ReviewWhen secondary comes first – The importance of non-canonical DNA structures
Introduction
This year is the 50th anniversary of the discovery of the G4 quartet. The 2012 FASEB Summer Research Conference on Dynamic DNA Structures in Biology commemorated this event by dedicating a large fraction of the meeting to the subject. Talks ranged from Martin Gellert's (NIH) first hand account of how studies of a jelly-like substance formed by guanylic acid led to the identification of G-quadruplexes in 1962 [1] to more recent work demonstrating the functional significance of such structures in vivo. In addition, this meeting, organized by Nancy Maizels (University of Washington) and Sergei Mirkin (Tufts University) at Saxtons River, VT, June 17–22, covered a wide variety of other alternate DNA structures including triplexes, hairpins, cruciforms, RNA:DNA hybrids and Holliday junctions and their roles in the metabolism of prokaryotic and eukaryotic cells. Through a series of talks and poster sessions, the meeting emphasized that unusual DNA secondary structures are widespread in all living organisms where they have profound effects on replication, transcription and genome stability. Some of these effects are positive, affecting normal development and the generation of genetic diversity, whilst other effects are negative and result in a variety of genetic disorders and cancer in humans (Fig. 1).
While much has been learned about the behavior of many of these structures, our understanding of their incidence in the genome is still incomplete. As was highlighted in the keynote address by Jeffrey Strathern (NCI), the inability of some of these DNA motifs to be propagated in Escherichia coli (e.g. long palindromes) and to be amplified or sequenced has resulted in their underrepresentation in whole-genome sequencing analyses of complex genomes including humans. However, as was accentuated in the keynote address and other talks in the meeting, the field is entering an exciting new era where more accurate sequencing technologies and bioinformatics tools for analysis of these sequences are emerging.
Below we briefly describe these topics as well as other new findings discussed at this meeting that contribute to our understanding of the dynamic nature of DNA.
Section snippets
G-quartets – the birthday boy
G-rich DNA molecules can form inter- or intra-molecular hydrogen bonds to form square planar arrays of 4 guanines known as G-quartets. A series of G-quartets results in a quadruplex structure frequently referred to as a G-quadruplex, G-tetraplex or G4-DNA. The guanines in the quadruplex are held by non-Watson–Crick hydrogen bonds, termed Hoogsteen base-pairs. The topology of the quadruplex varies depending on the orientation of the DNA strands involved, the length of the G-rich region and its
Triplex forming repeats – the split personality
Triplex DNA (H-DNA) is formed by homopurine-homopyrimidine sequences that have mirror symmetry. In the secondary structure, a third strand is folded into the major groove of the duplex DNA, an interaction that is stabilized by Hoogsteen-base pairing. The best known triplex structure-forming repeat is the GAA/TTC tract, whose expansion down-regulates the frataxin (FXN) gene and causes Friedreich ataxia (FRDA) in humans [8].
Similar to G4-DNA, it has been shown that GAA/TTC repeats can block
Hairpins and cruciforms – intra-strand acrobatics prone to instability
Palindromic DNA sequences or inverted repeats are sequences with internal symmetry such that they can switch between inter-strand and intra-strand base pairing. Consequently, these repeats can form hairpins when only one DNA strand is involved, a cruciform structure when both strands are involved, or slipped DNA when both strands form hairpins that are offset from one another. Several talks addressed the following questions: how to identify loci containing palindromes, what nucleases lead to
Branches, forks and head-on collisions: hazards on the road to replication, recombination, repair and transcription
The genome is employed in a variety of often simultaneous metabolic operations including replication, transcription and recombination which besides aiding formation of secondary structures as described above, can yield other transient deviations from the canonical B-DNA conformation. Various talks at this meeting discussed how defects in such operations can lead to the accumulation of intermediates that result in genetic instability. Another interesting related topic that attracted attention
Concluding remarks
Although G4 quartets were described half a century ago, it is only recently that we have begun to appreciate the dynamic role that they and other non-B DNA structures play in the evolution and function of the genomes in which they are found. This conference provided an excellent forum for discussion on the progress that has been made in this area and provided many fascinating ideas for new avenues of research that it is hoped will make the next meeting in the series, planned for June of 2014,
Acknowledgments
We are grateful to all the participants at the meeting who agreed to present unpublished results in this review. On behalf of the organizers, we would also like to thank ABCAM, American Society for Biochemistry and Molecular Biology, Annual Reviews, Elsevier, New England Biolabs, Inc., Public Library of Science and Tufts University, School of Arts and Sciences for their generous support for the meeting. The studies in KL laboratory were supported by the grants MCB-0818122 from NSF and
References (10)
- et al.
MutSalpha binds to and promotes synapsis of transcriptionally activated immunoglobulin switch regions
Curr. Biol.
(2005) - et al.
Helix formation by guanylic acid
Proc. Natl. Acad. Sci. U. S. A.
(1962) Dynamic roles for G4 DNA in the biology of eukaryotic cells
Nat. Struct. Mol. Biol.
(2006)- et al.
Formation of pearl-necklace monomorphic G-quadruplexes in the human CEB25 minisatellite
J. Am. Chem. Soc.
(2012) Structure, location and interactions of G-quadruplexes
FEBS J.
(2010)
Cited by (54)
Biophysical evaluation of antiparallel triplexes for biosensing and biomedical applications
2024, International Journal of Biological MacromoleculesOligonucleotides-transformers for molecular biology and nanoengineering
2022, GeneCitation Excerpt :However, the tendency of some DNA motifs to form hairpins may be associated with replicative fork blocking. The results of experiments using yeast have suggested that hairpins form in the S-phase of mitosis (Saini et al., 2013). Satellite DNA regions (the typical component of eukaryotic genomes, which consists of nucleotide tandem repeats in a non-coding DNA region) are structurally unstable and may trigger the untwisting of a double helix into two linear regions of DNA, each of which capable of forming hairpins of different sizes (Mitas, 1997).
Regulatory role of Non-canonical DNA Polymorphisms in human genome and their relevance in Cancer
2021, Biochimica et Biophysica Acta - Reviews on CancerCitation Excerpt :During different biological processes like replication, transcription, and chromatin remodeling, the DNA unwinds from the histone core and gives rise to negative supercoiling. This mechanism drives the transition of B form to non-canonical DNA form [2,4,5]. In normal conditions, the cells divide in a controlled and regulated manner under tight regulation of cell division mechanism and remain constant.
Rational design of Red fluorescent and selective G-quadruplex DNA sensing probes: The study of interaction signaling and the molecular structural relationship achieving high specificity
2020, Sensors and Actuators, B: ChemicalCitation Excerpt :It has been known that nucleic acids can form a variety of secondary structures. In addition to the classical double helix structure, they can also form other non-canonical structures [4–7]. Among various structures, the G-quadruplex (G4) structure has been an attractive research area since its first discovery in 1960s [8].
Modulation of DNA structure formation using small molecules
2019, Biochimica et Biophysica Acta - Molecular Cell ResearchCitation Excerpt :Although most non-B DNA structures exist in higher energy states compared to the B-DNA structure, negative supercoiling generated by the unwinding of DNA from histone cores behind the replication and transcription machinery or other chromatin remodeling processes, can drive the B-DNA to non-B DNA transition and maintain non-B structures. Importantly, non-B DNA is involved in wide range of biological processes, such as DNA replication, transcription, recombination and telomere maintenance [7,19,37,38], such that modulation of and/or alterations in DNA conformation could lead to significant biological outcomes (Fig. 2). While triplet repeat-forming hairpins have been implicated in a number of neurological disorders, largely via expansion of the repeats, here we will focus on Z-DNA, H-DNA and G4-DNA structures (Fig. 1) that have been implicated in cancer etiology.