Hoogsteen and reverse Hoogsteen base pairs

The A·U (or A·T) Hoogsteen pair is a well-known type of base pair (bp), named after the scientist who discovered it. As shown in the Figure below (left), in the Hoogsteen bp scheme, adenine uses its N7 (acceptor) and N6 (donor) atoms at the major groove edge to form two H-bonds with the N3 (donor) and O4 (acceptor) atoms from uracil, respectively. Interestingly, if the uracil base ring is flipped around the N7(A)…N3(U) H-bond by 180 degrees, N6(A) now forms an H-bond with O2(U), i.e., N6(A)…O2(U): this pairing scheme is called the reverse Hoogsteen bp (right).

Hoogsteen and reverse Hoogsteen base pairs

I first knew about the Hoogsteen bp from Saenger’s book titled “Principles of Nucleic Acid Structure”. My knowledge of the Hoogsteen bp deepened as I tried to categorize different types of bps, especially in RNA-containing structures, in a consistent and rigorous computational framework. Thus, in the 3DNA NAR03 publication, we discussed specifically the bp (M+N type) and compared it with the A·U Watson-Crick bp (M–N type), as shown in the Figure below:

Watson-Crick vs Hoogsteen base pairs

Antiparallel and parallel combinations of adenine (A) and uracil (U) base pair ‘faces’: (a) the antiparallel Watson–Crick A–U pair with opposing faces (shaded versus unshaded) and a 1.5 Å Stretch introduced to separate the two base reference frames; (b) the parallel Hoogsteen A+U pair with base pair faces of the same sense. Black dots on bases denote the C1′ atoms on the attached sugars.

However, only recently did I read the two original publications by Hoogsteen:

  • The two-page long preliminary report, titled The structure of crystals containing a hydrogen-bonded complex of 1-methylthymine and 9-methyladenine [Acta Cryst. (1959). 12, pp.822-3]. It contains only a single reference, i.e. the 1953 Watson-Crick DNA structure Nature paper. Reading carefully through the two pages, I know why Hoogsteen used the methylated derivatives of thymine and adenine, and how the failed initial interpretation of the experimental “vector-density map” based on the Watson-Crick A-T bp led to the discovery of the new base-pairing scheme:

The fact that the first trial structure could not be refined led to a more critical scrutiny of the generalized projection and a greater emphasis on the significance of certain spurious peaks and on relatively large variations in the heights of peaks that were assumed to represent atoms. The correct structure was finally discovered by changing the positions of a few atoms in the 9-methyladenine portion of the asymmetric unit.

I enjoyed reading these two papers a lot. More generally, I like such focused articles where authors get directly to a point and addressed it thoroughly and clearly.

As a side note, the term Hoogsteen “edge” appears frequently in nowaday’s publications of RNA structures: in the Leontis-Westhof bp classification scheme, this term simply means the major groove edge in what would be a Watson-Crick bp geometry.





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