The distant shielding effect in trinucleoside diposphates
A comparative study on the proton magnetic resonance of the dinucleoside monophosphates TpT, dApT, TpdA, the trinucleoside diphosphates dApTpT, TpTpdA, and poly T has been made. The purpose of this investigation was to establish whether in a trimer the proton chemical shifts of one terminal residue are influenced by the magnetic anistropy of the other terminal residue. The conformation of the trimers was first studied and shown to the similar to that of the corresponding dimer, except that of the percentage of the lefthanded conformers in the population of the trimers is probably lower than in the population of the dimers. The methylprotons, H‐6, and H‐1′ of the 3′‐terminal T residue in TpTpdA (or the 5′‐terminal T residue in dApTpT) are found to be more upfield than the same protons on the dimer TpT up to a magnitude of about 0.1 ppm. The shielding of these protons of the terminal T(s) in these trimers is even larger than those corresponding protons in the poly(T) at the same condition. From these results, it is concluded that a distant shielding effect is exerted by the 5′‐terminal. A residue (or by the 3′‐terminal A residue) on the other terminal residue in the trimers studied.
Thermal perturbation differential spectra of ribonucleic acids. III. Chain length effect.
Thermal perturbation differential spectra of several adenylic acid oligomers, two single-strand polyribonucleotides, poly(A) and poly(C), and five trinucleoside diphosphates, U-A-A, U-A-G, U-G-A, C-U-C and C-U-A, were obtained and analysed. It is shown that these differential spectra cannot be entirely described by the nearest-neighbour approximation devised from the appropriate mononucleotides and dinucleoside monophosphates. In an attempt to determine the origin of this discrepancy, we have examined the possible optical changes arising from increased electronic interactions, changes in conformation, solvent accessibility or thermodynamic properties. This study indicates that dinucleoside monophosphates on one the hand and trinucleoside diphosphates on the other hand, are separate classes from the conformational point of view. The capacity to assume stacks, absent or negligible in higher oligomers or polymers, makes them poor models for the stacking interaction in longer nucleic acids. It is also shown that in trinucleoside diphosphates, interaction between the two terminal bases arising from bulging out of the middle base is very likely to occur. This type of interaction has to be taken into account in the description of the temperature perturbation differential spectra of trimers.
220 MHz nuclear magnetic resonance spectra of oxidized and reduced pyridine dinucleotides.
Abstract 1. The two C4 protons of the dihydropyridine ring of reduced coenzymes appear as an AB spectrum in the 220 MHz nuclear magnetic resonance system. This indicates that they are chemically and magnetically nonequivalent. 2. When the oxidized coenzyme is converted to the reduced coenzyme, the coupling constant of C'1H of ribose adjacent to the pyridine increased by about 3.5 Hz, whereas the same of the ribose adjacent to the adenine remained constant. This indicates that, when the oxidized pyridine dinucleotide is reduced, the ribose attached to the pyridine ring undergoes a conformational change, the conformation of the ribose attached to the adenine remaining the same in both oxidized and reduced coenzymes. 3. The C'1H of the ribose adjacent to pyridine of reduced coenzymes is substantially broadened, and this broadening increased at elevated temperatures. This is due to onset of unresolved nitrogen spin-spin coupling as a result of the alteration of the relaxation time of nitrogen dominated by quadrupole coupling. This observation provides the most unequivocal method for assigning the chemical shift of the C'1H of ribose attached to the pyridine of reduced coenzyme. 4. Startling changes take place in the shape and position of the ribose protons as a result of the reduction of the oxidized coenzyme. It is thought to result from an alteration in the geometric posture of the diphosphate backbone as a result of the reduction.