Form Of Poly Research Articles

UV resonance Raman contribution to structure determination of the X form of double-stranded poly(dA-dT)

Double-stranded poly(dA-dT) in aqueous solution and in the presence of a sufficient amount of a water soluble porphyrin (i.e. Cu(TMpy-P4)) can adopt a structure different from all canonical A-, B- and Z-DNA conformations. The corresponding circular dichroism (CD) spectra yield the same features as those of the so-called “X form” observed in highly concentrated CsF solutions of the same polymer. Resonance Raman spectra of this form were compared with those of the canonical B form of poly(dA-dT) obtained using the same UV excitation wavelengths (257 and 281 nm). No spectral modification of the adenine bands was observed which would imply any C2′-endo/anti to C3′-endo/anti or C3′-endo/syn sugar-pucker reorganization of the purine residues, as would be expected for the A or Z forms, respectively. Consequently, it is assumed that the conformation of adenine residues remains C2′-endo/anti, i.e characteristic of the B-DNA structure. In contrast, there is much spectral evidence that the sugar-puckering of thymine residues is different in the X form compared with that in the B form. Shifts and intensity changes in the ring and sugar coupled modes at 665, 745 and 784 cm −1 are interpreted in terms of a C3′-endo/anti reorganization of thymine residues. This B–X structural transition also induces modifications in the thymine C4O hydrogen-bond network with opposite adenine bases, as reflected in the variation in intensity of the 1370 cm −1 band and splitting of the 1660 cm −1 band.

Comparison of base inclinations for left‐handed DNA and RNA

AbstractThe Z'‐form of poly(dG‐m5dC) · poly(dG‐m5dC) in 85% ethanol/MOPS and the Z‐form poly(rG‐rC) · poly(rG‐rC) in 4.8 M NaClO4, 20% ethanol are studied by flow linear dichroism. Simulataneous analysis of the isotropic absorption and linear dichroism data yields the angle of inclination of the base normal relative to the helix axis, and the orientation of the axis around which the bases incline. For the Z'‐form of poly(dG‐m5dC) · poly(dG‐m5dC) the inclination angles are 31.3° for guanine, and 27.9° for cytosine; for the Z‐form of poly(rG‐rC) · poly(rG‐rC) they are 25.0° for guanine, and 23.3° for cytosine. The inclination angles for the Z'‐form DNA are similar to those for the Z‐form, and the angles for Z‐form RNA are somewhat smaller. The axes of inclination for guanine and cytosine are similar in all three left‐handed forms. © 1995 John Wiley & Sons, Inc.

Laser Desorption Mass Spectrometry of Chemically and Electrochemically Prepared Poly(2-vinylthiophene)

We have used laser desorption Fourier transform mass spectrometry to determine the molecular weight distributions of three forms of poly(2-vinylthiophene): polymer A, the classic, free radical-initiated form, polymer B, produced as a precipitate during the anodic oxidation of the monomer, and polymer C, formed as an insoluble film on the anode during the same oxidation. We have obtained molecular weight distributions for all three of these products in the form of Na + -attached species. Analysis of the mass spectral data allows us to reach several conclusions. For polymer A, initiation takes place by benzoate radicals, and this reaction is faster than decomposition of benzoate radicals to phenyl radicals and carbon dioxide

Synthesis of functionalized platinum complexes containing dimethylsulfoxide as leaving group. Observation of novel steric control of intrastrand versus interstrand cross-linking by use of bulky ligands

Dinuclear bis(platinum) cations, containing as potential leaving group dimethylsulfoxide (Me 2SO), were prepared. The general formula is [{ trans-Pt(Me 2SO)(NH 3) 2} 2NH 2(CH 2) nNH 2] 4+. These complexes were found to induce the Z form of poly(dG-dC).poly(dG-dC). The complexes also appear to bind to DNA forming interstrand cross-links by displacement of Me 2SO. In aqueous solution, rapid hydrolysis occurs to free diamine and the trans-[Pt(H 2O)(Me 2SO)(NH 3) 2] 2+ cation. In a surprising finding, this monomeric species (as the chloride trans-[PtCl(Me 2SO)(NH 3) 2] +) was found to be a much more efficient interstrand cross-linking agent than the parent trans-[PtCl 2(NH 3) 2]. Thus, steric control by bulky ligands such as Me 2SO may be used to affect relative tendencies to inter- or intrastrand cross-link formation in platinum complexes.

Polymorphism in poly(aryl ether ketone)s

Polymorphism in poly(aryl ether ketone)s (PEKs) has been studied by X-ray diffraction as a function of the chemical structure and the crystallization conditions. Two types of chemical variations were investigated: (1) the molar ratio of the keto/ether linkages (expressed as % ketone linkages) was varied from 33 to 67% using the wholly 1,4-substituted forms of poly(aryl ether ether ketone) (PEEK), PEK, poly(aryl ether ketone ether ketone ketone) (PEKEKK) and poly(aryl ether ketone ketone) (PEKK) and (2) the partial replacement of 1,4-substituted phenyl residues with their 1,3-substituted counterparts of PEKK and PEKEKK. As-polymerized polymers and materials prepared by melt crystallization, cold crystallization and crystallization induced by exposure to methylene chloride (solvent crystallization) were used. For all of the polymers investigated, the conventional structure, known as form 1, was observed in samples prepared by melt crystallization. In contrast, for polymers crystallized under one of the other conditions, the second polymorph, known as form 2, was sometimes observed. The occurrence of form 2 was found to be dependent on chain stiffness, which was systematically modified by changing the 1,3-substituted/1,4-substituted isomer ratio and/or by changing the ether/keto linkage ratio and molecular mobility during crystallization. With the increase of chain stiffness and the decrease of crystallization mobility, the ability to form the second polymorph was significantly enhanced. Polymorphism in poly(aryl ether ketone)s may be due to the nucleation control: the stable, form 1 phase has a slower nucleation rate, and thus a higher crystal surface free energy than the metastable form 2 phase.

Z-->B transition in poly[d(G-m5C)2] induced by interaction with 4',6-diamidino-2-phenylindole.

The Z form of poly[d(G-m5C)2], in presence of Mg2+ ion, is found to be transformed into B form upon interaction with 4',6-diamidino-2-phenylindole (DAPI). The Z-->B transformation is complete at a mixing ratio of about 0.07 DAPI per DNA base pairs, i.e., each DAPI molecule may be related to the conversion of 6-7 base pairs. An interaction between DAPI and poly[d(G-m5C)2] in its Z form at low drug: DNA ratios is suggested from optical dichroism and time-resolved luminescence anisotropy results. The spectroscopic behaviour of DAPI indicates that the Z conformation of DNA does not provide normal binding sites for DAPI, such as groove or intercalation sites, but that the initial association may be of external nature.

Infrared spectroscopy and stereochemical structure of poly(P-phenylene vinylene)

Theoretical infrared (ir) spectra of trans- and cis- forms of poly(p-phenylene vinylene) (PPV) are presented, based on a single-period-chain model and harmonic potential with parameters transferred from p-divinyl benzen molecule. The out-of-plane degrees of freedom and the infrared intensities were included in the calculations. The calculations of polarized infrared spectra of cis- and trans-PPV do not show practically any difference. However, as the calculations evince the absence of the in-plane C-H bending infrared absorption band of trans-vinylene portion of experimental infrared spectrum of PPV, which is a consequence of a delocalized π-electron system (similarly to the case of trans-polyacetylene but not cis-polyacetylene), it seems that stereochemical structure of PPV is of the trans-form. Additional X-ray analysis is still necessary to support our conclusion.

Soluble Conducting Polythiophenes for Charge Dissipation in Electron Beam Lithography

ABSTRACTIn electron beam lithography, charging on photoresist usually causes image distortion and placement error. To dissipate the charge, a conductive polymeric layer can be introduced either over or under the photoresist coating. In this paper, we will discuss the approach of using toluene and xylene soluble polyalkylthiophcne in combination with photoacid generator as a discharge underlayer or interlayer beneath photoresist to dissipate the accumulated charge during li-bcam exposure. We will also discuss the use of water soluble acid or ammonium salt form of poly 3- (cthanesulfonate) thiophene as discharge. toplayer. During the resist image developing process, the toplayer will be removed by aqueous base. Therefore, it is advantageous to use discharge toplayer due to its simplicity. In this study, the salt and acid form of poly 3- (ethanesulfonate) thiophene was synthesized through chemical polymerization of the corresponding methanesulfonate ester. It exhibits the same properties as that of electrochemically synthesized polymer reported in the literature.

Conformational energy studies of β‐sheets of model silk fibroin peptides. I. Sheets of poly(Ala‐Gly) chains

A new model structure is proposed for the silk I form of the crystalline domains of Bombyx mori silk fibroin and the corresponding crystal form of poly(L-Ala-Gly). It was deduced from conformational energy computations on stacked sheet structures of poly(L-Ala-Gly). The novel sheet structure contains interstrand hydrogen bonds but is composed of anti-parallel polypeptide chains whose conformation differs from that of the antiparallel beta-sheets that constitute the silk II structure. The strands of the new sheet have a two-residue repeat, in which the Ala residues adopt a right-handed and the Gly residues a left-handed sheet-like conformation. The computed unit cell is orthorhombic, with cell dimensions a = 8.94 A, b = 6.46 A, and c = 11.26 A. The model accounts for most spacings in the observed fiber x-ray diffraction patterns of silk I and of the silk-I-like form of poly(L-Ala-Gly), and it is consistent with nmr and ir spectroscopic data. As a test of the computations, the well-established beta-sheet structure of silk II and the corresponding form of poly(L-Ala-Gly) have been reproduced. The computed energies for the two forms of poly(L-Ala-Gly) indicate that the silk-II-like form is more stable, by about 1.0 kcal/mol per residue. The main difference between the two structures is the orientation of the Ala side chains of neighboring strands in each sheet. In the Pauling-Corey beta-sheet and in the silk II form, referred to as an "in-register" structure, the Ala side chains of every strand point to the same side of a sheet. In the silk I structure, referred to as "out-of-register," the side chains of Ala residues in adjacent strands point to opposite sides of the sheet.

Two new photoaffinity polyamines appear to alter the helical twist of DNA in nucleosome core particles

Two new photoaffinity derivatives of polyamines have been synthesized by the reaction of spermine or spermidine with methyl 4-azidobenzimidate. The new compounds were purified chromatographically and characterized by several methods including proton magnetic resonance spectroscopy. The spermine derivative is N1-ABA-spermine [(azidobenzamidino)spermine], and the spermidine derivative is a mixture of N1- and N8-ABA-spermidine. ABA-spermine stabilizes nucleosome core particles in thermal denaturation experiments, with similar but not identical effects when compared with the parent polyamine, spermine. In circular dichroism experiments, ABA-spermine was capable of producing a B----Z transition in poly(dG-m5dC) at a concentration of 30 microM, compared with 5 microM required to produce the same effect with spermine. On the other hand, ANB-spermine [(azidonitrobenzoyl)spermine; Morgan, J. E., Calkins, C. C., & Matthews, H. R. (1989) Biochemistry 28, 5095-5106] stabilized the B form of poly(dG-br5dC). ABA-spermine is a potent inhibitor of ornithine decarboxylase from Escherichia coli, giving 50% inhibition at 0.12 mM, while ANB-spermine is a modest inhibitor, comparable to spermine or spermidine. Under conditions of nitrogen-limited growth, yeast take up ABA-spermine and ABA-spermidine at approximately one-third to half the rate of spermidine or spermine. In contrast, ANB-spermine was not significantly taken up. The photoaffinity polyamines were used to photoaffinity label the DNA in nucleosome core particles, and the sites of labeling were determined by exonuclease protection. All photoaffinity reagents showed both nonspecific labeling and specific sites of higher occupancy. However, the positions of the sites varied: the ANB-spermine sites confirmed those previously reported (Morgan et al., 1989); the ABA-spermine and ABA-spermidine sites were spaced at 9.8 bp intervals from the 3' end of each DNA strand. This observation, together with the effect of spermine on the circular dichroism of DNA in nucleosome core particles, implies that polyamines alter the helical twist of DNA in nucleosome core particles. The ABA-polyamines are offered as general-purpose photoaffinity polyamine reagents.

Crystal transition and structure of poly (γ‐n‐alkyl glutamate)s

AbstractThe nature of the crystal transition of the α‐helical forms of poly (γ‐n‐alkyl glutamate)s (alkyl = ethyl, propyl, and butyl) is described. The transition is thermally reversible, and its temperature T2 is much higher than the glasslike transition temperature T1 associated with the side‐chain motion. The main chains undergo large‐scale motion (librational about the chain axis and translational along the axis) above T3 ≈ 200°C. The structure observed below T2 is anomalously disordered compared with that observed between T2 and T3. The crystal structure emerging above T2 is analyzed for a typical sample of poly(γ‐n‐propyl L‐glutamate). The trigonal unit cell contains three α‐helices so that each helix is surrounded by other helices in the same fashion, but the helices are not interrelated by a crystallographic symmetry element. The side chains suffer no particular change at T2. The main‐chain motion gives rise to the T2 transition by inducing attractive forces between interpenetrating side chains.

Observation of strain-induced β form in poly(β-hydroxyalkanoates)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTObservation of strain-induced β form in poly(β-hydroxyalkanoates)W. J. Orts, R. H. Marchessault, T. L. Bluhm, and G. K. HamerCite this: Macromolecules 1990, 23, 26, 5368–5370Publication Date (Print):December 1, 1990Publication History Published online1 May 2002Published inissue 1 December 1990https://doi.org/10.1021/ma00228a014RIGHTS & PERMISSIONSArticle Views412Altmetric-Citations126LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (868 KB) Get e-Alerts Get e-Alerts

Characterization of a bipolaronic form in poly(2-methylaniline)

The electropolymerization of 2-methylaniline gave uniform electroactive polymer films which were analyzed by cyclic voltammetry and spectroelectrochemistry in different acidic conditions. It has been found that a protonated (bipolaronic) form can be stabilized in the fully oxidized polymer at pH < −0.5 and this new electronic structure is characterized by an absorption band at 630 nm. However, in-situ conductivity measurements have shown an insulating behaviour for this protonated fully oxidized form whereas the partially oxidized (polaronic) structure is conducting.

X‐ray diffraction studies on the cross‐β form of poly (O‐benzyl‐L‐serine)

AbstractPoly(O‐benzyl‐L‐serine) of degree. polymerization 90 in oriented film cast from dichloroacetic acid (DCA) solution yielded the x‐ray patterns of the intramolecular cross‐β form, in which the extended segments stand upward and downward to the surfaces of a thin film. These x‐ray photographs further suggest that residual solvent molecules are bound to the polymer, and it may provide an important clue in understanding the nature of the cross‐β conformation in a diluted DCA solution.

Conformational Isomerizations of the Poly(dA-dT) and Poly(amino2dA-dT) Duplexes Involving the Unusual X-DNA Double Helix: A Fourth Derivative Spectrophotometric Study

Fourth derivative spectrophotometry has been applied to monitor conformational isomerizations of polynucleotides for the first time. The transitions studied have been the B-A and A-X isomerizations of poly(dA-dT) and the B-X one of poly(amino2dA-dT). Parameters obtained from the fourth derivative spectra have been used to follow these conformational changes. The A form of poly(dA-dT) has been characterized by a new fourth derivative peak at 293.0 nm which can be associated to interstrand adenine-adenine interactions. Furthermore, some of the fourth derivative peaks in the long wavelength region (270-310 nm) can be related to stacking interactions present in the polynucleotide double helices. The tentative assignment of these peaks, particularly that at 299.0 nm in the derivative spectra of poly(amino2dA-dT), to n----pi electronic transitions is discussed.

Stabilization of the Z′ form of poly(dGdC):poly(dGdC) in solution by multivalent ions relates to the Z¶form in crystals

Both multivalent ions and 85% ethanol are required to produce the original Z' form of poly(dGdC):poly(dGdC) in solution. When multivalent impurities are removed by dialysis against 0.5 M NaCl and 1 mM EDTA, the circular dichroism retains features of the standard Z form. Addition of Ca+2 nearly reverses this effect. Analysis by singular value decomposition of near-ultraviolet circular dichroism spectra collected during titrations of polynucleotide in 60% ethanol with multivalent ions reveal that, at concentrations below .5 per nucleotide, they stabilize Z'-like forms in a two-state equilibrium with the Z form. Differences among the Z' spectra produced by the different ions suggest that at least three families of Z' structures exist. Furthermore, comparison with crystal data indicates that the Z' form in solution is related to the ZII form in crystals.

Divalent cations are not required for the stability of the low-salt Z-DNA conformation in poly(dG-ethyl5dC).

It is demonstrated that poly(dG-ethyl5dC) adopts Z form in low-salt solution like poly(dG-methyl5dC). Its existence is, however, not contingent on the presence of divalent cations in the polynucleotide solution. The Z form is transformed into B form below room temperature. The arising B form cannot be transformed back into Z form by millimolar MgCl2 concentrations. On the contrary, the addition of MgCl2 at room temperature converts the low-salt Z form of poly(dG-ethyl5dC) into B form. It follows from the results that Z form is a stable DNA conformation not only at high but even at low ionic strengths.

Electroinitiated polymerization of bis(4-bromo-2,6-dichlorophenoxo) N, N, N′, N′-tetramethylethylenediamine copper(II) complex

Electroinitiated polymerization of bis(4-bromo-2,6-dichlorophenoxo) N, N, N′, N′-tetramethylethylenediamine copper(II) complex was achieved upon oxidation. Prior to polymerization a cyclic voltammogram (CV) of the complex was obtained. Polymerization potentials were selected as the oxidation and reduction peak potentials of the complex, obtained by CV. Polymers in the form of poly(dihalophenylene oxide), were obtained by constant potential electrolyses carried out at redox peak potentials of the complex. No ligand or copper was found to incorporate into the final polymer product. The mechanism of polymerization was found to be free radicalic. It was also found that post-polymerization proceeds in the absence of current, when current is ceased after approximately 10 minutes of electrolysis. Percent conversions of polymerization had been measured by an electrochemical technique via simultaneous measurement of reacted monomer concentration. In order to follow the reacted monomer concentration by simultaneous CV measurement, a special H-type electrolysis cell with six electrodes was constructed. Polymers were characterized by 1H-n.m.r., 13C-n.m.r. and FTi.r. spectroscopy along with molecular weight measurements by the isopiestic method.

Application of polarography to the study of complexation and stacking interactions of bases in the BZ helical transition of poly[d(GC)] and poly[d(G-m 5C)] induced by Ni(II) and Mn(II)

The complexation of polynucleotides, poly[d(GC)] and poly [d(G-m 5C)], by transition metal ions, Ni(II) and Mn(II), was studied by polarographic methods (dc and DP) at the conditions of the BZ helical transition of these polymers. In the case of Ni(II), the appearance of two peaks or waves corresponding to the reduction of (Ni 2+-base) aq complex and Ni 2+ aq, respectively, allows the monitoring of the complexation of the bases independently from the complexation of phosphate groups of polynucleotides. The changes in the stacking interactions of nucleic acid bases in nucleosides and dinucleotides in the presence of Ni(II) and Mn(II) were studied by ac polarography, as changes in “pits” or “wells” on double layer capacitance curves due to adsorption and association of bases on the electrode. Simultaneously, changes in complexation of these metal ions with the addition of nucleic acid components were monitored by DPP. The results were used to predict the stacking interactions in the B and Z form of poly[d(GC)] and [poly[d(G-m 5C)]. It was found that there exists a good correlation between the stacking pattern predicted from our ac polarographic data and that known from crystal structure data of these polynucleotides. The nature of the B to Z transition was explained as a change in stacking interactions between nucleic acid bases due to their complexation by transition metal ion. The proposed mechanism of the B to Z transition of polynucleotides resembles Calladine and Drew's explanation of the B to A transition based on the analysis of appropriate crystal structures.

Application of polarography to the study of complexation and stacking interactions of bases in the B–Z helical transition of poly[d(G–C)] and polyld(G-m 5 C)] induced by Ni(II) and Mn(II)

The complexation of polynucleotides, poly[d(G–C)] and poly [d(G-m 5 C)], by transition metal ions, Ni(II) and Mn(II), was studied by polarographic methods (dc and DP) at the conditions of the B–Z helical transition of these polymers. In the case of Ni(II), the appearance of two peaks or waves corresponding to the reduction of (Ni 2+-base) aq complex and Ni aq 2+, respectively, allows the monitoring of the complexation of the bases indepently from the complexation of phosphate groups of polynucleotides. The changes in the stacking interactions of nucleic acid bases in nucleosides and dinucleotides in the presence of Ni(II) and Mn(II) were studied by ac polarography, as changes in “pits” or “wells” on double layer capacitance curves due to adsorption and association of bases on the electrode. Simultaneously, changes in complexation of these metal ions with the addition of nucleic acid components were monitored by DPP. The results were used to predict the stacking interactions in the B and Z form of poly[d(G-C)] and poly[d(G-m 5 C)]. It was found that there exists a good correlation between the stacking pattern predicted from our ac polarographic data and that known from crystal structure data of these polynucleotides. The nature of the B to Z transition was explained as a change in stacking interactions between nucleic acid bases due to their complexation by transition metal ion. The proposed mechanism of the B to Z transition of polynucleotides resembles Calladine and Drew's explanation of the B to A transition based on the analysis of appropriate crystal structures.