concentrated salt media. A simple quantitative treatment shows that k = 8GC/SAT decreases from a value of 4.14 (in 0.01MN(a)) to 1.86 (in 3M Na) and from 4.18 (in 0.01M Cs) to 1.42 (in 3M Cs). SAT is the equilibrium constant for the formation of a hydrogen-bonded AT base pair from a pair of unbonded bases at the junction between a helical region and a denatured region and SGC is the like constant for the formation of a GC base pair. These results corroborate our previous findings of a strongly reduced composition dependence of the negative logarithm of the methylmercuric hydroxide concentration necessary to produce 50% denaturation when the helix-coil transition of DNA is studied in concentrated Cs(s)SO(4)(ultracentrifugation) instead of in dilute N(a)(2)SO(4) (ultraviolet spectrophotometry).

Stereochemistry of nucleic acids and polynucleotides. VI. Minimum energy conformations of dimethyl phosphate

Abstract: As part of a study on the conformation of polynucleotides and nucleic acids the preferred conformations of the model conpound dimethyl phosphate are worked out using potential energy functions. In calculating the total potential energy associated with the conformation, nonbonded, torsional, and electrostatic terms have been considered. The variation of the total conformational energy is represented as a function of two torsion angles #x03D5; and Ψ which are the rotations about the two phosphoester bonds. The most stable conformations are found to be the gauche-gauche conformations about these bonds. The conformations observed for phosphodiesters in the solid state and in the proposed structures of polynucleotides and nucleic acids cluster around the minimum. Also, regions of minimum energy correspond well with the typical allowed regions of a representative dinucleotide.

Nuclear magnetic resonance investigation of the helix in random coil transformation in poly-alpha-amino acids. I.

Abstract: High-resolution nuclear magnetic resonance spectra at 100 MHz and 220 MHz have been obtained on two samples of poly-L-alanine of differing molecular weights (2500 and 42 500) in the chloroform–trifluoroacetic acid system under various conditions of solvent composition, temperature, and polypeptide concentration. Separate helix and random coil peaks are observed for the α-CH and peptide NH backbone proton resonances, thereby permitting the determination of helix content. This observation of separate peaks demonstrates that the lifetimes of the helix and random coil portions of poly-L-alanine have lower limits of about 10−1 sec. It is suggested that solvent–peptide versus peptide–peptide hydrogen bond competition, coupled with a destabilizing effect of the trifluoroacetic acid on the helix, is responsible for the helix–random coil transformation.

Optical rotatory dispersion of mucopolysaccharides and mucopolysaccharide--dye complexes. II. Ultraviolet cotton effects in the amide transition bands.

Abstract: Ultraviolet optical rotatory dispersion curves of mucopolysaccharides exhibit particular Cotton effects in the spectral region of the n–π and π–π amide transitions. Two general patterns emerge: (1) enhancement of negative rotation and of the first negative Cotton effect (troughs 217–220 mμ) and (2) relative dominance of the positive Cotton effect in the π–π transition region (peak ∼198 mμ). Groups (1) and (2) can be correlated with a structural difference in the linkages of the amino sugars: (1) occurs with polymers containing 3-1-linked glycosamino sugars and (2) with glycosamino moieties linked 4–1 by either α- or β-glycosidie bonds. Measurements of the circular dichroic absorption bands support the qualitative conclusions from optical rotation. All mucopolysaccharides exhibit a first, negative band centered at 208–211 mμ, while only those in group (2) show, in addition, a positive band centered at 189–192 mμ. A suggested unifying model considers that difference in kind and/or degree of preferred geometry of the amide groups obtains from two forms of secondary order: (1) having a linear hydrogen bond from the N (acceptor) to the (C2)O—H of the preceding uronic acid and (2) having a linear hydrogen bond from the N (acceptor) to the (C2 or 3) O—H of the following sugar. The hydrogen bonds would have similar strength but opposite directions in two systems towards the nonreducing end (1) or towards the reducing end (2)], closing eight-membered rings