Methods to detect replication-dependent and replication-independent DNA structure-induced genetic instability

Abstract

DNA can adopt a variety of alternative secondary (i.e., non-B DNA) conformations that play important roles in cellular metabolism, including genetic instability, disease etiology, and evolution. While we still have much to learn, research in this field has expanded dramatically in the past decade. We have summarized in our previous Methods review (Wang et al., Methods, 2009) some commonly used techniques to determine non-B DNA structural conformations and non-B DNA-induced genetic instability in prokaryotes and eukaryotes. Since that time, we and others have further characterized mechanisms involved in DNA structure-induced mutagenesis and have proposed both replication-dependent and replication-independent models. Thus, in this review, we highlight some current methodologies to identify DNA replication-related and replication-independent mutations occurring at non-B DNA regions to allow for a better understanding of the mechanisms underlying DNA structure-induced genetic instability. We also describe a new web-based search engine to identify potential intramolecular triplex (H-DNA) and left-handed Z-DNA-forming motifs in entire genomes or at selected sequences of interest.

Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability

“…These sequence patterns allow for the identification of potential non-B DNA-forming sequences in the genome. With the advances in DNA genome sequencing, researchers have used this information to develop computer-based algorithms to develop search engines for potential non-B DNA structure-forming sequences [21, 22] (reviewed in [23]). Most search algorithms allow for user-defined settings to adjust the search parameters, and some can provide predicted free energy costs for such B- to non-B transitions.…”

“…However, the extent to which of the polypurine/polypyrimidine mirror repeat tracts form H-DNA at any given time and their direct contribution to the high mutation frequencies is difficult to determine. Another example is the human c-MYC promoter region (Figure 2), where multiple overlapping non-B DNA-forming sequences have been identified within a small region (~400 bp) surrounding the promoter P0 [23]. These include sequences with the capacity to adopt H-DNA [39], G-quadruplexes [37] and Z-DNA conformations [92], and each of these non-B DNA elements individually has been shown to be mutagenic in simplified models.…”

Leukemogenic rearrangements at the mixed lineage leukemia gene (MLL)—multiple rather than a single mechanism

“…A broader look at the intron 11/exon 12 boundary reveals that the whole region harboring major therapy-related translocation breakpoints is predicted to fold into a complex secondary structure with hairpins (Figure 1D ). Such non-B DNA structures can form during DNA replication when longer runs of single-stranded DNA are transiently formed as well as in a replication-independent manner (Wang et al, 2013 ). When left unresolved, such structures can obstruct progression of the DNA replication and/or RNA transcription machinery (Le et al, 2009 ; Wang et al, 2013 ), both of which could contribute to MLLbcr breakage and further rearrangements (Le et al, 2009 ) as discussed in more in detail below.…”

Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome

“…Indeed, when embedded in plasmids and examined in vivo (especially in bacteria), strong evidence supports the adoption of alternative conformations by sequences with non-B potential (Jaworski et al, 1987;Kouzine et al, 2008;Krasilnikov et al, 1999;Panayotatos and Fontaine, 1987). Based on biochemical and biophysical principles and experiments in vitro, various algorithms have been devised to identify sequence motifs of non-B DNA (SMnB) that might fold into non-B DNA structures (Cer et al, 2011;Kikin et al, 2006;Wang et al, 2013), and in some cases to assign a probability of such isomerization in naked DNA (Figure 1). Genome sequencing has revealed pervasive SMnB, especially in metazoans (Cer et al, 2011;Du et al, 2014;Huppert and Balasubramanian, 2007;Zhabinskaya et al, 2015).…”