Close encounters for the first time: Helicase interactions with DNA damage

Abstract

DNA helicases are molecular motors that harness the energy of nucleoside triphosphate hydrolysis to unwinding structured DNA molecules that must be resolved during cellular replication, DNA repair, recombination, and transcription. In vivo, DNA helicases are expected to encounter a wide spectrum of covalent DNA modifications to the sugar phosphate backbone or the nitrogenous bases; these modifications can be induced by endogenous biochemical processes or exposure to environmental agents. The frequency of lesion abundance can vary depending on the lesion type. Certain adducts such as oxidative base modifications can be quite numerous, and their effects can be helix-distorting or subtle perturbations to DNA structure. Helicase encounters with specific DNA lesions and more novel forms of DNA damage will be discussed. We will also review the battery of assays that have been used to characterize helicase-catalyzed unwinding of damaged DNA substrates. Characterization of the effects of specific DNA adducts on unwinding by various DNA repair and replication helicases has proven to be insightful for understanding mechanistic and biological aspects of helicase function in cellular DNA metabolism.

Yeast Helicase Pif1 Unwinds RNA:DNA Hybrids with Higher Processivity than DNA:DNA Duplexes

“…For some other helicases, the interaction with the displaced strand can result in sensitivity to DNA damage. For example, RECQ1, WRN, and other helicases are impeded by DNA adducts in the nontranslocating strand (48,49).…”

Methods to study the coupling between replicative helicase and leading-strand DNA polymerase at the replication fork

“…For example, helicases that move unidirectionally along single-stranded (ss) DNA separate the strands of double-stranded (ds) DNA and aid in DNA replication and repair, whereas those tracking along dsDNA catalyze DNA recombination and genome packaging reactions [1–7]. Given their involvement and importance in practically all nucleic acid metabolic pathways, methods have been developed to understand the fundamental properties of helicases [8–12]. However, in almost all cases, DNA or RNA helicases work in conjunction with associated proteins that affects helicase activities [13, 14]; therefore, it is essential to study the biochemical properties of helicases not only in isolation, but also in the context of the partner proteins.…”

Biochemical Activities and Genetic Functions of the Drosophila melanogaster Fancm Helicase in DNA Repair

“…Using the free energy derived from the hydrolysis of a 5ʹ nucleoside triphosphate, generally ATP, the helicase catalyzes the unwinding of duplex DNA to yield single-stranded DNA (ssDNA), a process that is required in replication, transcription, recombination, and repair. Thus, helicases are involved in essentially all metabolic pathways that require the separation of duplex DNA (Brosh 2013;Khan et al 2015).Helicases exhibit a diversity of structure and mechanism that may be related to the often unique and specialized roles that these enzymes can play in the cell (Brosh 2013;Daley et al 2013). Importantly, distinct helicases can interact with specific DNA substrates.…”

“…Using the free energy derived from the hydrolysis of a 5ʹ nucleoside triphosphate, generally ATP, the helicase catalyzes the unwinding of duplex DNA to yield single-stranded DNA (ssDNA), a process that is required in replication, transcription, recombination, and repair. Thus, helicases are involved in essentially all metabolic pathways that require the separation of duplex DNA (Brosh 2013;Khan et al 2015).…”