Showing papers in "Biopolymers in 1971"

Estimation of the relative stiffness of the molecular chain in polyelectrolytes from measurements of viscosity at different ionic strengths.

Abstract: A method was developed that allowed comparison of the stiffness of the chain in different polyelectrolyte from measurements of the intrinsic viscosity at different concentrations of added monovalent (sodium) salt. The response to salt was quantitatively expressed as the slope of straight lines relating the intrinsic viscosity to the reciprocal of the square-root of the ionic strength. This slope increased considerably with increasing molecular weight of the polyelectrolyte, and could serve to characterize the response to salt of different substances only when comparison was made at a constant molecular weight. An empirical parameter, B, which is the slope corresponding to an intrinsic viscosity of 1.0 at an ionic strength of 0.1 M could be correlated to the unperturbed dimensions of the molecules. A method of extrapolation, enabling the determination of B from measurements of viscosity on only one sample of unknown molecular weight, was evaluated. The empirically found correlation between Band some well established parameters of stiffness did not contrast predictions from the “fuzzy-sphere model” of Fixman, provided that reasonable assumptions regarding ion-binding and the interaction between polymer and solvent were made.

Statistical thermodynamics of nucleic acid melting transitions with coupled binding equilibria

Abstract: Equations are developed to describe the shift in the temperature of the helix–coil transition when small molecules bind to nucleic acids. Included are high polymers, oligonucleotides, and oligomer–polymer interactions. The equations prescribe simple ways of plotting experimental data to evaluate transition and binding parameters.

Stereochemistry of Nucleic Acids and Their Constituents. X. * Solid-state Base-Stacking Patterns in Nucleic Acid Constituents and Polynucleotides

Abstract: The base-stacking patterns in over 70 published crystal structures of nucleic acid constituents and polynucleotides were examined. Several recurring stacking patterns were found. Base stacking in the solid state apparently is very specific, with particular modes of interaction persisting in various crystalline environments. The vertical stacking of purities and pyrimidines in polynucleotides is similar to that observed in crystals of nucleic acid constituents. Only partial base overlap was found in the majority of the structures examined. Usually, the base overlap is accomplished by positioning polar substituents over the ring system of an adjacent base. The stacking interactions are similar to those found in the crystal structures of other polar aromatic compounds, but are considerably different from the ring–ring interactions in nonpolar aromatic compounds. Apparently, dipole-induced dipole forces are largely responsible for solid-state base stacking. It is found that halogen substituents affect base-stacking patterns. In general, the presence of a halogen substituent results in a stacking pattern which permits intimate contact between the halogen atom and adjacent purine or pyrimidine rings. Considering differences in the stacking patterns found for halogenated and nonhalogenated pyrimidines, a model is proposed to account for the mutagenic effects of halogenated pyrimidines.

Conformational dependence of the Raman scattering intensities from polynucleotides. III. Order-disorder changes in helical structures

Abstract: Raman spectra are presented on ordered and presumably helical structures of DNA and RNA as well as the poly A·poly U helical complex, polydAT, and the helical aggregates of 5′-GMP and 3′-GMP The changes in the frequency and the intensity of the Raman bands as these structures undergo order-disorder transitions have been measured In general the changes we have found can be placed into three categories: (1) A reduction in the intensities of certain ring vibrations of the polynucleotide bases is observed when stacking or ordering occurs (Raman hypochromism) Since the ring vibrational frequencies are different for each type of base, we have been able to obtain some estimate of average amount of order of each type of base in partially ordered helical systems (2) A very large increase in the intensity of a sharp, strongly polarized band at about 815 cm−1 is observed when polyriboA and polyriboU are formed into a helical complex Although this band is not present in the separated chains at high temperature, a broad diffuse band at about 800 cm−1 is present The 815 cm−1 band undoubtedly arises from the vibrations of the phosphate-sugar portions of the molecule and provides a sensitive handle to the back-bone conformation of the polymer This band also appears upon ordering of RNA, formation of the helical aggregate of 5′-riboGMP, and to some extent in the selfstacking of the polyribonucleotides polyA, polyU in the presence of Mg++, PolyC, and polyG No such intense, polarized band is found, however, in ordered DNA, polydAT, or the 3′-riboGMP aggregate, although there is a conformationally independent band at about 795 cm−1 in DNA and polydAT (3) Numerous frequency changes occur during Conformational changes In particular the 1600–1700 cm−1 region in D2O shows significant conformationally dependent changes in the CO stretching region analogous to the changes in this region which have been observed in these substances in the infrared Thus, Raman scattering appears to provide a technique for simultaneously observing the effects of base stacking, backbone conformation and carbonyl hydrogen bonding in nucleic acids in moderately dilute (10–25 mg/ml) aqueous solutions

Nägeli amylodextrin and its relationship to starch granule structure. I. Preparation and properties of amylodextrins from various starch types

Abstract: Nageli-type amylodextrins were prepared from various starch types: native starch granules from potato, waxy maize, wrinkled pea, and high-amylose maize, and from a commercial amylose (“Superlose”). The granular starches and retrograded amylose were treated with 15% sulfuric acid at 22°–25° for 3 months, the undissolved residues were washed free of acid and air dried. X-ray diffraction patterns showed that amylodextrin from waxy maize starch (A-type) and potato starch (B-type) retain the same diffraction type as that of the parent starch. On conversion of a starch to an amylodextrin, the sharpness and intensity of the diffraction patterns are either retained (waxy maize starch), improved (slightly with potato, significantly with high-amylose maize, and very markedly with wrinkled pea) or developed (amylose). The results indicate that the crystalline regions of a native starch granule, retrograded amylose, or amylodextrin are exceedingly resistant to acidic hydrolysis at room temperature. In contrast to the parent starches, native amylodextrins stain little if at all with dilute iodine solution. The iodine stains of dissolved amylodextrins were red (waxy maize), red-purple (potato), or purple (amylose, high-amylose maize, and wrinkled pea).

Variation of the NH–CαH coupling constant with dihedral angle in the NMR spectra of peptides

Abstract: Proton magnetic resonance data and conformational calculations of a series of model compounds containing a NH-CαH group substituted as in peptides have been used to generate a proton–proton coupling constant–dihedral angle relation for the peptide unit. For those substances used in which the dihedral angle about the N-Cα bond is not fixed, the angle distribution was calculated from conformational theory. Using eight examples in which the number of theoretical assumptions were least, the best values of the coefficients A, B, and C in the expression J(θ) = Acos2θ + B cosθ + Csin2θ were found by a least-squares procedure to be 7.9, −1.55, and 1.35, respectively. This relation gives reasonable values for the dihedral angles ϕ in cyclic oligopeptide structures for which the availability of both NMR data and other structural information allow comparison. When applied to N-acetylamino acid N-methylamides having side chains extending beyond Cβ, however, agreement with the calculated conformational distribution was found for Leu, Met, and Trp, but observed values of J were larger than expected for Val, He, Phe, and Tyr, These disagreements are considered to be the result of interactions not yet taken into account in the usual conformational calculations.

Conformational dependence of the Raman scattering intensities from polynucleotides.

Abstract: The intensity of Raman scattering from the various Raman active vibrations of poly-(riboadenylic acid), poly(ribocytidylic acid), poly(ribouridylic acid), and poly(riboinosinic acid) in moderately dilute solutions were examined as the temperature was changed to alter their conformation. It was found that certain highly intense, highly polarized Raman bands from the totally symmetric, i.e., in-plane, ring vibrations of the nucleic acid bases become less intense as the chains become more ordered in solution. Since these vibrations occur at frequencies which are markedly different for each type of base, Raman spectroscopy appears to provide a new method for the characterizing of the average conformation of each of the bases in solution. A theory for the resonant Raman effect is given in which it is shown that, a decrease in resonant Raman intensity is to be expected if one obtains a decrease in the intensity of the corresponding ultraviolet absorption band with which the incident light is resonant. If it is assumed that certain Raman bands derive their intensity predominantly from the first few ultraviolet absorption intensities, then a qualitative explanation of our observed conformational dependence of the ordinary Raman intensities can be obtained.

Kinetic and hydrodynamic studies of the complex of proflavine with poly A-poly U.

Abstract: Relaxation kinetic experiments reveal general similarity between the mechanism of binding of proflavine to poly A·poly U and DNA. There are differences in detail, however. For example, the rate constants are roughly an order of magnitude smaller for the former, and the thermodynamic parameters of the individual steps are also different. The total heat and free energy for intercalation of free dye are quite similar in the two cases. As was the case with DNA, considerable dye (up to 25% of the bound form) is attached externally to the double helix, even in the strong binding region of the isotherm. Sedimentation measurements on small, rodlike fragments of poly A·poly U reveal a length increase on binding proflavine of a magnitude similar to that found with DNA. This length increase seems to become smaller under conditions (high temperature) where the relaxation measurements indicate a higher fraction of externally bound dye.

Thermodynamic analysis of thermal transitions in globular proteins. I. Calorimetric study of ribotrypsinogen, ribonuclease, and myoglobin

Abstract: Thermal confonnalional transformations of globular proteins, chymotrypsinogen, ribo-nudcase and myoglobin in solutions at different pH values were studied microcalorimetrically. It was shown that the heat effects observed in the process of heating have a complicated form and their explanation necessitates an assumption on the existence of two stages of the process separated by temperature: (I) a pre-denaturational stage where the protein partial heat capacity changes are probably connected with a labilization of the globule structure and (II) a denaturational stage representing a single-step transition of the protein into a state with a higher enthalpy. Transitions without enthalpy change, the existence of which is shown for the first time in globular proteins, necessitates a more cautions approach to the thennudynamical analysis of different physical parameters on the basis of the van't Hoff equation.

Conformation of amylose in aqueous solution: Optical rotatory dispersion and circular dichroism of amylose–iodine complexes and dependence on chain length of retrogradation of amylose

Abstract: The dependence on chain length of two characteristic properties of amylose, i.e., retrogradation and complex formation with iodine, have been studied by using enzymatically synthesized, homodisperse amyloses. The association rates of amyloses in water containing 5% dimethyl sulfoxide have a sharp maximum at a degree of polymerization Pn of 80; shorter and longer molecules are much more soluble. The iodine complexes of amylose exhibit a strong Cotton effect in the range of the long-wave absorption maximum (position depending on chain length) and two weaker Cotton effects at 480 and 350 nm. The long-wave Cotton effect is most intense at about Pn 50 and decreases rapidly for shorter and longer chains. This behavior is unexpected and is not in accordance with the further increase of λmax and λmax. The experiments can best be interpreted by assuming well ordered, stiff chains in the low molecular weight range (Pn 50–80). For longer chains, the findings are discussed in the light of current concepts of amylose conformation in aqueous solution, namely the model of the broken helical chain (alternating stiff helical segments and unordered regions) and the model of a flexible coil without a significant helical content. However, according to the results given in this paper, a wormlike helical chain seems to be the most adequate model for amylose conformation in neutral solution.

Correction of light-scattering errors in spectrophotometric protein determinations.

Abstract: Errors due to light scattering are a feature of spectrophotometrie methods of protein determination. The experimental conditions may be chosen to allow calculation of the scatter contribution, which is obtained essentially from the linear relationship between log turbidity and log incident wavelength, together with knowledge of the slope of such functions. Using this information, the scatter corrections may be obtained by various simple and rapid methods, applicable to single or multicomponent protein solutions.

The infrared spectrum and water binding of collagen as a function of relative humidity.

Abstract: The infrared spectra of undenatured bovine tendon collagen were investigated at 25°C and relative humidities from 0 to 95%. Suitable samples were prepared by forcing frozen suspensions of the material in distilled water through a stainless steel capillary. The samples were investigated by electron microscopy before and after the spectra were obtained to ascertain that no denaturation had taken place while the sample was exposed to infrared radiation. Temperature controlled absorption cells were constructed which permitted the passing of air with a known water content over the sample film. Gradual changes were observed in the frequencies and intensities of characteristic amide bands over the relative humidity range of 0 to 75%. These changes are particularly pronounced for the amide II band, associated with bending motions of peptide NH bonds. They lead to the conclusion that water molecules are gradually attached to peptide NH bonds within the triple helix over a wide range of relative humidity. Changes in CH deformation bands suggest that CH to O hydrogen bonding does occur and that it is more pronounced in collagen exposed to high relative humidity.

Cooperative nonenzymic base recognition II. thermodynamics of the helix-coil transition of oligoadenylic + oligouridylic acids

Abstract: The properties of oligonucleotide helices of adeuylic- and uridylic acid oligomers have been investigated by measurements of hypo-and hyperchromieity. High ionic strengths favor the formation of triple helices. Thus, the double helix-coil transition can be studied (without interference by triple helices) only at low ionic-strength. A “phase diagram” is given representing the Tm-values of the various transitions at different ionic strengths for the system A(pA)17 + U(pU)17. Oligonucleolides of chain lengths <8 always form both double and triple helices at the nucleotide concentrations required for base pairing. For this reason the double helix-coil transition without coupling of the triple helix equilibrium can only be measured for chain lengths higher than 7. Melting curves corresponding to this transition have been determined for chain lengths 8, 9, 10, 11, 14 and 18 at different concentrations. An increase in nucleotide concentration leads to an increase in melting temperature. The shorter the chain length the lower the Tm-value and the broader the helix-coil transition. The experimental transition curves have been analysed according to a staggering zipper model with consideration of the stacking of the adeuylic acid single strands and the electrostatic repulsion of tlip phosphate charges on opposite strands. The temperature dependence of the nucleation parameter has been accounted for by a slacking factor x. The stacking factor expresses the magnitude of the stacking enthalpy. By curve fitting xwas computed to be 0.7, corresponding to a stacking enthalpy of about S kcal/mole. The model described allows the reproduction of the experimental transition curves with relatively high accuracy. In an appendix the thermodynamic parameters of the stacking equilibrium of poly A and of the helix-coil equilibria of poly A + poly U at neutral pH are calculated (ΔHA = −7.9 kcal/mole for the poly A stacking and ΔH12 = −10.9 kcal/mole for the formation of the double helix from the randomly coiled single strands). A formula for the configurational entropy of polymers derived by Flory on the basis of a liquid lattice model is adapted to calculate the stacking entropies of adenylic oligomers.

DNA-copper (II) complex and the DNA conformation.

Abstract: Spectrophotometric, sedimentation, infrared, optical rotatory dispersion (ORD), and circular dichroism (CD) methods have been used to demonstrate the structural changes in DNA induced by the interaction of copper(II) with bases and to elucidate the complex binding sites. As shown by the electrolyte-induced reversion (addition of salts) of temperature-denatured copper DNA the effectiveness of re-formation of the double-stranded structure depends on the temperature, copper(II) ion concentration, and on the base composition of the DNA. Exposure of heat-denatured copper DNA to higher temperatures decreases the reversion effect on addition of electrolyte. The results indicate that a greater fraction with a cooperative transition appears on heating DNA to 80 or 100°C at a Cu2+/DNA-P ratio of 2 : 1 than at a Cu2+/DNA-P ratio of 1 : 1. With AT-rich copper DNA, reversion to the native DNA structure was not observed. Selective methylation of guanine residues in DNA also affects the electrolyte-induced reversion, indicating the importance of GC pairs for copper(II) binding and the reversion to the native structure. Temperature-denatured copper DNA shows an increased sedimentation coefficient Which decreases again after electrolyte-induced reversion. This change in s is reduced by selective methylation of DNA. Complex formation between copper(II) and the bases is accompanied by a conformational change of the DNA double-helical structure as demonstrated by ORD and CD experiments. The ORD profile of GC-rich DNA is much more affected by copper(II) than that of AT-rich ones. Even at very low copper(II) concentrations, e.g., at 0.02 and 0.2 Cu2+/DNA-P, the ORD and CD measurements exhibit conformational changes of the DNA secondary structure at room temperature. By comparing the infrared spectra of deoxynucleosides with that of DNA of different GC content it has been shown that both guanine and cytosine are involved in the formation of the complex of copper(II) with DNA. N-7 and O at C-6 in guanine and N-3 as well as O of C-2 in cytosine are discussed as the most probable binding sites in DNA. A binding model for the coordination of the copper(II) ion between guanine and cytosine of the opposite strands is suggested. The results are in good agreement with the assumptions and predictions made by Eichhorn and Clark about the complexing of copper(II) with DNA. The recent proposal made by Schreiber and Daune about an interaction of the type guanine–Cu2+–guanine cannot be excluded as an additional kind of coordination of copper(II) in DNA.

Circular dichroism studies of isoleucine oligopeptides in solution.

Abstract: A conformational analysis was carried out on a series of L-isoleucine oligomers having the general formula BOC-(Ileu)n-OMe (n = 2–8). These oligopeptides were examined in trifluoroethanol, trifluoroethanol-acid and mixed organic-water media. The results indicate that these oligomers form β-conformations beginning at the heptamer. The stability of the β-conformations was found to be greater than those formed by oligopeptides derived from L-alanine.

Stereochemistry of nucleic acids and polynucleotides III. Electronic charge distribution

Abstract: Calculation of σ- and π-charges were made on nucleotides and nucleic acids. The σ-charges were calculated using LCAO MO method suggested by Del Re, making use of Berthod and Pullman parameters. The π-charges were calculated by Huckel's method, making use of suitable parameters which gave a good qualitative correlation of calculated bond orders with experimentally determined bond lengths. General features of the charge distribution are discussed.

The binding of Mg++ ions to polyadenylate, polyuridylate, and their complexes.

Abstract: The binding of Mg ++ to polyadenylate (poly A), Polyuridylate(poly U), and their complexes, poly (A + U) and poly (A + 2U), was studied by means of a technique in which the dye eriochrome black T is used to measure the concentration of free Mg−. The apparent binding constant KX = [MgN]/[Mg++][N], N = site for Mg++ binding (the phosphate group of the nucleotide), was found to decrease rapidly as the extent of binding increased and, at low extents of binding, as the concentration of Na− increased in poly A, poly (A + U), and poly (A + 2U), and somewhat less so in poly U. Kx is generally in the range 104 > KX > 102. The cause of these dependences is apparently, primarily, the displacement of Na+ by Mg++ in poly U and poly (A + U) on the basis of the similarity of extents of displacement measured in this work and those measured potentiometrically. was calculated and was found to approach zero as the concentration of Na+ increased. In poly U, poly (A + U), and poly (A + 2U) at low ΔH′ v.H. > 0, about + 2 kcal/“mole.” In poly A, also at low salt, ΔH′ v.H. ≈ −4 kcal/“mol” for the initial binding of Mg++, and increases to +2 kcal/“mol” at saturation. This enthalpic variation probably accounts for the anticooperativity in the binding of Mg++ not ascribable to the displacement of Na++.

The circular dichroism in the ultraviolet of aminoacridines and ethidium bromide bound to DNA.

Abstract: The circular dicrosim (CD) spectra of complexes of DNA with ethidiun bromnide, profiavine, 9-aminoacridine and 4-etliyl-9-amino-acridine have been determined between 220 and 450 nm, the range lieing extended to 600 nm for ethidiufm bromide. The variation of the magnitude of the visible and near—ultraviolet CD spectra of ethidium bromide—DNA complexes with the amount of ligand bound (r) suggests a common binding position with profiavine. On the other hand, 4-ethyl-9-aminoacndine complexed to DNA shows CD spectra not distinguishable from those of 9-aminnoacnidmc in both the visible and ultraviolet. The interpretation of these results with respect to the stereochemistry of the DNA-ligand complexes is discussed.

Experimental thermodynamics of the helix–random coil transition. IV. Influence of the base composition of DNA on the transition enthalpy

Abstract: The helix–coil transition of DNA of various base compositions has been followed by measuring the heat capacity and the ultraviolet absorption as a function of temperature through the transition region. The results of these measurements indicate that the transition enthalphy ΔH for a given pH value and salt concentration depends considerably on the base composition of the various DNA samples. The values of the transition enthalpies vary from ΔH = 7.73 kcal/mole base pair (MBP) for 31% GC base pairs to ΔH = 8.52 kcal/MBP for 72% GC base pairs. The results of the heat capacity measurements are discussed in relationship to the theoretical models suggested by various authors. Some peculiarities of the measured heat capacity versus temperature curves are reported. The correlation between these peculiarities and the results of the transcription experiments of DNA is discussed.

Raman scattering of some synthetic polypeptides: Poly(γ-benzyl L-glutamate), poly-L-leucine, poly-L-valine, and poly-L-serine

Abstract: The Raman spectra of poly-γ-benzyl-L-glutamate, poly-L-leucine, poly-L-valine, and poly-L-serine are reported. For the α-helical polymers, the conformationally sensitive amide I, II, and III modes are observed in the Raman as, well as the infrared. For the β form, the Raman effect, supplies the infrared inactive inphase motion which is useful for the determination of a parallel or antiparallel chain alignment. Modes characteristic of the specific polypeptide are also observed which are insensitive to conformation.

Calorimetry of rat tail tendon collagen before and after denaturation: the heat of fusion of its absorbed water

Abstract: The specific heat, of rat tail tendon at various water contents was measured as a function of temperature. The resulting graphs showed peaks arising from the melting, near 50°C, of helical material in the collagen, and from the melting of absorbed water in the range -40°C to 0°C. The heat of melting of helical material was 11.7 cal per gram of dry tendon. Determination of the heat and temperature of fusion of the absorbed water allowed resolution of the water into four states in the case of tendon before denaturation, and three states after denaturation. The four states are (1) water not freezable on cooling to - 70°C, (2) freezable water with-both heat and temperature of fusion different from the values for ordinary water, (3) freezable water with the heat of fusion of ordinary water, but a different temperature of fusion, and (4) water not distinguished from ordinary water. The fourth state was absent in denatured tendon. The results are discussed in terms of increasing size of clusters of absorbed water molecules.

Optical rotary dispersion of mucopolysaccharides III. Ultraviolet circular dichroism and conformation al specificity in amide groups

Abstract: The circular dichroism of glycosaminoglycans and ganglioside in distilled water are described, showing two bands in the region of amide and carboxyl transitions. The first, negative hand is common to all polymers and the amino sugar derivatives. The characteristics of the second band depend upon polymer structure. Those containing 4–1-linked amino sugars show a second, positive, resolved band about 190 mμ, while those with 3–1-linked amino sugars show a second, negative band less resolved from the first usually ≤185mμ, but clearly centered at 188mμ for dermatan sulfate. Ultraviolet optical absorption from 300 to ∼183 mμ showed inflection regions around 190 mμ for most compounds.

The effects of aqueous neutral-salt solutions on the melting temperatures of deoxyribonucleic acids.

Abstract: The helical stability of a variety of DNA samples, ranging in base composition from 0 to 72 mole-% GC, has been studied by heat denaturation at neutral pH in increasing concentrations of LiCl, NaCl, KCl, CsCl, Li2SO4, and K2SO4. The variation of melting temperature with average base composition, dTm/dXGC, was found to decrease drastically in the concentrated salt media, e.g., from 41°C in 0.006M LiCl to 29°C in 3.2M LiCl, and from 39°C in 0.003M Li2SO4 to 18°C in 1.6M Li2SO4. At the same time, the thermal transition is much more cooperative in the concentrated salt solutions than at low ionic strength. Indeed, at limiting salt concentrations, the transition breadth seems to reach a minimum value irrespective of the compositional heterogeneity of the DNA samples. Attempts to correlate the observed decrease of dTm/dXGC with predicted changes in the enthalpy of melting, deduced from a simple theoretical treatment, experimental data on the binding of counterions and water to DNA, and experimental data on thermal denaturation, were unsuccessful. However, the strongly reduced composition dependence of the melting temperature can be understood in terms of a destabilizing effect of the concentrated salt media on GC-base pairs. It is suggested, though not proven, that the destabilization involves the displacement of water molecules from the DNA helix.

Phonon dispersion curves and normal coordinate analysis of -poly-L-alanine.

Abstract: The vibrational frequencies of α-helical poly-L-alanine and its N-deuterated analog have been assigned by normal coordinate analyses. The phonon dispersion curves and frequency distribution of α-poly-L-alanine have been calculated by using a model which includes hydrogen bonding. The frequency distribution was used to interpret the inelastic neutron scattering data and to calculate the heat capacity. The low-frequency chain modes involving accordian-like motions of the whole helix have been calculated and their dispersion investigated by means of a simplified model.

Conformational studies of β-glucans

Abstract: Steric and energy contour diagrams have been plotted for disaccharide-like and for helical structures of linear β-D-glucans having (1 → 2), (1 → 3) and (1 → 4) linkages. The allowed conformations constitute only about. 4% of the total conformations, indicating that the freedom of rotation of glucose residues is highly restricted in all the three polysaccharides. The additional restrictions of the monomer unit, as one passes from disaccharide to polysaccaride structures, are severe in the case of (1 → 2) and (1 → 3) linked polysaccharides but not in (1 → 4) linked polysaccharide. The difference in the nature of linkages also has shown to affect the energetically preferred conformations: (1 → 2) linkages lead only to left handed helical conformations; (1 → 3) linkages lead to both right and left handed wide and extended helical conformations, (1 → 4) linkages lead to both right and left handed extended helical conformations. The possible hydrogen bonds between adjacent residues are also dependent on the nature of linkage.

The chain length dependence of the conformation for oligomers of L-lysine in aqueous solution: optical rotatory dispersion studies.

Abstract: The optical rotatory dispersion of L-lysine oligopeptides (Lysn, n = 2–22) in solution was measured in water and in 50% methanol. A gradual change with increasing chain length in the ORD curves of the oligomers was observed at pH 4. 3. Not even a chain of 22 residues had ORD identical with that of high molecular weight poly-L-lysine. A plot of the average molar residue rotation at 233 nm versus 1/n (where n is the chain length) resulted in a straight line with an intercept of −1900, representing the internal residue rotation of a lysine residue in the random conformation, and a slope of +6200 representing the large end effect. At pH 11.9 a stright line is obtained up to n = 12 after which it deviates from the initial slope indicating onset of helicity. Extrapolation of the initially straight line to tire higher n's provided the necessary zero-helicity values for calculation of helicity. The highest oligolysine (n = 22) showed at pH 11. 9 13% helicity, which on adding methanol to 50% increased to about 50% helicity. It is shown that helix-coil data which are usually obtained from the temperature dependence of helicity can be obtained from the dependence of helicity on chain length applying the statistical theory. For the methanol-water system the cooperativity parameter v was calculated to be in the range 0.024–0.060, with corresponding equilibrium constants w of 1.32–1.43. The helical structure was calculated to be less stable in water than in methanol-water by about 250 calories per residue.

Circular dichroism of superhelical DNA.

Abstract: The circular dichroism (CD) spectra of a number of superhelical DNA's have been measured The introduction of negative superhelical turns causes an increase in magnitude of the positive band around 280 mμ, while the trough around 250mμ is little affected For two samples of λb2b5c DNA (20 Mdalton) containing different number of negative superhelical turns, the magnitude of the positive band relative to that of the nicked control increases with increasing number of superhelical turns In 2M NaCl, the small (145 Mdalton) superhelical DNA from E coli 15 shows an unusually large difference in CD compared with that of the same DNA with a few single-chain scissions per molecule This large difference is not observed in a medium containing p 011M NaCl These results indicate that the double helix in a superhelical DNA is perturbed somewhat due to the bending and torsional forces in such a molecule The magnitude of such structural alteration seems to depend on the number of superhelical turns per unit length, the size of the DNA molecule, as well as the ionic medium

Density‐gradient sedimentation equilibrium of DNA and the effective density gradient of several salts

Abstract: The various treatments of sedimentation equilibrium are compared on a theoretical and an experimental basis. Particular attention is paid to the polyelectrolyte nature of the problem and the choice of a neutral component. The effective density gradients of several cesium salts for DNA are measured. Two previous theories for the effective density gradient are shown to be equivalent, and the experimental values are interpreted with respect to these theories. It is clear t hat sedimentation equilibrium in a density gradient may be used for the determination of unambiguous molecular weights.