The hydrogen bonding of cytosine with guanine: Calorimetric and ¹H‐NMR analysis of the molecular interactions of nucleic acid bases

Abstract

synopsisThe enthalpy of hydrogen-bond formation between guanine (G) and cytusine (C) in o-dichlorobenzene and in chloroform at 25°C has been determined by direct calorimetric measurement. We derivatized 2'-deoxyguanosine and 2'-deoxycytidine at the 5'-and 3'-hydroxyls with triisopropylsilyl groups; these group increase the solubility of the nucleic acid bases in nonaqueous solvents. Such derivatization also prevents the r i b hydroxyls from forming hydrogen bonds. Consequently, hydrogen-bond formation in our system is primarily between the bases, and to a lesser extent, between base and solvent, and can be measured directly with calorimetry. To obtain the data on baae-pair formation, we first took into account the contributions from self-association of each base, and where possible, have determined the AH of self-association. From isoperibolic titration dorimetry, our measured AH of C2 formation in chloroform is -1.7 kcal/mol of C. Our measured AH of C : G base-pair formation in o-dichlorobenzene is -6.65 0.32 kcal/mol. Since o-dichlorobenzene does not form hydrogen bonds, the AH of C : G base-pair formation in this solvent represents the AH of the hydrogen-bonding interaction of C with G in a nonassociating solvent. In contrast, our measured AH of C : G basepair formation in chloroform is -5.77 f 0.20 kd/mol; thus, the absolute value of the enthalpy of hydrogen bonding in the C : G base pair is greater in o-dichlorobenzene than in chloroform. Since chloroform is a solvent known to form hydrogen bonds, the decrease in enthalpic contribution to C : G base pairing in chloroform is due to the formation of hydrogen bonds between the bases and the solvent. The AH of hydrogen bonding of G with C reported here differs from previous indirect estimates: Our measurements indicate the AH is 50% less in magnitude than the AH based on spectroscopic mensurements of the extent of interaction. We have also observed that the enthalpy of hydrogen bonding of C with G in chloroform is greater when G is in excess than when C is in excess. This increased heat is due to the formation of C : G, > complexes that we have observed using H-nmr. Although C:G2 structures have previously been observed in triplestranded polymeric nucleic acids, higher order structures have not been observed between C and G monomers in nonaqueous solvents until now. By using monomers as a model system to investigate hydrogen-bonding interactions in DNA and RNA, we have obtained the following results: A direct measurement of the AH of hydrogen bonding in the C : G complex in two nonaqueous solvents, and the first observation of C : G,, , complexes between monomers. These results reinforce the importance of hydrogen bonding in the stabilization of various nucleic acid secondary and tertiary structures.

A study of 7-deaza-2′-deoxyguanosine–2′-deoxycytidine base pairing in DNA

“…As mentioned above, the electronic nature of the 7-zG purine ring system is different than that of G. In order to experimentally evaluate the H-bonding properties of 7-zG relative to G, we prepared 3′,5′- bis (triisopropylsilyl) substituted 2′-deoxynucleoside analogs of C, G and 7-zG that afford sufficient solubility in a non-polar environment, such as CDCl 3 , under conditions that are essentially devoid of base stacking interactions (34). The 1 H-NMR studies, at mole fractions up to 0.5:0.5, show that the silylated dG–dC and 7-z-dG–dC pairs have similar chemical shift changes for G-N1-H, C-N 4 -H 2 and G-N 2 -H 2 protons, which are indicative of H-bonding (Figure 8).…”

“…The syntheses of the 2′-deoxy-3′,5′- bis (triisopropylsilyl) derivatives of C, G and 7-zG were performed based upon methods previously reported (34). …”

“…The experimental design closely followed that previously described (34) using a 500 MHz instrument. A solution of the 2′-deoxy,3′,5′- bis (triisopropylsilyl)cytidine in anhydrous CHCl 3 was mixed with 2′-deoxy,3′,5′- bis (triisopropylsilyl)guanosine or 2′-deoxy,3′,5′- bis (triisopropylsilyl)-7-deazaguanosine in anhydrous CDCl 3 to give mixtures with mole fractions ranging from 100:0 to 0:100 while maintaining the same concentration of deoxynucleotides.…”

Controlling the transmembrane transport of nucleosides

“…Organic soluble C and G derivatives form stable Watson-Crick base pairs in low dielectric solvents, with high association constants (K A ¼ 10 4 -10 5 M 21 in CDCl 3 ) (30). Under the conditions of our U-tube transport experiments, the G 1·C 2 base pair is the dominant species in solution when the two lipophilic nucleosides are mixed together in CHCl 3 at mM concentrations.…”

Pair Formation of Free Nucleobases and Mononucleosides in the Gas Phase

“…Several experimental investigations of substituted nucleobase pairs in the gas phase [14] and in different solvents [15,16,17,18] have been performed. The proportion of substituted nueleobases and nucleobase dimers in solution was determined by IR spectroscopy [19,20] and N M R studies [21,22].…”