J_NH Values Show that N1···N3 Hydrogen Bonds Are Stronger in dsRNA A:U than dsDNA A:T Base Pairs

Abstract

Here, we show that 1JNH values are on average 0.4 Hz less negative for double-stranded RNA A:U than for DNA A:T base pairs, which, according to existing theory, suggests that RNA N1...N3 hydrogen bond distances are about 0.02 A shorter than those of DNA. Also, there is a statistically relevant trend between 1JNH and 2hDelta13C2 values, which supports the original hypothesis that 2hDelta13C2 values are also sensitive to hydrogen bond distances. Finally, a context dependence is observed for these values, which suggests that hydrogen-bonding and base-stacking interactions are coupled.

Probing the role of hydrogen bonds in the stability of base pairs in double‐helical DNA

“…Our investigation does not support this theoretical prediction since the Φ values for GC/CG base pairs do not differ significantly from those for AT/TA base pairs (Table I). Variations in the strength of NH···N hydrogen bonds induced by the base sequence have been observed previously from isotopic shifts of adenine 13 C 2 NMR resonance and from one‐bond 15 N 1 H J‐coupling constants 33. According to this previous study, the NH···N hydrogen bonds may be the strongest in polypyrimidine‐polypurine tracts of at least four base pairs.…”

“…This enhancement could result from the binding of the third “strand” in the major groove of the DNA double‐helical structure. The enhancement may also be due to the presence of long polypyrimidine and polypurine tracts in this Y·RY triple helix, as previously suggested for DNA duplexes containing such tracts 33…”

2′‐Fluoro RNA Shows Increased Watson–Crick H‐Bonding Strength and Stacking Relative to RNA: Evidence from NMR and Thermodynamic Data

“…1 J NH coupling constants for imino groups were measured following published methods and by adapting the two-dimensional in phase anti phase (IPAP) technique to an 15 N-filtered, 1D proton detected, one-dimensional NMR measurement. [15] The 1 J NH coupling values for imino groups from the three internal base pairs are depicted in Figure 1. As expected we could not measure the 1 J NH values for terminal C:G base pairs due to rapid exchange with solvent.…”

“…Our observations are also in-line with those by others who had used a similar strategy based on measurements of 1 J NH coupling constants to establish the increased strength of [A]N 1 ⋯H-N 3 [U/T] H-bonds in duplex RNA relative to duplex DNA. [15] Thus, it appears that the more electronegative fluorine polarizes imino moieties more strongly than the RNA 2'-hydroxyl group, thereby tightening W-C H-bonds and contributing to the previously established, favorable ΔH term underlying the higher RNA affinity of 2'-F RNA relative to RNA. [9] …”

Isotope effect on chemical shifts in hydrogen‐bonded systems

“…A correlation is also found between 1 JNH and hydrogen bond isotope effect. 43 It has been demonstrated most recently that hydrogen bonding and pi-pi stacking are coupled in DNA using isotope effects.…”