Geometry and Strength of Hydrogen Bonds in Complexes of 2‘-Deoxyadenosine with 2‘-Deoxyuridine

Abstract

NMR studies have been performed on the association of 3′,5′-di-O-acetyl-2′-deoxyuridine with a 2′-deoxyadenosine derivative in solution. Using a CDClF 2 /CDF 3 solvent mixture, measurements at very low temperatures allowed the observation of individual complexes in the slow-exchange regime. From 2D NOE connectivities of the imino proton resonances at 125 K the predominant species could be assigned to a Watson-Crick geometry. However, concentration-dependent 15 N chemical shifts of specifically labeled uridine and adenosine nucleosides indicate a considerable population of Hoogsteen base pairs at ambient temperatures. These results together with a more downfield chemical shift of the Watson-Crick bound imino proton point to a stronger hydrogen bond in Watson-Crick when compared to Hoogsteen base pairs.

Intramolecular hydrogen bond directed stable conformations of benzoyl phenyl oxalamides: unambiguous evidence from extensive NMR studies and DFT-based computations

“…In such situations the spin magnetization transfer is relayed through the HB. [57][58][59][60] For molecules 2 and 4, a doublet was detected for the proton of NH(1) with a frequency separation of 13.4 Hz (Fig. 5a).…”

Synthesis and complementary self-association of novel lipophilic π-conjugated nucleoside oligomers

“…[23][24][25][26][27] Nucleosides A and U, having a symmetric ADA:DAD H-bonding pattern (Figure 4), associate in CHCl3 (or CDCl3) with Ka = 1.8-3.1 x 10 2 M -1 . In the less polar CHCl3 (or …”

“…In this work we also study the hydrogen-bonding dimerization and hetero-association processes between complementary units (G-C, iG-iC, G-iC, iG-C and A-U) by both 1 H NMR and absorption spectroscopies, and analyze the binding isotherms by adequate fitting programs in order to obtain the relevant association constants. 22 Guanine-cytosine and adenine or 2-aminoadenineuracile binding has already been studied by a number of authors, [23][24][25][26][27] so this work offers new quantitative data on their association constants studied and analyzed by diverse methods. However, to the best of our knowledge, no data has been reported so far on the association between isoguanine and isocytosine in organic solvents, or on the interactions between these nonnatural bases and cytosine or guanine.…”

Hydrogen bonding in complexes of adenosine and 4-thiouridine: a low-temperature NMR study

“…Even with uridine present in large excess, Hoogsteen binding always occurs to a minor extent and competes with the formation of uridine homodimers. 13 The larger tendency of self-association for uridine might be partially attributed to its more negative free enthalpy G of homodimerization when compared with the 4-thio analog. 12 On the other hand, imino proton signals in hetero complexes of the thio derivative are already in slow exchange on the NMR chemical shift time-scale at T Ä 163 K and thus at higher temperatures when compared with AÐU complexes.…”

“…12 On the other hand, imino proton signals in hetero complexes of the thio derivative are already in slow exchange on the NMR chemical shift time-scale at T Ä 163 K and thus at higher temperatures when compared with AÐU complexes. 13 This increased kinetic stability may be the result of stronger hydrogen bonds involving the more acidic imino function of 4-thiouridine.…”