A library of IR bands of nucleic acids in solution.

Conformations of nucleosides and nucleotides

The cellular form of prion protein is a precursor of the infectious isoform, which causes fatal neurodegenerative diseases through intermolecular association. One of the characteristics of the prio...

Raman spectroscopic study on the copper(II) binding mode of prion octapeptide and its pH dependence.

Oriented fibers drawn from aqueous gels of calf-thymus DNA were maintained at constant relative humidites of 75 and 92% to yield canonical A-DNA and B-DNA structures, respectively. Raman spectra of the two forms of DNA were recorded over the spectral range 300–4000 cm−1. The authenticated DNA fibers were deuterated in hygrostatic cells containing D2O at appropriate relative humidities, and the corresponding spectra of deuterated DNAs were also obtained. The spectra reveal all of the Raman scattering frequencies and intensities characteristic of A- and B-DNA structures in both nondeuterated and deuterated froms, as well as the frequencies and intensities of adsorbed solvent molecules from which the hydration content of DNA fibers can be calculated. Numerous conformation-sensitive vibrational modes of DNA bases and phosphate groups have been identified throughout the 300–1700-cm−1 interval. Evidence has also been obtained for conformation sensitivity of deoxyribosyl CH stretching modes in the 2800–3000-cm−1 region. Raman lines of both the backbone and the bases are proposed as convenient indicators of A- and B-DNA structures. The results are extended to Z-DNA models investigated previously. Some implications of these findings for the determination of DNA or RNA structure from Raman spectra of nucleoproteins and viruses are considered.

Characterization of DNA structures by laser Raman spectroscopy.

The M2 protein of influenza A virus forms a homotetramer ion channel in the lipid membrane. The channel is specific for proton conductance and is activated by low pH with a transition midpoint at pH 5.7. We have studied the structure of the transmembrane domain of the M2 ion channel by using UV resonance Raman spectroscopy, with special attention to the side chains of histidine (His37) and tryptophan (Trp41) residues. The Raman spectra provide direct evidence that the imidazole ring of His37 is protonated upon channel activation at low pH. Concomitantly, the UV resonance Raman scattering from Trp41 shows an unusual intensity change, which is ascribed to a cation-pi interaction between the protonated (cationic) imidazole ring of His37 and the indole ring of Trp41. The protonation of His37 and the Raman intensity change of Trp41 do not occur in the presence of amantadine that blocks the M2 ion channel. These observations clearly show that the protonation of His37 and concomitant cation-pi interaction with Trp41 is a key step in the activation of the M2 ion channel. The His37-Trp41 interaction associated with the channel activation is explained by assuming a conformational transition of His37 induced by electrostatic repulsion among the protonated imidazole rings of four His37 residues in the tetramer channel. Trp41 may play a role in stabilizing the channel open state through cation-pi interaction with His37. A molecular model for the activation of M2 ion channel is proposed on the basis of the gating mechanism.

Protonation of histidine and histidine-tryptophan interaction in the activation of the M2 ion channel from influenza a virus.

CHAPTER 11 – Infrared and Raman Spectra of Nucleic Acids—Vibrations in the Base-residues

The Raman spectra of L-histidine, L-histidine- 13C (labelled at C2 of the imidazole ring) and related compounds, namely, imidazole, 4-methylimidazole, N-acetyl-L-histidine methylamide, were observed in H2O and D2O solutions at various pH and pD values. A strong Raman band at around 1410 cm−1 was found for these compounds in acidic D2O solutions, and it was assigned to a mode characteristic of the N-deuterated imidazolium ring (Im+) in which the N1C2N3 symmetric stretching and ND bending vibrations are mixed. It is concluded that this band would be useful as a probe for studying the ionization states of histidine residues in proteins.

Raman studies of L‐histidine and related compounds in aqueous solutions

Infrared and Raman spectra of aqueous poly(rA-rU)·poly(rA-rU), the double-helical complex containing strands of alternating riboadenylate and ribouridylate residues, display significant differences from one another and from corresponding spectra of poly(rA)·poly(rU), the double-helical complex of riboadenylate and ribouridylate homopolymers. Parallel studies on the copolymer and homopolymer complexes by cesium sulfate density gradient centrifugation, ultraviolet absorption spectroscopy, hydrogenion titration, 1-N oxidation of adenine residues by monoperphthalic acid and X-ray diffraction reveal, however, that the geometry of base pairing between adenine and uracil is closely similar in each complex and apparently of the Watson-Crick type. Therefore the differences observed between vibrational spectra of poly (rA-rU)·poly (rA-rU) and poly(rA)·poly(rU) are not due to different base-pairing schemes but may be attributed to differences in vibrational coupling between vertically stacked bases. Vibrational coupling may also account for the differences between infrared and Raman spectra of the same complex. Thus, the present results indicate that infrared and Raman frequencies of RNA in the region 1750–1550 cm−1 should be dependent on the base sequence.

The vibrational spectra and structure of poly(rA-rU)-poly(rA-rU).

The phosphorus-31 nuclear magnetic resonance spectrum of β-adenosine-39-β-adenosine-59-phosphoric acid in its aqueous solution ( p H = 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 59 carbon, and one on the 39 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.

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

Raman spectrum of purified formylmethionine transfer RNA from Escherichia coli has been
 observed in its aqueous solution. In the 1800 to 200 cm-l range, about 30 Raman
 lines are found, each of which can be assigned to one of the constituent nucleotide
 residues. From the positions and intensities of the lines, information on the
 intramolecular environments of these base residues can be obtained.

Seizo Takahashi

Papers

CHAPTER 11 – Infrared and Raman Spectra of Nucleic Acids—Vibrations in the Base-residues

Raman studies of L‐histidine and related compounds in aqueous solutions

The vibrational spectra and structure of poly(rA-rU)-poly(rA-rU).

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

Raman Spectrum of a Transfer RNA