Figure 1. Hydrogen bonds found in tetraloop structures. (a) and (b) Watson–Crick and (c) GU wobble base pairs drawn for comparison. (d) Bifurcated hydrogen bond between the first U and the fourth G in UUCG tetraloop. (e) Sheared base pair found in GNRA tetraloops. (f) G·A mismatch found in the GNRN-like structure of the AMP–aptamer complex. (g)–(i) Ribose–base hydrogen bonds. The hydrogen bonds between 2′-OH of the first U and O6 of the fourth G in UUCG (g) and between 2′-OH of the first G and N7 of the third A in GCAA (h) tetraloops stabilize the backbone turn. The amino group of the fourth A and O2′ of the first G also makes a hydrogen bond in the GCAA (i) tetraloop. (j) Ribose–phosphate hydrogen bond found in the UGAA tetraloop. (k)–(n) Base–phosphate hydrogen bonds found in the UUCG (k), GNRA (l) and (m) and UGAA (n) tetraloops.
Figure 2. UUCG (a) and GCAA (b) tetraloop structures. Hydrogen bonds are shown as dotted green lines. Carbon atoms are shown in green, phosphorus purple, nitrogen blue, oxygen red and hydrogen white.
Figure 3. U turn motif in a GAAA tetraloop. The backbone turn occurs at the GpA step and the turn is stabilized by a ribose–base (2′-OH of the first G and N7 of the fourth A) and a base–phosphate (amino proton of the first G and phosphate of the fourth A) hydrogen bonds. Carbon atoms are shown in green, phosphorus purple, nitrogen blue, oxygen red and hydrogen white.