Search

One of the dilemmas in predicting the secondary structure of proteins from their amino acid propensity for a given conformation is the presence of all amino acids in all types of secondary structure, regardless of their propensity for that specific structure. One explanation is the nucleation hypothesis that only a few residues with a strong propensity for the secondary structure, such as the alpha-helix structure, initiates its formation and propagates the structure through indifferent sequences until strong breakers terminate the growth on both ends. Eight 15-mer peptides were studied to examine the alpha-helix nucleation hypothesis. The nucleation sequence of VAEAK, with high helix propensity, was mixed with an indifferent sequence of TSDSR in all possible permutations. From the percent alpha-helix structure derived from the CD at 222 nm, it appears that helicity does not propagate through the indifferent sequence.

CD spectra have been measured as a function of temperature for a number of ApA analogues with modified backbones. Oligonucleotides with these modified backbones are being used as antisense agents having potential as viral therapeutics. Results of these studies show that when a carbonyl is substituted for the phosphate to produce an uncharged backbone, the analogues that have either sugar or morpholino substitution do not stack. In contrast, when a morpholino group is substituted for the sugar and the phosphate is modified so as to be uncharged, there is strong base stacking. Stacking interactions in the phosphorus-linked morpholino analogues are at least as strong as those found in d(ApA). The stacking interactions in ApA are weak by comparison. Singular value decomposition demonstrates that the stacking is two state, and Taylor series decomposition yields a coefficient that measures base stacking interactions. The van't Hoff equation is applied to the base stacking coefficient from the Taylor series fitting to give thermodynamic parameters.

Flow linear dichroism measurements extended into the vacuum uv region yield inclinations for the base normal from the helix axis of 21° for dA and 40° for dT in the X-form of poly (dAdT) · poly (dAdT). These inclination angles are similar to the B form of the synthetic polymer, but the axes around which the bases incline are different. Hydrogen-bonded base pairs are consistent with the geometry for the standard B, C, D, and Z forms of natural DNA, but will not fit into the A form. Fourier transform ir spectra indicate that the X form has sugar pucker and phosphate geometry similar to B-form DNA, and supports the dinucleotide repeat with two kinds of phosphates seen in earlier work, in analogy to Z-form DNA. Clearly, X-form DNA has a unique geometry. © 1994 John Wiley & Sons, Inc.

One of the dilemmas in predicting the secondary structure of proteins from their amino acid propensity for a given conformation is the presence of all amino acids in all types of secondary structure, regardless of their propensity for that specific structure. One explanation is the nucleation hypothesis that only a few residues with a strong propensity for the secondary structure, such as the alpha-helix structure, initiates its formation and propagates the structure through indifferent sequences until strong breakers terminate the growth on both ends. Eight 15-mer peptides were studied to examine the alpha-helix nucleation hypothesis. The nucleation sequence of VAEAK, with high helix propensity, was mixed with an indifferent sequence of TSDSR in all possible permutations. From the percent alpha-helix structure derived from the CD at 222 nm, it appears that helicity does not propagate through the indifferent sequence.

Flow linear dichroism is used to measure specific inclinations for each of the four bases in poly[d(AC)].poly[d(GT)] and poly[d(AG)].poly[d(CT)] in both the B and A forms. For the B form in solution the bases are found to have a sizable inclination. Inclination is increased in the A form, as expected. In all cases the pyrimidines are more inclined than the purines.

In previous work, it was shown that poly[d(AC).d(GT)] could be forced into the Z form by strong dehydrating conditions, provided EDTA was not present. Presumably multivalent impurities were also necessary for the transition. In order to gain control over the B to Z transition for this DNA, we carefully removed all divalent contaminants from the sample and asked the obvious question: What ions are necessary for the transition under dehydrating conditions? We systemically investigated the effect of various multivalent ions. The common contaminants Ca2+, Mg2+, and Fe3+ will not cause the transition, but Co2+ and Ni2+ facilitate the transition, undoubtedly because of their well-known propensity to bind to purine N7. Since the transition also depends on the synergistic dehydrating action of sodium perchlorate and ethanol, we include CD spectra for the independent variations of these two factors. In addition, vacuum-uv CD spectra for the A form and various B forms of poly[d(AC).d(GT)] are presented for the first time.

The P-Form of DNA has been studied by use of ir spectroscopy and electron microscopy (EM). The ir data show that the P-form has little or no hydrogen bonding, while the data from EM show that the P-form has a condensed tertiary structure. In earlier work, we demonstrated that the P-form is devoid of base stacking. When that information is combined with the new ir data, we conclude that the P-Form is denatured because it lacks any of the interactions associated with a normal secondary structure. This is in apparent contradiction to earlier work that showed that the P-form may be easily transformed back to a native state by adding water. However, the lack of secondary structure can be overcome by the presence of a collapsed tertiary state that does not allow non-hydrogen-bonded strands to separate. Thus, the complementary strands can renature quickly on addition of water. The collapse to a condensed tertiary structure occurs when roughly 90% of the charge on the DNA molecule is neutralized by counterion condensation, as calculated by the Manning polyelectrolyte theory, and is consistent with other collapsed DNA states in this respect. This structure explains all physical properties of the P-form that have been observed.

A method is described which relates the circular dichroism of a polymer to its conformation. The method takes into account near and accidental degeneracies and eliminates the artificial distinction between degenerate and nondegenerate systems. Comparison of this method with perturbation theory indicates that the errors inherent in nondegenerate perturbation theory tend to cancel when a circular dichroism spectrum is calculated. The method is applied to dinucleoside phosphates.

A particularly simple theory of circular dichroism is described and applied to the polynucleotides. It works surprisingly well and predicts the conservative spectrum of DNA and the more intense nonconservative spectrum of RNA. The anomalously low intensity of the CD of the nucleic acids is shown to be a natural consequence of the cancellation of the rotational strengths of the many CD bands. The theory's many successes and predictions as well as its weaknesses are discussed.

The large change in the electronic absorption spectrum of cytidine on going from an aqueous to an aprotic medium is attributed to the existence of a hydrogen bonded solvent-solute complex in solvents capable of donating a proton. The spectrum of cytidine in a variety of solvents and the spectra of a number of nontautomerising model compounds are presented. The tautomerisin of cytidine and its biological implications are discussed.

Working within the restrictions of a model, we have calculated the circular dichroism of the dinucleoside phosphates ApA, CpC, and CpA for various conformations. Comparing the calculated curves with those measured in aqueous solution we find agreement for (1) ApA as a right-handed helix with both bases either as in B-form DNA, or else rotated 180° around the glycosidic bond, (2) CpC as the right-handed conformation with both bases as in DNA, (3) ApC as either the right-handed conformation with both bases as in DNA, or else as a left-handed helix with both bases rotated 180°, and (4) CpA as either a left-handed helix with both bases in a left-handed DNA, or else in the right-handed conformation with both bases rotated 180°. In addition, we have investigated circular dichroism as a measure of unstacking. We find that opening the bases to a 90° total angle (base planes perpendicular) reduces the intensity of the calculated bands to 20% of their original value. Further, we find that allowing the sliding of one base past the other does not lead to a temperature dependence consistent with experiment.