Yoshimasa Kyogoku

Infrared absorption spectra of protonated and deprotonated nucleosides

Abstract Infrared absorption spectra have been observed in the 1800-1450 cm−1 region of four nucleosides: cytidine, adenosine, uridine, and guanosine, in their deuterium oxide solutions at various pDs. The spectra have also been observed in their solid states obtained from acidic, neutral (H2O and D2O), and alkaline solutions. The authors discuss (a) the identity and non-identity of the general features of the spectra obtained at different pHs and pDs, (b) the double-bond stretching frequencies observed in the deuterated nucleosides, (c) the NH2 and NH bending frequencies observed in the undeuterated nucleosides, and (d) the probable configurations of the protonated or deprotonated nucleosides with their correlations to the observed spectra.

A preliminary investigation on the molecular structure of rice dwarf virus ribonucleic acid

X-Ray diffraction and infrared absorption measurements have been made of a ribonucleic acid obtained from rice dwarf virus which was isolated from the infected rice leaves. On a fibre diagram obtained at 75% relative humidity, 52 independent reflections were observed. All of them are indexed on a hexagonal lattice with a = 40·0 A and c = 30·5 A. It was found that the unit cell contains three molecules, each of which is displaced along the c-axis direction by c /3 from the neighbours. Intensities of the reflections were used to calculate the cylindrically symmetrical Patterson function. From this Patterson function it was concluded that the ribose-phosphate chains form two intertwined helices one of which is displaced along the helix axis by 13·0 A from the other. Each helix has its axis parallel to the c -axis, a pitch of 30·5 A, and ten nucleotide residues per turn. On the basis of the infrared dichroism observed for the 1225 cm −1 and 1084 cm −1 bands, the orientation of the PO 2 − group has been determined. The O…..O line makes an angle of about 70° and the bisector of 2 − group in the A and B forms of DNA.

Intra-red absorption spectra of the single crystals of 1-methyl-thymine, 9-methyladenine and their 1:1 complex

Abstract Infra-red absorption spectra have been observed of thin sections of the single crystals of 1-methylthymine, 9-methyladenine, and their hydrogen-bonded 1:1 complex (AT dimer) by using the polarized radiation in the spectral region of 4000-400 cm −1 . The absorption bands due to the in-plane and out-of-plane vibrations are distinguished in the spectra of the sections perpendicular to the molecular plane. The directions of the transition moments were determined of some of the absorption bands in the spectra of the sections parallel to the molecular plane. Assignments of the absorption bands due to the NH and NH 2 deformation were made on the basis of the observed N-deuteration effects. A marked difference was observed between the spectra of the AT dimer and an equimolar mechanical mixture of 1-methylthymine and 9-methyladenine. The frequencies assignable to the out-of-plane vibrations of the NH and NH 2 groups were found to be sensitive to the manner of their hydrogen bonding.

Phosphorus-Proton Spin-Spin Coupling and Conformation of a Dinucleoside Phosphate

The phosphorus-31 nuclear magnetic resonance spectrum of β-adenosine-3-β-adenosine-5-phosphoric acid in its aqueous solution (pH = 9.2) was studied. The signal consisted of eight peaks caused by the spin-spin coupling of the phosphorus nucleus with three protons, two on the 5 carbon, and one on the 3 carbon. The coupling constants were 3.4, 6.5, and 8.1 hertz; from these values the dihedral angles of the three P-O-C-H systems were estimated.

Infrared spectra of formamide-treated nucleic acids.

The effects of formamide treatment on the infrared absorption of sodium salts of calf thymus DNA, yeast ribosomal RNA, and yeast soluble RNA have been examined. The effects are found to be very similar to the effects of heating the aqueous solutions of these sodium salts of the nucleic acids. On the basis of the characters of the absorption bands where these effects are observed, it is concluded that the formamide treatment causes a cleavage of the base pairings, a change in the electronic structure of the base portions and a change in the molecular conformation of the phosphate and sugar portions of NaDNA.

Infrared spectra of transfer RNA's: II. Formylmethionine transfer RNA from Escherichia coli in aqueous solution

Abstract Infrared absorption spectrum has been observed in the 1450–1750 cm −1 region of formylmethionine transfer RNA (tRNA) from Escherichia coli in deuterium oxide solution with 0.2 M Na + or 0.005 M Mg 2+ . At 33°, the spectrum shows seven absorption peaks in the spectral region in question. On the basis of the positions and relative intensities of these peaks, the amounts of the adenine-uracil (AU) base pair, guanine-cytosine (GC) base pair, free adenine, uracil, guanine and cytosine residues are estimated. A calculated spectrum of 2 AU+17 GC+13 A+6 U+7 G+8 C (which corresponds to the “clover leaf” arrangement of the nucleotide sequence of this tRNA determined by Dube et al. 11,12 , is in agreement with the observed spectrum. On heating the solutions, marked changes are observed in the positions and intensities of the absorption peaks. These changes are explained as what are caused by breaking down the AU and GC hydrogen-bonded base pairs. The amounts of the remaining base pairs are estimated at each temperature.

A double-beam grating spectrophotometer with a CsBr fore-prism and wavelengths of absorption lines of water vapour in the region from 16 to 30 μ

Abstract A double-beam single path grating spectrophotometer is described. It covers the spectral region from 5 to 40 μ. In order to eliminate the energy of unwanted orders a CsBr foreprism monochromator, a LiF reststrahlen crystal and a polyethylene grating transmission filter are used. The spectrophotometer is flushed with dry air from which water vapour and carbon dioxide are removed with molecular sieve. Adjustment and calibration procedures are described and the wavelengths of the absorption lines of water vapor between 16 and 30 μ, which have been determined by the calibrated spectrophotometer, are given.

Complex formation of d-amino acid oxidase with barbiturates and uracil derivatives

1. n1. Phenobarbital and barbital modified the absorption and circular dichroism (CD) spectra of d-amino acid oxidase [d-amino acid:O2 oxidoreductase (deaminating), EC 1.4.3.3] and inhibited the enzyme in competition with the substrate, but barbituric acid did not. 1-Methyl-5-bromouracil, 1-methyluracil, 1-methyl-4-thiouracil and 9-ethyladenine also produced changes in the absorption and CD spectra of the enzyme, and acted as inhibitor. Among these, 1-methyl-4-thiouracil was unique in that it produced diffuse absorption extending to 700 nm and positive CD in the corresponding wavelength region. However, uridine, 5-bromouridine and adenosine did not affect the absorption and CD spectra of the enzyme, indicating that bulky, hydrophilic groups attached to bases disturbed the binding. n n2. n2. The Ki of phenobarbital was not lowered with decreasing pH from 8 to 6. Since the pKa of phenobarbital is 7.5, this result indictes that the non-ionized form of the compound effectively combines with the enzyme. No correlation was found between the Ki values (at pH 8.3) and the pKa values of barbiturates and uracil derivatives. Thus, these compounds are considered to bind to the enzyme without essential participation of an anionic group, in contrast to the other known inhibitors such as benzoate.