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The structure of the three-stranded helix poly(A+2U)

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... Depending on experimental conditions (temperature, polymer concentration, ion content), poly(rA) and poly(rU) polymers can form a wide range of single, double, and triple helices as well as coils. 22,36,[100][101][102] The next three sections will be devoted to these RNA forms and their computed VCD spectra. They will be discussed in the order of increasing complexity both from the structural and from the computational points of view. ...
... At the conditions of increased salt concentrations or at the simultaneous action of salt and temperature the double-stranded poly(rA)*poly(rU) helix can disproportionate into a triple-stranded poly(rU)*poly(rA)*poly(rU) helix (Fig. 7a) and a single strand of poly(rA). 22,36,100,101,103,110 While triple-stranded structures of nucleic acids are somehow intriguing and might be thought of as untypical, they have been shown to play an important biological role as regulators of eukaryotic gene expression. 111 A site-specific nucleic acid recognition by specially designed oligonucleotides, which can bind to a host DNA molecule forming triple-helical structures (antigene strategy), can be used as a new class of pharmacologically active compounds. ...
... 103,109,110 However, an alternative model, formation of a reverse Hoogsteen-type base pairing, better fits many IR and VCD profiles and their interpretation by the coupled-oscillator model. 29,36,101 The triple-helical RNA was the most computationally challenging due to the large size and uncertainty about its solution geometry. Because this structure was not a canonical one, it could not be easily constructed by available molecular modeling software. ...
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Infrared and Raman spectra of the Mg2+ salt of poly(U) in D2O were recorded in the 1600-1800 cm−1 region and between 1 and 20C. The ir spectra showed a melting curve similar to the uv melting curves with a temperature of transition of about 6.5°C. This spectral change is assumed to be associated with the formation of the secondary structure of Mg2+-poly(U) in D2O at this temperature. Three double-helical and two triple-helical structures were used as inputs to compute the normal modes of vibration. A double-helical structure was found to give the best agreement with the observations. Knowledge of the C=0 eigenvectors, and of the expression for transition probability from quantum mechanics, was used to explain the so far unanswered question of H. T. Miles [(1964) Proc. Natl. Acad. Sci. USA 51, 1104–1109; (1980) Biomolecular Structure, Conformation, Function and Evolution, Pergamon, Oxford, pp. 251–264] as to why there is an increase in the ir vibrational wave number of a carbonyl band when that group is H-bonded to another polynucleotide chain in a helix. Such considerations also explain why a predicted band at about 1648 cm−1 is not to be seen in the ir spectra but is present in the Raman spectra. The model incorporating the CO transition dipole-dipole coupling interaction is able to explain also the observed higher intensity of the higher wave-number ir band. The experimental results demonstrate that the complete picture of vibrational dynamics of Mg2+-poly(U) in D2O is obtained only by looking simultaneously at ir and Raman spectra and not at only one of them. Weak ir bands were found to be as useful as the strong ones in understanding structure and vibrational dynamics. On the bases of our ir and Raman spectra, of the normal-mode analyses, and of the literature data, it is concluded that Mg2+-poly(U) in D2O is present in a double-helical structure at temperatures below the temperature of transition, whereby the uracil residues are paired according to arrangement (a) (see Fig. 1). This structure is rodlike and arises by refolding of one poly(U) chain. The computations show that no normal mode is associated with a single CO group vibration; all CO group vibrations are heavily mixed motions of various CO groups.
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Combining two-color infared pump-probe spectroscopy and anharmonic force field calculations we characterize the anharmonic coupling patterns between fingerprint modes and the hydrogen-bonded symmetric NH$_2$ stretching vibration in adenine-thymine dA$_{20}$-dT$_{20}$ DNA oligomers. Specifically, it is shown that the anharmonic coupling between the NH$_2$ bending and the CO stretching vibration, both absorbing around 1665 cm-1, can be used to assign the NH$_2$ fundamental transition at 3215 cm-1 despite the broad background absorption of water.
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Raman spectra of aqueous solutions of uridine and cytidine have been recorded as a function of pH with the band intensities and vibrational frequencies monitored to determine bands which may be considered as diagnostic of the concentration of the various species. Quantitative band intensity measurements indicate that not all pH-sensitive bands can be considered as diagnostic of the pK value for the acid form of the nucleoside, and for the percent species in solution. Although the accuracy of the Raman band intensity method is inherently less than that of the titrimetric or visible-ultraviolet spectrophotometric methods, the pK values and percent species agree well with those obtained from these methods. The utility of the results obtained from the pH profiles for cytidine is discussed in terms of the effect of acidification on the structural and conformational characteristics of polycytidylic acid in solution.
Article
The resonance Raman spectra of a DNA containing bromodeoxy-uridine (BrdUrd), the poly d(BrU-A), are reported, using U.V. laser as a source of excitation. The conformational change from the ordered, base paired form of poly d(BrU-A) (at 25°C) to the melted form at high temperature (63°C) is reflected in a pronounced hyperchromism of Raman bands at 1627 cm−1, 1352 cm−1 and 1230 cm−1. Particularly the band at 1627 cm−1 assigned to the vibrations of C4 carbonyl which is hydrogen bonded to adenine increases strongly its intensity upon melting. This represents a new approach for a detection of base unpairing and of modifications in geometry of selective molecules (BrdUrd) in a DNA chain in dilute solutions (10−4 M).
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Infrared linear dichroism studies of A-and B-DNA films reveal six bands between 2800 and 3000 cm-1 which must arise from deoxyribose and thymine methyl CH stretching motions. The band at 2890 is perpendicularly polarized in A-DNA but parallel polarized in B-DNA. This band most probably originates in the C'(5)H2 symmetric stretch; the polarization flip is consistent with the structural change occurring at C'(5) during the A to B transition, according to models derived from x-ray work.
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Detailed models are presented for the triple-stranded polynucleotide helices of poly (U)-poly (A)-poly (U) (two forms), poly (U)-poly d (A) -poly (U), poly d(C)-poly d(I)-poly d(C), poly d(T)-polyd(A)-poly d(T) and poly (I)-poly (A)-poly (I). The models were genrated using a computerized, linked-atom procedure which preserves standard bond lengths, bond anglesand sugar ring conformations, constrains the helices to have the pitches and symmetries observed in X-ray diffraction experiments, and optimises the non-bonded interatomic contacts including hydrogen bonds. The possible biological sigificance of such complexes is discussed.
Article
Raman spectra of AMP, UTP, GMP, and CMP, and of their bromo-derivatives (8 Br-ATP, 8-bromo-adenosine, 8-bromo-guanosine, 5-bromo-deoxyuridine, 5-bromo-cytidine), are reported. They are obtained using excitation wavelengths of 457.9 nm (ionized continuous argon laser) and of 300 nm (tunable pulsed dye laser). Comparison of spectra leads to the following observations: (1) preresonances Raman effects on nucleotides spectra at 300 nm; (2) resonance Raman effects on bromoderivatives spectra at 300 nm; (3) in dilute solution (10−4M), shifts and enhancements of Raman lines of the bromo-derivatives with respect to the corresponding lines of nucleoctides. On the basis of these comparisons, the assignments of the Raman lines are discussed, This provide the necessary background for the understanding of the properties of selected groups in DNA in dilute solution. The new experimental set-up for measurements of Raman spectra using excitation in the uv regions is described. It is specially designed to incorporate the pulsed feature of the excitation laser and for correcting of the instabilities of the sourse.
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Intermolecular interactions of guanine-containing dinucleoside monophosphates in aqueous solution have been investigated by Raman spectroscopy. The measurements show that the dinucleotides ApG, GpA, UpG, GpC and GpG can form ordered structures under the conditions used. The association of these dinucleotides can be monitored by changes of the frequency and intensity of the C=O stretching vibrations due to hydrogen bond formation and by hypo- and hyper-chromic effects in the ring vibrations of the bases.
Using the “melting curve” technique, we have been able to demonstrate partial denaturation of the secondary structure of irradiated poly-(A + U): γ rays, 3.5 · 10−4 M nucleotides. The Tm decreases rapidly as the dose of radiation increases. The radiochemical yields (G) for the destruction of the bases in the presence of oxygen are, respectively: G(−A) = 1.11; G(−U) = 1.11; the G value (number of breakages of phosphodiester bonds) is 0.19. However, this denatured poly-(A + U) structure is still able to form a triple helix with another chain of unirradiated poly-U. It has been shown that a single strand of irradiated poly-A or poly-U can easily combine with the complementary unirradiated chain. As the oxygen renders the bases more sensitive to radiation, the recombination is more efficient when the irradiation has been carried out in the absence of oxygen. Moreover, the association of two complementary irradiated chains seems quite difficult. The G values for bases destroyed within the irradiated polymer (when the irradiation is done in twice-distilled water at pH 7) are, for poly-A: G(in the presence of oxygen), I; G (in the absence of oxygen), 0.47; for poly-U: G (in the presence of oxygen), 2.1; G(in the absence of oxygen), 1.
Chapter
In the IR spectra coupling of vibrations leads to band splitting and bands shifting in opposite directions, thus providing information on the orientation of groupings of macromolecules relative to each other. — With polynucleotides base pairing is indicated by such coupling effects with the C=O stretching vibrations. — With ribo(polynucleotides) coupling of the 2’OD bending vibration with the C—O—C stretching vibration of the ether group of ribose residues proves that the ribose residues may be cross-linked via hydrogen bonds, which are formed by the 2’OD groups with the ether O atom of neighboring ribose residues. These H-bonds stiffen the backbone of RNA, inducing, for instance with homoribo (polynucleotides) in neutral medium, rod-like structures. The influence of cations is discussed. Two conformations of the backbone are observed: (a) The groups can be turned outward at the backbone. (b) The groups can be turned toward the base residues. The latter may be induced by cations with strong fields. - It is shown that the conformation of Mg2+ poly(U) is probably a triple and not a double helix. - Melting of base pairing and backbone structure of t·RNAPhe with temperature and dialysis against distilled water are discussed. It is shown that Mg2+ ions increase the melting temperature by 40°C. This effect is preferentially caused by a change of the tertiary and not the secondary structure. In contrast to this result, with 23 S RNA the double helical regions become more compact and strong hydrogen bonds are formed between the 2’OH groups and the ether O atom of neighboring ribose residues, which is due to the influence of Mg2+ ions. Finally, vesicles from excitable membranes are investigated. It is shown that in the presence of K+ ions the conformation of relatively large parts of the membrane proteins occur as an antiparallel β-structure, whereas in the presence of Na+ and Ca2+ ions the proteins are largely helical. Thus it seems highly probable that during the action potential membrane proteins change their conformation, depending on the cations present in the membrane.
Chapter
Nucleic acids are an important class of compounds, which have been studied in great detail. Pauling and Corey (1953) proposed a helical model composed of three chains, each having ribofuranose, phosphate ion, and pyrimidine or purine moieties. The chains wound around the axis to form a rope-like molecule, the core of which was formed by the phosphates with hydrogen bonds and ribose rings connecting them. The pyrimidine and purine rings were connected to the sugars along the outer periphery of the polymer. The Watson-Crick (1953) model for DNA was a hydrogen-bonded one which involved two chains. Each chain had a backbone of sugar-phosphate-sugar-phosphate-sugar, etc. In this model the pyrimidine and purine rings were attached to the sugar molecules in such a way that the bases projected inward toward the core of the polymer. The hydrogen bonds formed in such a manner that two hydrogen bonds linked each purine to a pyrimidine on the opposite chain, and vice versa. Pauling and Corey (1956) then proposed a model in which instead of two hydrogen bonds between guanine and cytosine there were three (Fig. 12.1). The original Watson-Crick model has since been revised by Wilkins and his co-workers (see Mahler and Cordes, 1966).
Chapter
Immunization of an animal with bacterial ribosomes generally elicits the formation of antibodies capable of precipitating not only the homologous ribosomes used for immunization but also ribosomes of different origin (Barbu et al., 1961; Panijel and Barbu, 1961). However, for a given antiserum, the qualitative aspects of the immune reaction vary with the species of bacteria being tested. In addition, as shown in Figure 1 (A, B, C), the amount of antibody precipitable by a given bacterial ribosome varies with the antiserum used. It is evident that ribosomes even from distant species possess common antigenic determinants, thus explaining the cross-reactions observed. With a given antiserum, such as the E. coli K12 ribosome antiserum, one can distinguish the following: (a) homologous ribosomes, e.g., those from various strains of E. coli or even other enteric bacteria; (b) close heterologous ribosomes, e.g., ribosomes of Proteus vulgaris; and (c) distant heterologous ribosomes, e.g., ribosomes of Clostridia. Such a “classification” of ribosomes relative to a given antiserum seems to be genetically significant. Indeed, McCarthy and Bolton (1963), who used the hybridization technique to study the relationship between messenger RNAs extracted from E. coli and DNAs of other origin, subsequently arrived at a classification in agreement with ours.
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The heats of mixing of polyriboadenylic acid (Poly A) and polyribouridylic acid (Poly U) in various proportions by changing the mole ratio n = [Poly U]/[Poly A] in 0,001, 0,1, and 0,5 molar NaCl solutions containing 0,1 molar tris-HCl buffer solution were measured. Constant values for the heats of mixing of the (Poly A+n Poly U) system are found for n ≤ 1 and n ≥ 2. From the results of UV and CD spectra, it may be considered that the mixing of Poly A and n (Poly U) leads to the formation of Poly(A+U) for n ≤ 1, and to that of Poly(A+2U) for n ≥ 2, even at [NaCl] = 0,001 mol/l.The enthalpies of formation of Poly(A+U) and that of Poly(A+2U) depend on the concentration of NaCl. This dependence may be attributed to the differences in conformation of Poly(A+U) in NaCl solution.
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The purpose of this review is to show the extent to which infrared spectroscopy has been and will be useful for elucidating the molecular structures of nucleic acids.
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Interaction of adenosine and poly U† was studied by equilibrium dialysis, solubility, optical rotation, ultracentrifugation and viscosity measurements. Only when a threshold concentration of adenosine is reached does binding of adenosine to poly U take place in a co-operative manner, with a stacking energy of 5 to 6 kcal. estimated from the adsorption isotherm. The complex thus formed has an ordered structure, presumably helical, and, as expected, a molecular weight higher than that of poly U. The stability of the complex, besides being highly dependent on the concentration of adenosine, is influenced by ionic strength and temperature in a manner similar to the system of polynucleotide interaction. The stoichiometry of the complex is 1A to 2U at 5°C and becomes 1A to 1U at 20°C. This interaction is specific, with the possible involvement of N-1,6-amino and N-7 of adenosine in the hydrogen-bonding scheme, while the pentose moiety has a relatively insignificant role. Other studies from our laboratories have shown that both purines and nucleosides associate to form stacks in aqueous solution as a result of hydrophobic and stacking energy. It is proposed that these adenosine stacks are bound to poly U through specific hydrogen bonding. Thus, both hydrogen bonding and hydrophobic stacking energy co-operate and complement each other in providing the driving forces for this interaction.
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The blue complexes produced by reaction of cis-diamminediaquoplatinum(II) nitrate, [cis-Pt(NH3)2(H2O)2](NO3)2, with disodium 5′-uridine monophosphate, 5′-UMP(Na2), in H2O and D2O have been investigated by FT-IR spectroscopy. On the basis of the spectral changes observed in the CO stretching region during the reactions, chelation of the amidate N(3)··O(2) moiety to Pt(II) appears to be more likely than N(4)··O(4) chelation. The antisymmetric PO stretching mode of the PO32− group of 5′-UMP splits into a triplet on complex formation indicating that PO32− plays an important role in the structure of the platinum blue complexes. In addition, the sugar moiety of 5′-UMP apparently adopts a predominantly C(3′)-endo conformation in the solid blue complex. Finally, Raman microprobe spectroscopy of the solid provides some evidence for PtN(3) bond formation.
In the first part of this work, we found that on adding poly(U) to a solution of poly(A) (the molecular weight of poly(U) being smaller than that of poly(A)), the poly(U) macromolecules are randomly distributed on poly(A) macromolecules. This was shown by removing from the solution the completely free poly(A). Free poly(A) is precipitated by increasing the salt concentration of the solution.The second part of the work deals with poly(A) · 2 poly(U) + poly(A) obtained by heating a solution of poly(A) · poly(U) (). For poly(A) larger or identical in molecular weight to poly(U), the transition occurs according to an intramolecular process. For poly(U) larger than poly(A), free poly(A) is found. Molecular weights and radii of gyration of the mixtures were measured by light scattering. We interpreted our results assuming a folding of poly(U) on poly(A). Experimental results on poly(A) · 2 poly(U) prepared by direct mixing of poly(A) and 2 poly(U) give evidence of a similar structure of the complex.
Article
F.t.-i.r. and laser-Raman spectra of thymine and thymidine in the solid state were recorded. Assignments were proposed for the frequencies observed. The influence of the deoxy sugar on the vibrations of the nucleoside are discussed as a function of its particular puckering. The aim of this work is to elucidate the differences between the molecules constituting the nucleic acids, in order the better to comprehend their biological functions.
Article
Light-scattering studies on buffered aqueous solutions of the triple-stranded polyribonucleic acid poly(A)·2poly(U) were carried out at neutral pH and during titration. At pH 7.1 and 22°C, a sample of commercially available polymer in 0.005M phosphate buffer gave a Zimm plot which yielded values for the weight-average molecular weight, Mw, of 874,000 ± 1800 g/mol, a root-mean-square radius, ρ of 930 ± 22 Å, and a second viral coefficient of 0.51 ± 0.05 × 10 −3 cm3g−1 mol. The light-scattering data were also analyzed by serval linear and nonlinear least-squares programs which were devised to determine the model (e.g., rod, coil, or zigzag) which could best describe the shape of the molecule. It was found that a rodlike model, perhaps with a few bends, was in best overall agreement with the data. The assumption that the molecule is a thin rod leads to a value for the linear density of 206 g mol−1 Å−1 and a translation of 3.3 Å per residue. These values are also in close agreement with those expected for a triple-stranded, thin, base-stacked molecule. During titration from neutral pH with 0.1M HCl, the observed apparent molecular weight slowly increased until at about pH 3.5 a sudden, large increase (about 30-fold) occurred. The root-mean-square radius, on the other hand, after an initial small decrease (of about 25%), also exhibited a large increase (about 4-fold). Upon back titration with 0.1M NaOH, the molecular parameters did not retrace the original path, but instead exhibited hysteresis—the Mw and ρz are both larger on the basic branch than on the acid branch at a corresponding pH. A plot of long ρz against log(Mw) during the interval in which the high-moelcular-weight form was present (below pH 3.5 on the acid branch, and on the basic branch) gave a straight line with a slope of ⅓. This suggests that the aggregates were composed of some tens of rather open radom coils, presumably of poly(A)·poly(A), and that the hysteresis may be caused under conditions by the metastability of the entangled coils.
Article
A normal mode analysis has been carried out on the in‐plane vibrations of uracil and three isotopic molecules, N,N‐dideutero, C,C‐dideutero, and perdeutero uracil, using a molecular orbital calculation (MNDO) to constrain the ratios of off‐diagonal to diagonal elements in the compliance matrix (MOCIC). The 81 observed frequencies are calculated with a mean error of 9.7 cm−1. The force constants and normal mode patterns are discussed. The characteristic up‐shift of the 1236 cm−1 mode upon N,N deuteration is reproduced by the calculation, and is ascribable to a change in mode composition from predominantly C=O deformation to predominantly C–N stretching, in agreement with the pattern observed for other cyclic imides. The analogous mode in flavin is variable in different flavoproteins and has been suggested to be sensitive to hydrogen bonding at flavin N3. This effect of hydrogen bonding is modeled in the present calculation by increasing the N–H deformation force constant. A similar perturbation of the C=O deformation constants shows that the 1236 cm−1 mode frequency may also be somewhat sensitive to hydrogen bonding at C4=0, but not at C2=0.
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The infrared spectrum of monomeric uracil, trapped in Ar and N2 cryogenic matrices, is presented and compared with the infrared and Raman spectra recorded for this same compound in associated forms, as observed in its pure solid state and in solution. The monomeric molecules are all in the 2,4-diketotautomeric form and are planar, as can be deduced indirectly from the absence of band multiplicity due to conformeric equilibrium. The assignment is based on comparison with previous works on uracil and with matrix isolation studies on other cis- and trans-imides and is supported by spectral comparison with N,N-dideuterouracil trapped in the same cryogenic matrices. With few exceptions, the assignment is consistent with that obtained by theoretical approaches. On passing from an Ar to an N2 matrix, the bands due to νNH and γNH shift to lower and higher wavenumbers, respectively, as a result of a specific interaction between the NH groups and the N2 molecules.
Article
It has been found that highly syndlotactic PVU has a greater hypochromism and fluorescence emission Intensity along with a different dimethyl sulfoxide denaturation profile than the less syndlotactic polymer in aqueous solutions. These results are probably attributable to an interrelation between the configurational arrangement of uracils, the conformation of the polymers, and base stacking between uracils. In the neutral pH range, before the onset of aggregation and precipitation, the polymers are thought to be in tightly packed coillike conformations which are stabilized by intramolecular base stacking forces. The reaction of highly syndlotactic PVU with Poly A was thought to form a triple stranded PVU:2 Poly A complex, while the less syndlotactic polymer formed a metastable double stranded 33.3% Poly A complex which on equilibration rearranged into a 25% Poly A complex probably containing PVU loops. In the presence of 20% DMSO this system formed a 13% Poly A complex indicative of partial denaturation of the base pairs with DMSO. PVU was also
Patent
The chapter discusses various synthetic polynucleotides. Synthetic polynucleotides are of considerable interest from the biological viewpoint of code cracking, and, also, as grossly simplified models for the study of the numerous physical properties, manifested by nucleic acids. This chapter is discusses the physical studies of the structure in synthetic polynucleotides, including homopolymers of naturally occurring nucleotides and of various analogs. The chapter very briefly reviews some technical aspects of the physical chemistry of polynucleotides. The various random coil and structured forms of polynucleotides, containing a single naturally occurring purine or pyrimidine base, are discussed in this chapter. Under suitable conditions of pH or salt concentration, all such polymers form hydrogen-bonded, multi stranded, secondary structures. The chapter discusses various polynucleotide complexes, such as complexes between Poly G and Poly C. All homopolynucleotides are derived from natural or almost natural nucleotides form multistranded secondary structures under appropriate conditions. In case of the “basic” (or 6-amino) nucleosides (A and C), slightly acidic conditions are necessary, whereas the “acidic” (or 6-keto) polymers (G, U, I, X), all give defined secondary structures at pH 7 albeit, with vast different stabilities.
Article
The optical rotatory dispersion (ORD) and absorption spectra of poly-I, poly-C, poly-(I + C), poly-(A + 2I), and poly-(G + C) were measured at various temperatures. All the polymers exhibited multiple Cotton effects below 300 mμ, but poly-I is the first polynucleotide studied that shows two troughs and one peak between 240 and 300 mμ instead of two peaks and one trough in the same wavelength range, as observed for nucleic acids and other polynucleotides. The complex formations of poly-I with poly-C or with poly-A immediately inverted the ORD profile to one characteristic of other polynucleotides. This must be attributed to the difference in base interactions, since an inverse ORD profile for polynucleotides does not necessarily indicate a change in the handedness of the helices. In all cases the temperature curves of ORD paralleled those of the hyperchromic effect of the polymers. Poly-I showed a broad melting temperature in 0.01 M NaCl but a sharp transition in 1 M NaCl. This supports the contention that poly-I in low salt solution has very little, although not negligible, secondary structure. The three complexes, poly-(I + C), poly-(A + 21), and poly-(G + C), all showed sharp helix-coil transitions, some of which were irreversible and some partially reversible.
Article
Data on complex formation between synthetic polynucleotides and complementary oligo(mono)nucleotides are reviewed and analysed. The principal methods for the investigation of complexes are examined and the limits of their applicability are estimated. Attention is concentrated on the complex formation conditions (temperature, ionic strength, pH, concentration, component ratio, etc.). The influence of the nature of the heterocyclic base and the sugar and of the length of the oligonucleotide chain on the stoichiometry and thermal stability of the complexes is discussed. The bibliography includes 150 references.
Article
The Zimm-Bragg theory is extended to treat the melting of the triple helix poly (A + 2U) for a solution with a 1 : 2 mole ratio of poly A to poly U. Only the case for long chains is considered. For a given set of parameters the theory predicts the fraction of segments in the triple helix, double helix, and random coil states as a function of temperature. Four nucleation parameters are introduced to describe the two order–disorder transitions (poly (A + 2U) ⇄ poly A + 2 poly U and poly (A + U) ⇄ poly A + poly U) and the single order–order transition (poly (A + 2U) ⇄ poly (A + U) + poly U). A relation between the nucleation parameters is obtained which reduces the number of independent parameters to three. A method for determining these parameters from experiment is presented. From the previously published data of Blake, Massoulié and Fresco8 for [Na+] = 0.04, we find σT = 6.0 × 10−4, σD = 1.0 × 10−3, and σσ* = 1.5 × 10−3. σT and σD are the nucleation parameters for nucleating a triple helix and double helix, respectively, from a random coil region. σσ* is the nucleation parameter for nucleating a triple helix from a double helix and a single strand. Melting curves are generated from the theory and compared with the experimental melting curves.
Article
Vibrational frequencies and IR band intensities for 18 isotopomers of uracil, including deuterated 15N and 18O species, have been calculated using the scaled ab initio force field of Ref. 1. The results obtained are compared with available experimental data, and a number of refinements in former assignments are proposed. The good agreement between the calculated and experimental frequencies confirms the reliability of the scaled quantum mechanical-force field.
Article
RNAase III, an endonuclease specific for double-stranded substrates, has been obtained in a highly purified form from extracts of Salmonella typhimurium. Poly (I-C) and a mixture of poly(A) and poly(U) (1 : 1), the latter in presence of 5 mM Mg2+, act as excellent substrates. Poly(I-C) is only partially hydrolysed by RNAase III and the product or products are acted upon by both RNAase I and RNAase II indicating that the products may be oligonucleotides. This conclusion is supported by two-dimensional chromatography on DEAE paper.
Article
IT has been found that the sodium salts of polyadenylic and polyuridylic acids interact1-4 with formation of a two-stranded helix1 with a structure very similar to deoxyribonucleic acid. More recently it was observed that the infra-red spectrum5 of the mixture of these two acids showed the following marked changes from the summation of the curves of the components : a 39 per cent reduction in intensity of the 1,627 cm.-1 band and a 7 cm.-1 shift to higher frequency ; a decrease in peak height (because of strong overlap the band was not integrated) and an 11 cm.-1 shift to higher frequency of the 1,661 cm.-1 band. The interaction of the sodium salts of polycytidylic and polyinosinic acids6 has now been observed in the infra-red7 with the following result : a marked decrease in intensity of the 1,651 cm.-1 peak of the sodium salt of polycytidylic acid (the intensities have not yet been put on a quantitative basis) and a 19 cm.-1 shift to higher frequency of the 1,678 cm.-1 peak of the sodium salt of polyinosinic acid.
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Article
Integrated infrared absorption intensities have been determined for some nucleosides, nucleotides, and polynucleotides in D2O solution.There are marked changes in the infrared spectra upon mixing the polynucleotides Poly A and Poly U. These changes are considered to result from hydrogen-bonding interaction between the two polynucleotides.The spectra indicate that the uracil residues in the nucleosides, nucleotides, polynucleotides, and in the mixture of polynucleotides are in the keto form and that the adenine units are probably in the amino form.
Article
The three-stranded helical complex of polyadenylic acid and polyinosinic acid, poly (A+ 2I), reacts with single-stranded polycytidylic acid to form a double-stranded helix, poly (I + C), with the release of single-stranded poly A according to the reaction, Poly (A + 2I) + 2 poly C → 2 poly (I + C) + poly A This strand displacement reaction was examined by ultraviolet and infrared spectroscopy of the reaction mixture and the reaction products were separated by sucrose gradient sedimentation and identified by ultraviolet spectroscopy. The reaction proceeds readily to completion at temperatures well below the Tm of the less stable reactant helix, poly (A + 2I).
Article
Guanosine has been demonstrated, by infrared and nuclear magnetic resonance spectroscopy, to have a keto-amino structure in neutral aqueous solution and to undergo protonation at N(7) in acid solution.
20 A clear statement of the importance of small deviations from "standard" dimensions has been made by Sasisekharan, drawing examples primarily from the amino acids and peptides
20 A clear statement of the importance of small deviations from "standard" dimensions has been made by Sasisekharan, drawing examples primarily from the amino acids and peptides, Collagen (Interscience, 1962), p. 46.
  • H Ziffer
  • E Charney
  • Spectrochim Acta Karabatsos
E. D., H. Ziffer, and E. Charney, Spectrochim. Acta, 19, 1891 (1963); Karabatsos, G. F., J. Org Chem., 25, 315 (1960).
13 For other examples of the use of 018 substitution as an aid in interpreting vibrational spectra, see, e.g
  • S Pincas
  • D Samuel
  • M Weiss-Broaday
13 For other examples of the use of 018 substitution as an aid in interpreting vibrational spectra, see, e.g., Pincas, S., D. Samuel, and M. Weiss-Broaday, J. Chem. Soc., 2382, 3063 (1961);
  • H T Miles
  • F B Howard
  • J Frazier
12 Miles, H. T., F. B. Howard, and J. Frazier, Science, 142, 1458 (1963).
  • F B Howard
  • H T Miles
14 Howard, F. B., and H. T. Miles, Biochem. Biophys. Res. Commun., 15, 18 (1964).
15 The two bands might, for example, be attributed to symmetric and antisymmetric modes of the C6 = C5 -C4 = 0 system. The relative intensities of the two bands would make it difficult simply to reverse the previous assignments
  • D R Davies
  • A Rich
15 The two bands might, for example, be attributed to symmetric and antisymmetric modes of the C6 = C5 -C4 = 0 system. The relative intensities of the two bands would make it difficult simply to reverse the previous assignments. 16 FeLsenfeld, G., D. R. Davies, and A. Rich, J. Am. Chem. Soc., 79, 2023 (1957). 17Rich, A., Nature, 181, 521 (1958).