A historical account of hoogsteen base‐pairs in duplex DNA

Abstract

In 1957, a unique pattern of hydrogen bonding between N3 and O4 on uracil and N7 and N6 on adenine was proposed to explain how poly(rU) strands can associate with poly(rA)-poly(rU) duplexes to form triplexes. Two years later, Karst Hoogsteen visualized such a non-canonical A-T base-pair through X-ray analysis of co-crystals containing 9-methyladenine and 1-methylthymine. Subsequent X-ray analyses of guanine and cytosine derivatives yielded the expected Watson-Crick base-pairing but those of adenine and thymine (or uridine) did not yield Watson-Crick base-pairs, instead favoring ‘Hoogsteen’ base-pairing. More than two decades ensued without experimental ‘proof’ for A-T Watson-Crick base-pairs, while Hoogsteen base-pairs continued to surface in AT-rich sequences, closing base-pairs of apical loops, in structures of DNA bound to antibiotics and proteins, damaged and chemically modified DNA, and in polymerases that replicate DNA via Hoogsteen pairing. Recently, NMR studies have shown that base-pairs in duplex DNA exists as a dynamic equilibrium between Watson-Crick and Hoogsteen forms. There is now little doubt that Hoogsteen base-pairs exist in significant abundance in genomic DNA where they can expand the structural and functional versatility of duplex DNA beyond that which can be achieved based only on Watson-Crick base-pairing. Here, we provide a historical account of the discovery and characterization of Hoogsteen base-pairs hoping that this will inform future studies exploring the occurrence and functional importance of these alternative base-pairs.

Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics

“…Thus, transient HG bps seem to be more abundant in less stable WC dinucleotide steps such as CA/TG and TA/TA steps. The energetic preference for HG bps at TA/TA steps observed here is consistent with a large body of data showing that HG bps are favored in A-T rich sequences, particularly TA/TA steps (reviewed in 8 ).…”

“…This can help explain how polymerases such as the human DNA polymerase iota can use HG pairing as a general mechanism to replicate DNA and thereby bypass lesions that diminish the ability to form WC bps 8,16 . Our findings also raise the possibility that HG bps may be widespread in genomic DNA, especially given that the energetic differences between WC and HG bps are small compared to forces in living cells, including those arising due to supercoiling, torsional stress, and protein binding.…”

“…1a). HG bps modify the structural and chemical presentation of DNA and thereby can play unique roles (reviewed in ref 8 ) in DNA-protein recognition 9–12 , damage induction 13 and repair 14,15 as well as replication 16,17 . For example, by narrowing the minor groove, HG bps have been shown to alter the DNA electrostatic potential “seen” by DNA-binding proteins at the bp edges in the DNA grooves in the context of p53-DNA complexes 12,18,19 .…”

Atomic structures of excited state A–T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations

“…Techniques based on spin relaxation in the rotating frame (R1ρ) 1–3 and chemical exchange saturation transfer (CEST) 4–6 are providing rare insights into short-lived (μs-ms) low-populated (<5%) excited states (ESs) 7 in nucleic acids that play important roles in gene expression and regulation 8,9 . For example, canonical Watson-Crick A–T and G–C base pairs (bps) in duplex DNA have been shown to exist in dynamic equilibrium with non-canonical Hoogsteen bps 10 (Figure 1A).…”

“…For example, canonical Watson-Crick A–T and G–C base pairs (bps) in duplex DNA have been shown to exist in dynamic equilibrium with non-canonical Hoogsteen bps 10 (Figure 1A). The Hoogsteen bps are proposed to play important roles in DNA recognition 11 , damage repair 12 , and replication 9,13 . RD studies have also uncovered an inverse process, whereby non-canonical G–T/U wobble mismatches morph into canonical Watson-Crick-like tautomeric and anionic mismatches 14 .…”