Oligonucleotide studies: optical rotatory dispersion of normal and 2'-O-methylated diribonucleoside monophosphates

The optical rotatory dispersion (ORD) of several diribonucleoside monophosphates (NpN) and the corresponding 2′-O-methyl substituted dinucleoside monophosphates containing 2′-O-methyl ribosyl 3′-nucleotide and a 5′-nucleoside (NmpN) were measured at pH 1, 7, and 11.2, at 0.1 ionic strength in order to examine the role of the 2′-hydroxyl group of the ribose in the conformation of the oligoribonucleotides. The optical measurements are reported from 210 to 340 mμ. The pH effect on the ORD spectra of NpN as well as NmpN are large. No dramatic changes are seen in the shapes of the ORD spectra of the NmpN to the corresponding NpN at pH 7. However, a decrease in the amplitude is seen in most of the NmpN over that of the corresponding NpN ranging from 7 percent in the case of UmpG to 46 percent in AmpA. The differences seen in the NpN and the corresponding NmpN ORD results are best explained as a consequence of a change in the ribosyl conformation on 2′-O-methylation, rather than the involvement of the 2′-hydroxyl group in intramolecular hydrogen bonding in the ribo dimmer. The NmpN behave like NpN and not dNpdN, suggesting that the geometry of the stack in NpmN and NpN depends on the oxygen at the 2′-carbon and not on what is attached to it.     

Conformational studies on copolymers of L-lysine and L-leucine: circular dichroism and potentiometric titration studies

Conformational aspects of a series of copolymers of L -Leucine and L -leucine [poly-(Lys^xLeu^y)] containing 0 to 0.41 mole fraction L -leucine have been studied by circular dichroism (CD) and potentiometric titration in 0.05M KF solution. CD studies on the α-helical conformation showed a dependence of the magnitude of the CD ellipticity band at 222 nm on copolymer composition; the [θ]₂₂₂ decreasing with higher leucine contents. This was interpreted as the result of an increase of the hydrophobicity of the environment of the amide group due to the presence of the leucyl residues. Values of the Zimm-Rice parameter, σ, for the copolymers were obtained from the potentiometric titrations and used to fit theoretical curves to the experimental data. Using the variation of σ with polymer composition, a value of σ for the leucyl residue was estimated to be 6.3 × 10^?2, assuming independence of σ on the amino acid sequence in the copolymer. The free energy change for the conversion of one mole residue from uncharged helix to uncharged coil, ΔG_hc°, was also obtained from the titration data for each copolymer up to a leucine mole fraction of 0.16; a value of 385 cal mole^?1 was estimated for ΔG_hc° for a leucyl residue. These values for σ and ΔG_hc° are compared with other values in the literature for various amino acid residues obtained from titration and melting curve data.     

The optical rotatory dispersion of myosin a IV. Conformational changes in meromyosins

The effect of 8% dioxane on the optical rotatory dispersion of myosin A purified by treatment with DEAE-cellulose was measured in 0.6 M KCl and at pH 7.0 and 20°. The increase in the —b₀ term by 5% was followed by a gradual decrease to 0.88 of the original. The —b₀ term of L₁-meromyosin in 0.6 M KCl and at pH 7.0 and 20% was 575 and was unchanged by the addition of dioxane, ATP of PP₁. On the other hand, the —b₀ term of H₂-meromyosin in 0.3 M KCl and at pH 7.0 and 20% was 263. It increased by several percent immediately after the addition of 8% dioxane and decreased gradually with time. It increased by several percent on the addition of 4 moles p-chloromercuribenzoate, but decreased by several percent on the addition of 8 moles p-chloromercuribenzoate per 10⁵ g protein. It was also decreased by the binding of H₂-meromyosin with F-actin. ATP increased the —b₀ term of H₂-meromyosin by several percent, though PP₁ decreased the term by several percent. Thus these reagents change the helical content of H₂-meromyosin in ways similar to the case of myosin A. The extents of the changes in the helical content of H₂-meromyosin by F-actin and ATP were, however, higher than those observed in myosin A.     

Optical rotatory dispersion and circular dichroism of silver(I):Polyribonucleotide complexes

Optical rotatory dispersion (ORD) and circular dichroism (CD) spectra of single- and multistranded polyribonucleotides undergo extensive changes on binding of the silver ion. These changes are consistent with the proposition that Ag(I) binds to the heterocyclic bases and not to the phosphate groups of polynucleotides. ORD and CD of silver complexes of poly(A)·poly(U) and double-helical rice dwarf viral RNA display negative Cotton effects when there is more than one Ag(I) per two nucleotide residues in solution. These observations suggest a significant distortion of the double-helical conformation as a result of Ag(I) binding. Silver(I) binding sites of pyrimidine polynucleotides are apparently saturated when there is one Ag(I) per two nucleotide residues and those of purine polynucleotides at one Ag(I) per nucleotide in solution. These data are consistent with the supposition that some Ag(I) binding sites exist on the pyrimidine ring and additional sites on the imidazole ring of polynucleotides. The sedimentation coefficient of poly(A) increases by severalfold when one Ag(I) is present per nucleotide residue. Silver(I) may introduce intra- and interstrand cross-links (through bidentate chelates) in single-stranded polynucleotides, resulting in structures with high sedimentation coefficients. Among the polynucleotides studied, poly(U) was an exception. Silver(I) did not affect the optical properties (absorbance, ORD, and CD) of poly(U) at neutral pH.     

Conformational characteristics of luliberin. Circular dichroism and fluorescence studies.

By circular dichroism and fluorescence spectroscopy, the conformation of luliberin (luteinizing hormone-releasing hormone) has been investigated under various conditions of pH and solvents. Several structural parameters have been defined which seem predominant for the maintenance of the hormone in some privileged conformation(s). Formation of an intramolecular hydrogen bond between CO (His) and NH (Ser) seems likely when dissolving the hormone in organic solvent such as dioxane. Energy transfer has been demonstrated between Tyr and Trp residues. Calculation of the energy-transfer efficiency at different pH's allowed us to estimate in the range of 10 A the distance which separates these residues. Evidence is also provided for a charge-transfer interaction between protonated histidine and tryptophan. These data suggest that, when luliberin has organized structure (under appropriate surrounding conditions), its conformational pattern would resemble that of beta-turn structure in which a beta bend would exist at the level of the aromatic residues.     

Study by circular dichroism and optical rotatory dispersion of polypeptides with aromatic side-chain chromophores

Poly(ortho-, meta-, and para-γ-nitrobenzyl-L -glutamates) were studied by circular dichroism (CD) and optical rotatory dispersion (ORD) in two helicogenic solvents, hexafluoroisopropanol (HFIP) and dichloroethane (EDC), and two non-helicogenic solvents, dichloracetic acid (DCA) and trifluoroacetic acid (TFA). The corresponding glutamates were also studied in DCA and TFA. The symmetric nitrobenzylic chromophore is optically active when the polymers are in solution in DCA and TFA. The corresponding glutamates are also optically active under the same conditions. Thus, it was not possible to explain the origin of the optical activity of the side-chain chromophore when the polymer is in solution in a helicogenic solvent. Nevertheless, from a side-chain dichroic band, a helix–coil transition curve was determined and the stability of each poly(γ-nitrobenzyl-L -glutamate) given; this stability depends on the position of the nitro substituent on the aromatic ring.     

Circular dichroism and proton magnetic resonance studies of random chain poly-L-lysine

The 218-nm peak, characteristic of the circular dichroism of randomly coiled poly-α-amino acids can be demonstrated in solutions of penta-L -lysine, α-glycyl-L -lysine, as well as poly-L -lysine. The thermal stability of the particular state that gives rise to this 218-nm band in the CD is similar for all three peptides. These results eliminate the possibility that poly-L -lysine forms a structure with long-range order in acidic aqueous solution since the stability of such a structure would be expected to be greater for a higher molecular weight polymer than for a pentamer. The intrinsic viscosity of poly-L -lysine of molecular weight 180,000 varies only slightly between 25 and 60°C. The proton magnetic resonance spectra of poly-L -lysine and penta-L -lysine are indistinguishable on the basis of the chemical shift of all resonances, their line widths, and the exchange rates of the N? H protons. This demonstrates that poly-L -lysine does not possess a cooperatively formed ordered structure in acidic solutions. A weak band at 238 nm is observed in the circular dichroism of poly-L -lysine and other peptides. It is suggested that the effects of change in temperature, salt concentration, or polymer on both the magnitude and position of the 238-nm band may be explained if it is assumed that it is a shoulder of a lower wavelength peak.