Poly hypochromicity

Poly A form a complex with a 4 1 stoichiometry. The apparent hypochromicities of various mixtures are listed in Table 4. The mixtures of A12 with Poly U and of T12 with Poly A showed large hypochromicities compared with other mixtures, which suggests the importance of the hydrogen-bonding formation between complementary nucleic acid bases such as A-U and T-A. 

The important action of electrostatic forces between a cationic model and an anionic polynucleotide is clearly shown in Fig. 7. The hypochromicity sharply decreased with the ionic strength of the solution, which indicates that the base-base interactions between A12 and Poly U supported by the electrostatic attractive forces are weakened by the shielding effects of added salts. 

In order to develop compounds that can selectively target duplex RNA, Sinha et al. [ 194] studied the interaction of berberine with two different conformations of poly(rC) poly(rG) structures. Poly(rC) poly(rG) has been shown [15,215] to exist in two conformations depending on the pH of the solution, the A-form at physiological pH and the protonated form at pH 4.3. These two conformations have been characterized to have clearly defined but distinctly different circular dichroic and absorption spectral characteristics. Both the A-form and the protonated form of the RNA induced moderate hypochromic change and bathochromic shifts in the absorption maxima peaks at 344 nm and 420 nm of the alkaloid with three isosbestic points centered around 357,382 and 448 nm. Binding of berberine to both forms enhanced the fluorescence intensity, which was higher with the protonated form than with the A-from, suggesting clear differences in the nature of orientation... 

The heparin and poly-L-glutamate titrations show a markedly different behavior than do the DNA titrations. As polyanion is added, the fluorescence of the an-thrylpolyamine solution decreases until a well-defined minimum is reached. A new emission at 510 nm, which we assign to the anthracene excimer of 14, increases and decreases coincidently with the titrated fluorescence minimum. Likewise, the UV spectrum of 10 fiM 14 with added heparin shows hypochromism that occurs and disappears coincidently with the fluorescence minimum and a 2-nm red shift. We have proposed template-directed excimer formation as the physical basis for these observations. In the absence of heparin, fluorescence of the unassociated probe is observed. As heparin is added, the fluorescence decreases as a result of heparin-directed interaction between probe molecules. Additional heparin permits the fluorophore population to diffuse over the length of the poly anion, thus avoiding excimer formation and yielding a net CHEF. 

Table 14. Hypochromicity, (%) of the complex formed between poly(VAd) and RNA as a function of the molecular weight...

Complex formation between RNA and water soluble copolymers obtained in the copolymerization of methacryloyloxyethyl-type monomers containing nu-cleobases with water soluble monomers was also studied. Mixing curves between copolymers and between copolymers and RNA are shown in Figs. 14-16. The interaction between poly(MAOFU-co-AAm), poly(MAOT-eo-AAm), or poly-(MAOA-cn-AAm) with RNA was observed, as shown in Fig. 14. The overall stoichiometry of the complexes was about 1 1 and the hypochromicity was about 2% for the copolymer-RNA system under the conditions used. The observed interaction was not as strong as for the poly(VAd)-RNA system and poly(MAOA)-poly(MAOT) system [64], since the solubilizer, AAm, in the... 

A few of these UV resonance Raman studies have reported excitation profiles of oligonucleotides [158, 177], These studies show that the hypochromism in the resonance Raman intensities can be as large as 65% for bands enhanced by the ca. 260 nm absorption band for poly(dG-dC) and that the hypochromism can vary substantially between vibrational modes [177], In the duplex oligonucleotide poly(rA)-poly(rU) [158], similar hypochromism is seen. Although theUV resonance Raman excitation profiles of oligonucleotides have been measured, no excited-state structural dynamics have been extracted from them. 

The hypochromicity of Ad-Q-Ad and poly-VAd corresponds to the formation of the excimer which has also been concluded from the results of the fluorescence emission spectra. The stereomodel of Ad-Q-Ad shows that the conformation in which two adenine rings are situated plane-parallel and, thus, the formation of the excimer is possible. From these considerations, it can be inferred that there exist two kinds of interactions between adenine residues exhibiting either plane-to-plane or coplanar arrangements. Both interactions can be expected to be valid for poly-VAd which includes two kinds of interactions along the polymer chain corresponding to Ad-Q-Ad and Ad-Q-Ad. This effect may give rise to high hypochromicity in the spectra of the polymer. 

The existence of base stacking interaction for poly-VUr was also suggested from UV spectra25). At pH 12, the value of hypochromicity for poly-VUr was 29 to 51 % as compared to 1-ethyluradl. For poly-U solution, the value is only a few percent at room temperature while at lower temperature, about 30% of hypochromicity is observed which is attributed to the formation of a stacked helical polynucleotide structure. It seems therefore likely that the high value of hypochromicity observed for poly-VUr solution may be due to base stacking interactions. 

Figure 6 shows the clear interaction between atactic polyMAOA and atactic poly-MAOT in DMSO-ethylene glycol (3 2 v/v). The overall stoichiometry of the complex is 1 1 under the condition studied. The hypochromicity value obtained from Fig. 6, 14%, is greater than that obtained in trimethyl phosphate6. In DMSO, however, no interactions between these polymers were observed. 

Interactions of the paft copolymers of adenine and thymine on linear and branched polyethylenimine with polynucleotides, poly A and poly U, were studied.57 From the Job plots58 of the A-PEI/T-PEI system at pH 7.4, formation of the complex was observed, the overall stoichiometry of the latter being 1 1 hypochromicity of the 1 1 complex was about 16%. The melting profiles are reversible upon heating and cooling. 

It has been reported that the helicity of poly-L-lysine derivatives decreases with decreasing base content and the formation of complexes between polymers is affected by their helical content79. Effect of helicity of poly-L-lysine derivatives on the complex formation ability has also been observed (Fig. 27). The value of hypochromicity tends to decrease remarkably with falling thymine content in PLL-Ts. The overall stoichiometry of the complex of polyMAOA - PLL-T-65 was obtained as 5 1 (adenine thymine) it does not reflect the stoichiometry at the binding site (the theoretical stoichiometry of the binding sites for the polyMAOA-PLL-T-65 system is 3 2 (adenine thymine)). 

One interesting aspect of this helix-based hypochromicity is that equimolar amounts of right- and left-handed helices will mutually cancel in optical rotatory effect, but that this will not be the case for absorptivity. Indeed, Rosenheck and Doty deduce the existence of appreciable helical content in poly-oL-glutamic acid at pH 3.0 from the decrease in absorptivity (corrected for side chains) vis- -vis a pH 8 solution (random conformation). 

From various physical and biophysical properties of nucleic acid analogs the most important property for the present purpose is their interaction with nucleic acids. The spectrophotometric methods for detection of complex formation were applied to all combinations of polyvinyl polynucleotide analogs and natural polynucleotides (Fig. 3). In aqueous media hypochromic complexes were formed in combinations where the bases in the polynucleotide and analog were complementary. Poly-l-vinylcytosine is soluble in aqueous-propylene glycol base-pair type complexes were detected there also. An analog of polyinosinate, poly-9-vinylhypoxanthine, is soluble only in solutions of a detergent, sodium dodecylsulfate. This detergent intercalates into the polymer and conveys to it an... 

Polymerization and copolymerization of compounds, such as 8-12 with acrylamide, m.aleic anhydride, and 1-vinylpyrrolidone have been performed. The polymeric purine derivatives are generally hygroscopic poly(9-vinyladenine) is soluble in water and gives a hypochromic effect of 13% with ribonucleic acid in aqueous solution. For a review of polycondensation of functionalized purines see ref 234. 

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... 

Poly(I) and poly(C) form only a double helix, and hypochromicity is greatest at 250 nm. Since poly(I) can form helical structure by itself, this mixture of homopolymers is heated to 100° in a boiling water bath to melt the poly (I) structure, and the mixture is allowed to cool slowly to room... 

Poly(A)-poly(dT) shows hypochromicity at 260 nm a triple-helix can form with excess poly(dT) but only in solutions of high ionic strength. Poly(dA) and poly(U) form only a triple helix, with hypochromicity at all wavelengths from 220 to 285 nm. ... 

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