15 N and 13 C nuclear magnetic resonance of deoxynucleotide monophosphates. I. Protonation of d(CpG) in dimethylsulfoxide (original) (raw)
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Biochemistry, 1986
In order to evaluate models for the acid denaturation of D N A and to assess the potential importance of protonated bases in mutations and gene expression, an N M R investigation of D N A and nucleotides in the pH range 7-2 has been conducted. The changes in the imino proton spectral region are readily observed and quite dramatic on lowering pH. At pH 7.0, calf thymus D N A has imino proton signals for A T (13.6 ppm, 56% area) and GC (12.6 ppm, 44% area) base pairs but no peaks in the 10-12 ppm region. At pH 5 a broad peak(s) between 10 and 11 ppm was (were) observed, and it narrowed and shifted to 10.
European journal of biochemistry / FEBS, 1988
NMR and CD studies were carried out on the dinucleotides 5'-methylphospho-N6-dimethyladenylyl-uridine (mpm62-U) and 5'-methylphospho-uridylyl-N6-dimethyladenosine (mpU-m62A) and on the trinucleotide U-m62A-U. A detailed comparison is given of the conformational features of mpm62A-U and mpU-m62A with the corresponding 5'-nonphosphorylated dinucleotides m62A-U and U-m62A, respectively. The behaviour of the trinucleotide U-m62A-U is compared with the properties of the constituent dinucleotides U-m62A and mpm62A-U. Chemical-shift and CD data were used to determine the amount of stacking interactions. For each compound NMR spectra were recorded at two or three sample concentrations in order to separate intermolecular and intramolecular base-base interactions. The coupling constants of the ribose ring are interpreted in terms of the N/S equilibrium, and population distributions along the backbone angles beta, gamma and epsilon are presented. The combined data indicate a strong...
The Journal of Physical Chemistry B, 2013
Protonation of nucleobases in anions of canonical 2′-deoxyribonucleotides has been investigated by the DFT computational study at the B3LYP/aug-cc-pvdz level of theory. It is demonstrated that the protonation leads to a significant decrease of conformational space of purine nucleotides while almost all conformers found for non-protonated molecules correspond to minima of the potential energy surface for protonated mdTMP and mdCMP. However, in all nucleotides, only one conformer is populated. This applies to all tautomers of protonated molecules except the mdTMP and mdCMP with the proton attached to the carbonyl group where a minor population of second conformer is observed. Protonation of nucleobase leads to significant elongation of the N-glycosidic bond. These findings agree well with suggestions that protonation of nucleobase is a first step in cleavage of the glycosidic bond. The oxygen atoms of both carbonyl groups of thymine and the N3 atom of the pyrimidine ring of cytosine, guanine, and adenine represent the most preferable sites for protonation of anions of 2′-deoxyrobonucleotides. The highest proton affinity is observed for the base in mdGMP and the lowest for the thymine moiety in mdTMP. It should be noted that calculated values of the proton affinities in anionic nucleotides are significantly higher (by 2−3 eV) than for nucleosides and neutral nucleotides. This allows assuming that the proton affinity of the base in DNA macromolecule may be tuned by changing the extent of shielding or neutralization of negative charge of the phosphate group.
Nucleic Acids Research, 1986
The 1H, 13C, and 15N NMR sp ctra of neutral and protgnated forms of the nucleosides 1-methyladenosine (m A), 7-methylguanosine (m G) and ethenoadenosine (EA), as a mod ¶l compoynd, have been analyzed in order to assign the site of protonation in m A fnd m G. Protonation of these nucleosidls occurs in the pyrimidine ring of m A and EA and in the imidazole ring of m G, with the charge1being distributed rather than localized. Structural differences for both m A and m G were observed in solution and compared with those existing in the crystal state of monomers as well as in tRNA where these nucleosides occur quite often. The protonated nucleoside structures in solution compared favorably in sugar pucker and glycosidic bond conformations with x-ray crystallographic data. Methyl group carbon chemical shifts of the protonated mononucleosides corresponded to those of the methyls of the respective nucleosides in native tRNA structures. Therefore, the tRNA methyl group carbon chemical shifts are indicative of fully protonated nucleosides in the native, three dimensional structure of the nucleic acid.
Biophysical Journal, 1993
Circular dichroism (CD) spectra of d(CCCCGGGG) in the presence of Co(NH3)3+ are very similar to spectra of r(CCCCGGGG). In contrast, B-form characteristics are observed for d(CCCCGGGG) in the presence of Na+ and Mg2+, even at high salt concentrations. Spermidine induces modest changes of the CD of d(CCCCGGGG). The NMR chemical shifts of the nonexchangeable protons of d(CCCCGGGG) in the absence and presence of Co(NH3) 3+ were assigned by proton two-dimensional (2D) NOESY and COSY measurements. The chemical shifts of the GH8 protons of d(CCCCGGGG) move upfield upon titration with Co(NH3)6CI3. The sums of the sugar' coupling constants decrease with added Co(NH3)6CI3. Cross peak intensities in the 2D proton NOESY spectra show a transformation from B-DNA to A-DNA characteristics upon the addition of Co(NH3)6CI3. The temperature-dependent 59Co transverse and longitudinal relaxation rates demonstrate that Co(NH3)3+ is site-bound to the oligomer. Such localization is not a general feature of Co(NH3)6+ binding to oligonucleotides. 59Co NMR relaxation and CD measurements demonstrate chiral discrimination by d(CCCCGGGG) for the two stereoisomers of Co(en) 3+. Both stereoisomers bind tightly as judged by 59Co NMR, and both cause large (but nonequivalent) changes in the CD of this oligomer.
Inorganic Chemistry, 2001
The involvement of metal ions and their biological significance in nucleic acid processes has been well documented. [1][2][3][4][5] Metal ions counter balance the negative charges of the phosphate groups of the nucleotides, and they also affect the structure of these derivatives in the solid state. 3,5 There are three potential metal binding groups on a nucleotide: phosphate, sugar, and nuclear base moiety. [3][4][5] The crucial role of a direct metal ion binding to N(7) of the purine residue has been emphasized by several investigators. 3,5 However, one impediment to the definitive evaluation of the importance of the N(7) binding is the lack of effective direct spectroscopic criteria for its assessment. There is an indirect evaluation of metal-N(7) binding from satellite bands due to the metal-proton coupling constant, 6 however, this is applicable only in solution.
NMR Studies on the syn-anti Dynamic Equilibrium in Purine Nucleosides and Nucleotides
European Journal of Biochemistry, 1980
The s.yn + anti equilibrium conformation about the glycosidic bond of purine nucleosides and 5'-nucleotides in different solvent systems has been investigated by means of 'H NMR spectroscopy. Quantitative values for the conformer populations were improved, relative to previous results, by a detailed study of, and a resultant derived correction for, the influence of the sugar exocyclic group conformation on the chemical shifts of the sugar ring protons. This was achieved with the aid of nucleosides and nucleotides fixed in the conformations gauche-trans [derivatives of 8,5'-(R)-cyclo] and trans-gauclze [derivatives of 8,5'-(S)-cyclo]. The results of 13C NMR confirmed those obtained by 'H NMR. The measured values of the vicinal coupling constants between H-1 ' and the C-8 and C-4 carbons were employed to evaluate approximately the glycosidic angles x of the nucleosides in the conformations s,yn and anti. A critical examination is made of the applicability of relaxation methods, involving analysis of spin-lattice relaxation time of protons ( T I ) and the Overhauser effect, to determine the conformation of the base about the glycosidic bond; interpretations are provided for the lack of agreement between these methods and those based on chemical shifts in the present study. The foregoing results are also applied to an examination of the effect of the conformation of the base about the glycosidic bond on the enzymatic reactions catalyzed by 5'-nucleotidase and adenosine deaminase.