Association by hydrogen bonding of free nucleosides in non-aqueous solution

Quantum mechanical calculations of NMR chemical shifts in nucleic acids

During the last twenty-five years the development of quantum mechanical calculations and experimental measurements of chemical shifts of the different type of nuclei present in nucleic acids have run parallel in close relation to each other. The first calculations dealt with intramolecular effects on base proton shifts (Veillard, 1962) but the real breakthrough of the theory occurred with the advent of computations of intermolecular shielding due to the ring current effect of the nucleic acid bases (Giessner-Prettre & Pullman, 1970).

Hydrogen bonding between cytosine and peptides of threonine or serine: is it relevant to the origin of the genetic code?

13C, 15N, and 1H nuclear magnetic resonance measurements indicate that chloroform-soluble threonine-containing tripeptide derivatives, such as t-Boc-Thr-Gly-Gly-OBz, form three strong hydrogen bonds to the cytosine moiety of 2',3'-O-isopropylidene-5'-O-t-butyldimethylsilylcytidine. The C = O and NH of the central peptide residue plus the OH of the threonine side chain appear to form bonds to the N(4')H2, N(3), and C(2) = O, respectively, of the pyrimidine. An association constant calculated from the cytidine 15N(4') nuclear magnetic resonance response to added peptide is four times larger than the corresponding cytosine-guanine constant. It is suggested that cytosine-peptide bonding was part of the primitive genetic coding mechanism early in evolution and accounts for the origin of the cytosine-centered codons for the hydroxy amino acids, serine and threonine, in the present code.

The binding of DNA to water soluble carbodiimide modified proteins

Bovine serum albumin and human serum transferrin modified by the water soluble carbodiimides N-ethyl-N'-(3-dimethyl propylamino) carbodiimide (CDI) or N-ethyl-N'-(3-trimethyl propylammonium) carbodiimide (Me+CDI) to yield N-acylurea proteins bind pBR322 DNA reversibly showing electrostatic and non-electrostatic components in the binding energies (delta G overall). It is proposed that initially an electrostatic interaction arises from ion pair formation between the DNA phosphates and the N-acylurea entities. This is consolidated, in single stranded regions, by a second event in which it is suggested that the base guanine interacts with elements of the N-acylurea moieties through hydrogen bonding or a glyoxal-type addition.

Protonated base pairs explain the ambiguous pairing properties of O6-methylguanine

The base-pairing interactions of promutagenic O6-methylguanine (O6-MeGua) with cytosine and thymine in deuterated chloroform were investigated by 1H NMR spectroscopy. Nucleosides were derivatized at hydroxyl positions with triisopropylsilyl groups to obtain solubility in nonaqueous solvents and to prevent the ribose hydroxyls from forming hydrogen bonds. We were able to observe hydrogen-bonding interactions between nucleic acid bases in a solvent of low dielectric constant, a condition that approximates the hydrophobic interior of the DNA helix. O6-MeGua was observed to form a hydrogen-bonded mispair with thymine. Whereas O6-MeGua did not form hydrogen bonds with cytosine (via usual, wobble, or unusual tautomeric structures), it did form a 1:1 hydrogen-bonded complex with protonated cytosine. The pairing of unprotonated cytosine in chloroform is thus consistent with the known preference of O6-MeGua for thymine over cytosine in polymerase reactions. In contrast, the pairing of protonated cytosine is consistent with the greater stability of oligonucleotide duplexes containing cytosine.O6-MeGua as compared with thymine.O6-MeGua base pairs [Gaffney, B. L., Markey, L. A. & Jones, R. A. (1984) Biochemistry 23, 5686-5691]. Our observation that cytosine must be protonated in order to pair with O6-MeGua suggests that the cytosine.O6-MeGua base pair in DNA is stabilized by protonation of cytosine. Through this mechanism, methylation at the O6 position of guanine in double-stranded DNA could promote cross-strand deamination of cytosine (or 5-methylcytosine) to produce uracil (or thymine).

Hydrogen bond equilibrium constants for the complexes of benzotriazole and some nucleoside derivatives. A near infrared study

Approximate hydrogen bond association constants were determined by near infrared spectroscopy for pairs formed by benzotriazole and a number of nucleoside derivatives. The molecule of benzotriazole forms, in chloroform, hydrogen bonds with inosine, uridine and adenosine derivatives. The order of decreasing association constants for complexes formed by benzotriazole and uridine or inosine derivatives is the opposite of the one observed for pairs formed by adenosine and uridine or inosine derivatives.

Solution influence on biomolecular equilibria: nucleic acid base associations

This paper consists of two parts. In the first part, the general problem of biomolecular equilibria in solution is considered, stressing that molecular interactions ultimately determine the answer to this problem. It is discussed how computer simulation techniques can reliably treat the problem and several pitfalls of computer simulation to be avoided are pointed out. Other approaches based on modeling and conceptual simplifications such as perturbative methods, long-range interaction approximations, surface thermodynamic approaches, and hydration shell models are discussed. In the second part, the results of Monte Carlo calculations on the associations of nucleic acid bases in water and carbon tetrachloride are presented. Stacked self-associations are found to be preferred in water and hydrogen-bonded complexes are favored in nonpolar solutions, in agreement with experimental data. The influence of the solvent on base associations is explained in terms of solute-solvent and solvent-solvent contributions to the total energy. No enthalpic stabilization of the complexes by the solvent was found. The results are used to examine the validity of various approximations discussed in the first part of the paper.

Detection of proton-acceptor sites of hydrogen bonding in adenine X uracil base pairs by the use of 15N magnetic resonance

2',3',5'-Tri-O-acetyl[1,3,7,9,amino-15N]adenosine(ac3Ado) and its 8-2H and 8-bromo derivatives (ac3[8-2H]Ado and ac3br8Ado) were synthesized from 95% 15N-enriched adenosine which was obtained by microbial fermentation. The chemical shifts and nuclear Overhauser effects of 15N NMR of the adenosine derivatives were measured by changing the concentration of the mixed 1-cyclohexyluracil (cHxUra) in chloroform. The limiting shift of each 15N resonance was calculated by using the association constants obtained from proton magnetic resonances of the ac3Ado/cHxUra and ac3br8Ado/cHxUra systems. From the quantitative analysis of the 15N chemical shifts of the N-1 and N-7 atoms it could be concluded that ac3Ado X cHxUra dimers prefer the Hoogsteen-type pair while the Watson-Crick-type pairs are predominant in the ac3br8Ado X cHxUra dimers. The N-3 atom, which does not locate at the interaction site, showed a fairly large induced shift. Thus the induced shift of 15N resonance by association does not always mean the involvement of the corresponding nucleus to the interaction site. The effect of intermolecular hydrogen bonding on the nuclear Overhauser enhancement of the 15N-7 resonance was observed in the ac3[8-2H]Ado/cHxUra mixture. The presence of the Hoogsteen-type hydrogen bonding was proposed by the use of 15N NMR spectra. The present information will be useful for the elucidation of non-Watson-Crick-type base-pair interaction in transfer TNA and oligonucleotides.

Self-association and base pairing of guanosine, cytidine, adenosine, and uridine in dimethyl sulfoxide solution measured by 15N nuclear magnetic resonance spectroscopy

The self-association of guanosine, cytidine, and adenosine and base pairing between guanosine, cytidine, adenosine, and uridine in dimethyl sulfoxide have been investigated by the variation of their 15N NMR chemical shifts with concentration and temperature. Guanosine, cytidine, and adenosine all showed evidence of self-association by hydrogen bonding. In guanosine/cytidine mixtures, a hydrogen-bonded dimer is formed; however, no base pairing could be detected with adenosine/cytidine or adenosine/uridine mixtures.

Laser raman spectroscopy of a complementary base pair in the Hoogsteen configuration

Cocrystallization of m9Ade and m1Thy from water yielded crystals of te Hoogsteen base pair, m9Ade x m1Thy, as demonstrated by X-ray diffraction data. The Raman spectrum of the Hoogsteen base pair in the crystalline state was obtained and compared to the crystals of the individual monomers. Frequency changes between the heterobase dimer and both m9Ade and m1Thy are indicative of the base pairing interaction. Utilizing previously reported vibrational analyses for m9Ade, the frequency changes are clearly associated with modes involving the internal coordinates most sensitive to a Hoogsteen hydrogen bonding interaction. The spectrum of an equimolar mixture of e9Ade and ch1Ura in CHCl3 was also compared to the spectrum of the separate monomers in solution. The numerous frequency shifts and band intensity changes observed in the mixture from that of the individual monomers suggest a cyclic dimer is formed although the nature of the base pairing interaction is not clear.

Hydrogen bonding of amino acid side chains to nucleic acid bases

Absorption studies of hydrogen bonding association between nucleic acid bases and amino acid side chains show that association constants can be determined from difference absorption spectra in cyclohexane and chloroform. Association constants for the binding of 9-ethyladenine, 1-cyclohexyluracil and 1-cyclohexylcytosine to side chains of serine, threonine, aspartic acid, lysine, cystéine, methionine and tyrosine are reported. Results obtained in chloroform and cyclohexane are compared.

High-resolution nuclear magnetic resonance determination of transfer RNA tertiary base pairs in solution. 1. Species containing a small variable loop

Eight class I tRNA species have been purified to homogeneity and their proton nuclear magnetic resonance (NMR) spectra in the low-field region (-11 to -15 ppm) have been studied at 360 MHz. The low-field spectra contain only one low-field resonance from each base pair (the ring NH hydrogen bond) and hence directly monitor the number of long-lived secondary and tertiary base pairs in solution. The tRNA species were chosen on the basis of their sequence homology with yeast phenylalanine tRNA in the regions which form tertiary base pairs in the crystal structure of this tRNA. All of the spectra show 26 or 27 low-field resonances approximately 7 of which are derived from tertiary base pairs. These results are contrary to previous claims that the NMR spectra indicate the presence of resonances from secondary base pairs only, as well as more recent claims of only 1-3 tertiary resonances, but are in good agreement with the number of tertiary base pairs expected in solution based on the crystal structure. The tertiary base pair resonances are stable up to at least 46 degrees C. Removal of magnesium ions causes structural changes in the tRNA but does not result in the loss of any secondary or tertiary base pairs.

Theoretical study on the proton chemical shifts of hydrogen bonded nucleic acid bases

The variation of the proton chemical shifts due to the formation intermolecular hydrogen bonds is computed for a number of complexes which can be formed between the bases of the nucleic acids. The shifts expected for the isolated base pairs, in particular for the G-N1 H, T(or U)-N3H protons and the protons of the amino groups of A, G c, when combined with previous computations on the shifts to be expected upon base stacking, may enable a refined analysis of the high resolution NMR spectra of self complementary polynucleotides or tRNAs. Two examples are presented of a direct computation of proton shits associated with helix-coil transitions, helpful for deducing the helical structure in solution.

Tertiary hydrogen bonds in the solution structure of transfer RNA

The high resolution nuclear magnetic resonance (NMR) spectra of hydrogen-bonded protons in four tRNAs have been studied at 270 MHz. The relative intensity of the resonances between -11 ppm and -15 ppm of Escherichia coli tRNA1-Va1 indicate that there are 26 plus or minus 3 protons, while only 20 are expected from secondary structure Watson-Crick hydrogen bonds inthe cloverleaf structure. Several possible candidates for these extra resonances are suggested by tertiary interactions observed in recent crystallographic studies. Of the four tRNAs studied, three, e.g., E. coli tRNA1Va1, E. coli tRNA-Arg and E. coli tRNA-Phe have one "GU pair" in their cloverleaf structure, while the fourth, yeast tRNA-Asp,has three "GU pairs" and one "G pair". Correlating these with the NMR spectra in the -10 ppm to -11 ppm region allows us to conclude that the "GU pairs" are not hydrogen-bonded by tautomerization to the lactim form. At the very low field region, near -14.9 ppm, the three E. coli tRNAs show a single resonance which is attributed to the 4-thiouracil 8 to adenine 14 hydrogen bond of the tertiary structure, by analogy with the recent crystal structure of yeast tRNA-Phe. This assignment is confirmed by the disappearance of this resonance after treatment with cyanogen bromide.

Proton nuclear magnetic resonance investigations and ring current calculations of guanine N-1 and thymine N-3 hydrogen-bonded protons in double-helical deoxyribonucleotides in aqueous solution

Methods are outlined for assigning the guanine-N(1)H and thymine-N(3)H protons to particular base pairs in the proton nuclear magnetic resonance spectra of double-stranded oligodeoxyribonucleotides of known sequence in aqueous solution. Ring current calculations have been used to evaluate the upfield shifts of the guanine-N(1)H and thymine-N(3)H protons from the pyrimidine and purine rings of nearest-neighbor base pairs in DNA B-type double-helical structures. Chemical shifts of 13.6 +/- 0.1 ppm and 14.6 +/- 0.2 ppm are assigned to the guanine-N(1)H proton of an isolated G.C base pair and the thymine-N(3)H proton of an isolated A.T base pair, respectively.

Nuclear magnetic resonance study of hydrogen-bonded ring protons in Watson-Crick base pairs

We have studied the low-field proton magnetic resonance spectrum of the double-helical complex of d(A-A-C-A-A) with d(T-T-G-T-T). Well-resolved resonances for the thymidine N(3) and the guanosine N(1) protons are seen at 1 degrees C, which broaden by 4 degrees C and disappear above 9 degrees C. The actual T(m) of the complex was found to be 28 degrees C by measurement of UV-absorbance change. There are several factors that could limit the observed exchange broadening of the resonance lines; the model that best fits the data is one in which the rate of double-helix dissociation limits the rate of exchange of the H-bonding protons with water.

Hydroxyphenylazopyrimidines: characterization of the active forms and their inhibitory action on a DNA polymerase from Bacillus subtilis

The active forms of 6-(p-hydroxyphenylazo)-uracil and 6-(p-hydroxyphenylazo)-isocytosine were isolated and identified as their respective hydrazino derivatives. These arylhydrazino pyrimidines selectively inhibited a chromatographically distinct DNA polymerase from Bacillus subtilis. The actions of the reduced drugs on this polymerase were identical to those observed on ATP-dependent DNA synthesis in toluene-treated cells; dGTP competitively antagonized the inhibitory activity of the uracil derivative, and dATP competitively antagonized that of the isocytosine derivative. Analysis of the interactions of the arylhydrazinopyrimidines and nucleic acid bases by nuclear magnetic resonance suggested that hydroxyphenylhydrazino-uracil and hydroxyphenylhydrazino-isocytosine pair in a novel manner with, respectively, cytosine and thymine. A mechanism of inhibitor action, involving binding of the reduced drugs to enzyme and the pyrimidines of DNA template, is proposed.