Non-B DNA Secondary Structures and Their Resolution by RecQ Helicases

Abstract

In addition to the canonical B-form structure first described by Watson and Crick, DNA can adopt a number of alternative structures. These non-B-form DNA secondary structures form spontaneously on tracts of repeat sequences that are abundant in genomes. In addition, structured forms of DNA with intrastrand pairing may arise on single-stranded DNA produced transiently during various cellular processes. Such secondary structures have a range of biological functions but also induce genetic instability. Increasing evidence suggests that genomic instabilities induced by non-B DNA secondary structures result in predisposition to diseases. Secondary DNA structures also represent a new class of molecular targets for DNA-interactive compounds that might be useful for targeting telomeres and transcriptional control. The equilibrium between the duplex DNA and formation of multistranded non-B-form structures is partly dependent upon the helicases that unwind (resolve) these alternate DNA structures. With special focus on tetraplex, triplex, and cruciform, this paper summarizes the incidence of non-B DNA structures and their association with genomic instability and emphasizes the roles of RecQ-like DNA helicases in genome maintenance by resolution of DNA secondary structures. In future, RecQ helicases are anticipated to be additional molecular targets for cancer chemotherapeutics.

Figure 1

The RecQ helicase family. Proteins are aligned by their conserved helicase domain. Conserved domains and motifs in each group are shown by different colors as depicted at the bottom.

Figure 2

Schematic representation of certain non-B-form DNA structures. DNA can assume various alternate conformations depending upon the sequences. (a) Cruciform structures are formed at inverted repeats and also as intermediates of homologous recombination pathway, (b) Intermolecular triplex are formed by a triplex forming oligonucleotide (TFO, shown in blue) which binds to the purine-rich strand of the target duplex through the major groove. (c) Intramolecular triplex DNA structures can form at homopurine·homopyrimidine sequences with mirror symmetry, where a single-stranded region can bind in the major groove of the underlying DNA duplex to form a three-stranded helix. (d) G4 DNA is formed via parallel arrangement of four G-rich DNA strands; green boxes represent four guanine bases in planar arrangement via Hoogsteen base pairing. (e) Intermolecular G4 conformation is formed by DNA sequences with G-rich repeats forming hairpins that dimerize to stabilize bimolecular structure. (f) Intramolecular G4 DNA (or fold-over G quadruplex) is formed by single DNA strand with either four G-rich repeats or longer G tract that can fold upon themselves to form the G4 structure.

Figure 3

Proposed function of secondary structure resolution by RecQ helicases. Alternate DNA structures (indicated by red symbol) act as natural barrier to replication fork progression and can lead to fork stalling, collapse and ensue recombinogenic processing. Resolution by RecQ helicases is proposed to serve as roadblock remover for smooth progression of replication fork to avoid mutagenesis and/or genome rearrangements.