Poly double stranded helix

Clustering (association or aggregation) as a result of dissimilar parts within one chain molecule is well-known in the field of biopolymers a recent example in the field of synthetic polymers is provided by poly (p-nitrophenylmethacrylate) which in dimethylformamide (105) forms threefold clusters, presumably because of the difference in polarity of backbone and ester groups. Liquori (118) has presented proof for a double-stranded helix of isotactic and syndiotactic polymethylmethacrylate. 

Figure 2 shows the energy contour map for isotactic poly( methyl methacrylate). The lowest energy minimum was found at the position corresponding to a (12/1) helix contrary to the expectation of the (5/1) helix. The minimum corresponding to the (5/1) helix is higher than the (12/1) helix by 3 kcal/mole of monomer unit. This result led to the postulation of the double stranded helix for this polymer. 

Figure 7. Double-stranded helix of isotactic poly(methyl methacrylate) (30)...

In toluene solution, syndiotactic block copolymers of methyl methacrylate (PMMA) and allyl methacrylate were formed using triphenylphosphine and triethylaluminum as initiator [76]. In acetone solution, syndiotactic poly(methyl methacrylate) forms a stereocomplex with other syndiotactic polymers. The complex formed with syndiotactic poly(allyl methacrylate), upon separation from the reaction mixture and drying had a melting point of 141.5°C by DSC thermogram. From X-ray powder patterns of this and related complexes of PMMA with other polymethacrylates, the authors postulate that a double-stranded helix may represent a model of the structure of these complexes [77]. 

The stereocomplex formed from complementary strands of isotactic and syndiotactic poly(methyl methacrylate)s (it- and st-PMMAs) with an it st-stoichiometry of 1 2 represents another class of unique, polymer-hased helical supramolecules suitable for AFM studies. Although this stereocomplex has heen known for half a century, the molecular basis of the stracture and the mechanism of complex formation are still under dehate. In 1989, Schomaker and Challa proposed a double-stranded helix model for the stereocomplex based on the wide angle X-ray scattering (WAXS) analysis of the stretched fiber, which is composed of a 9i it-PMMA helix (nine repeating MMA units per turn) strrrormded hy an 18i st-PMMA helix, resulting in a double-stranded helix with a helical pitch of 1.84 nm. To verify the stmcture of the PMMA stereocomplex by the AFM technique, Kumaki et al. prepared a mixed monolayer of it- and... 

Keiderling reported the VCD spectra of triple helices in ribonucleic acids by investigating the temperature dependent VCD features of a mixture of poly(rA) and poly(rU) [54]. The spectra of the triple helix are more complicated than those of a double strand, as expected. We have reported the VCD of a number of oligo deoxynu-cleotides with between four and twelve base pairs. These studies will be elaborated upon after a detailed discussion of the VCD features of polymeric DNA and RNA samples, for which the solution structures are well established. 

The distortions induced in the DNA double helix by the interstrand cross-links have been characterized by several techniques. As judged by chemical probes (diethyl pyrocarbonate, hydroxylamine, osmium tetroxide), antibodies to cisplatin-modified poly(dG-dC)-poly(dG-dC), natural (DNase I) and artificial (1,10-phenanthroline-copper complex) nucleases, the cytosine residues are accessible to the solvent, and the distortions are located at the level of the adduct [48-50]. From the electrophoretic mobility of the multimers of double-stranded oligonucleotides containing a single interstrand cross-link [50] it is deduced that the DNA double helix is unwound (79°) and its axis is bent (45°). 

This K is considerably smaller than that of the single-strand polymer at neutral pH, and suggests that the molecules have a rather thick structure. Adopting the interrupted-helix model, we may apply Eq. (97) as in the case of poly-L-proline. Noting that the unit translation distance b0 is 1.70 A for the double-stranded Watson-Crick helix (263 ) [i. e., a distance of 3.40 A for two residues, one in each chain], and taking Mu = 328 for poly(adenylic acid), we obtain r = 22 residues per helical... 

To form double-stranded poly(A)-poly(U), equimolar amounts of the two homopolymers are mixed at a concentration of 0.6-1.5 fiM nucleotide (about 200-500 /iig/ml) in 0.1 A/ NaCl, 0.01 M phosphate pH 7 at room temperature and allowed to anneal for a few hours. Hypochromicity occurs at 260 nm when a double helix is formed and at both 260 and 280 nm when a triple helix is formed. At room temperature and 0.1 Af NaCl, only the stoichiometry determines which helix will form. At high ionic strength (0.7 M NaCl), and at high temperature, even a 1 1 mixture will form a triple helix with time triple-strand formation is also favored by... 

If neither DNA template nor Mg ions are present, then d-ATP and d-TTP give an antiparallel double helix of poly[d-(AT)], in which the d-Ap and d-Tp units alternate with one another in the individual strands [poly(alt-AT)]. A double strand is similarly produced from d-GTP and d-CTP, but in this case one stand is poly(d-G) and the other is poly(d-C). 

It is of interest to note that the model proposed by these authors for poly-L-lysine-DNA complex is quite different from the RNA to poly-L-lysine model described above. They concluded that a molecular model similar to that of deoxyribonucleoprotamine proposed by Wilkins (1956) would be acceptable for the poly-L-lysine DNA complex. In this model, an almost fully extended polypeptide chain also winds helically around the double-stranded polynucleotide chains. Unlike the RNA model, however, the pitch of the polypeptide helix is the same as that of the polynucleotide helices This model requires one amino acid residue per one nucleotide residue, i.e., NH tP = 1 1, as is experimentally observed. On the other hand, this... 

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