Dynamic alternative DNA structures in biology and disease

Wang, Guliang; Vasquez, Karen M.

doi:10.1038/s41576-022-00539-9

Cited by 196DNA and Nucleic Acid ChemistryDNA Repair MechanismsChromosomal and Genetic Variations

Dynamic alternative DNA structures in biology and disease

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Wang, Guliang, Vasquez, Karen M.·2023·Nature Reviews Genetics

DOI 10.1038/s41576-022-00539-9PMC PMC11634456

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Abstract

Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.

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G4s and non-B DNA structures in general have been shown to trigger genomic instability through wrongfully stimulating DNA damage and repair responses which initially maintain genome integrity.
“Notably, G4s and non-B DNA structures in general have been shown to trigger genomic instability through wrongfully stimulating DNA damage and repair responses which initially maintain genome integrity.”
From G-quadruplex-mediated genomic instability drives SNVs in cancer (2024) · cites this paper as [82]
In “Structure-specific repair cleavage models” (page unavailable), the review says non-B DNA can stimulate damage responses and may be recognized and cleaved by repair proteins that normally restore genome integrity. It presents resulting mutagenesis as a plausible model, not an established mechanism for non-B structures generally. In “Replication-dependent mutations” (page unavailable), it links G4 DNA to breaks and repair-associated deletions, but not specifically to wrongful stimulation of a damage response. (LLM, conf=0.86)
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DNA replication origins—where do we begin?Preprint
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Slipped (CTG)•(CAG) repeats can be correctly repaired, escape repair or undergo error-prone repair
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“were processed in cell extracts from multiple different human cells, including neuronal cells, independently of MSH2, MSH3, MSH6, MLH1, PMS2 or PMS1 (ref.(220)), despite the potential A–A or T–T mismatches formed in the loop-outs.”
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Replication of G Quadruplex DNA
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Mechanisms and implications of transcription blockage by guanine-rich DNA sequences
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Chemical profiling of DNA G-quadruplex-interacting proteins in live cells
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Impact of Alternative DNA Structures on DNA Damage, DNA Repair, and Genetic Instability
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Molecular analysis of the hotspot of recombination in the murine major histocompatibility complex.
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G-quadruplex formation at the 3′ end of telomere DNA inhibits its extension by telomerase, polymerase and unwinding by helicase
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A polymorphic dinucleotide repeat in the rat nucleolin gene forms Z-DNA and inhibits promoter activity
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G-Quadruplexes in DNA Replication: A Problem or a Necessity?
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Non-B-Form DNA Is Enriched at Centromeres
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A slipped-CAG DNA-binding small molecule induces trinucleotide-repeat contractions in vivo
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A Triplex-forming Sequence from the Human c-MYC Promoter Interferes with DNA Transcription
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Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis
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The Interplay between G-quadruplex and Transcription
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Large-scale expansions of Friedreich’s ataxia GAA repeats in yeast
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The nature of mutations induced by replication–transcription collisions
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Rif1 binds to G quadruplexes and suppresses replication over long distances
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Replisome stalling and stabilization at CGG repeats that are responsible for chromosomal fragility
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The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA reveals an unusual binding mode to Z-DNA
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Mutagenic consequences of a single G-quadruplex demonstrate mitotic inheritance of DNA replication fork barriers
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DDX5 helicase resolves G-quadruplex and is involved in MYC gene transcriptional activation
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Role of TLS DNA polymerases eta and kappa in processing naturally occurring structured DNA in human cells
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DNA triplet repeat expansion and mismatch repair
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“Mismatch repair (MMR) proteins, particularly the MSH2–MSH3 complex (MutSβ), sense heteroduplex DNA that contains small loops generated by slippage events at microsatellite repeats (reviewed in ref.(33)).”
Background
SbcCD causes a double-strand break at a DNA palindrome in the Escherichia coli chromosome.
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Transcription is associated with Z-DNA formation in metabolically active permeabilized mammalian cell nuclei.
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Transcription and DNA supercoiling.
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Chemical probing of homopurine-homopyrimidine mirror repeats in supercoiled DNA
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Endogenous oxidized DNA bases and APE1 regulate the formation of G-quadruplex structures in the genome
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MutSα Binds to and Promotes Synapsis of Transcriptionally Activated Immunoglobulin Switch Regions
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Integrative characterization of G-Quadruplexes in the three-dimensional chromatin structure
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Transcription-Induced CAG Repeat Contraction in Human Cells Is Mediated in Part by Transcription-Coupled Nucleotide Excision Repair
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BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes
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Promoter G-quadruplex folding precedes transcription and is controlled by chromatin
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Short Inverted Repeats Are Hot Spots For Genetic Instability: Relevance to Cancer Genomes
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Self-citation
Negative supercoiling induces spontaneous unwinding of a bacterial promoter.
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Human Origin Recognition Complex Binds Preferentially to G-quadruplex-preferable RNA and Single-stranded DNA*
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Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome
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The UvrD helicase and its modulation by the mismatch repair protein MutL
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Chromosome fragility at GAA tracts in yeast depends on repeat orientation and requires mismatch repair
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The Zalpha domain from human ADAR1 binds to the Z-DNA conformer of many different sequences.
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“The ZDBD of the ADAR1 protein binds to Z-DNA with high affinity and can convert even a short TA(3) repeat into a Z-DNA structure, which cannot form in the absence of ADAR1 (ref.(52)).”
Background
Nucleosome Assembly on CTG Triplet Repeats*
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Human XPA and RPA DNA repair proteins participate in specific recognition of triplex-induced helical distortions
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Defining R-loop classes and their contributions to genome instability
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Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase
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Recognition of nonhybridizing base pairs during nucleotide excision repair of DNA
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Evidence that vaccinia virulence factor E3L binds to Z-DNA in vivo: Implications for development of a therapy for poxvirus infection.
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Hotspot for deletions in the CGG repeat region of FMR1 in fragile X patients.
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Palindrome-mediated chromosomal translocations in humans.
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DNA repair in the trinucleotide repeat disorders
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Transcription-mediated organization of the replication initiation program across large genes sets common fragile sites genome-wide
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Combinatorial Regulation of Meiotic Holliday Junction Resolution in C. elegans by HIM-6 (BLM) Helicase, SLX-4, and the SLX-1, MUS-81 and XPF-1 Nucleases
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Mismatch repair and nucleotide excision repair proteins cooperate in the recognition of DNA interstrand crosslinks
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Self-citation
Contribution of a mutational hot spot to hemoglobin adaptation in high-altitude Andean house wrens
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Processing of G4 DNA by Dna2 Helicase/Nuclease and Replication Protein A (RPA) Provides Insights into the Mechanism of Dna2/RPA Substrate Recognition*
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DNA polymerases ζ and Rev1 mediate error-prone bypass of non-B DNA structures
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SRS2 and SGS1 prevent chromosomal breaks and stabilize triplet repeats by restraining recombination
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Somatic instability of the CTG repeat in mice transgenic for the myotonic dystrophy region is age dependent but not correlated to the relative intertissue transcription levels and proliferative capacities.
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Overcoming natural replication barriers: differential helicase requirements
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Length-dependent structure formation in Friedreich ataxia (GAA)n*(TTC)n repeats at neutral pH.
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Replication fork dynamics and dynamic mutations: the fork-shift model of repeat instability.
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The NEIL glycosylases remove oxidized guanine lesions from telomeric and promoter quadruplex DNA structures
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“Instead, G4 DNA has been shown to prevent the recognition and excision of 8-oxoG by NEIL1, NEIL3 and OGG1 (ref.(263)).”
Background
Induction of large DNA palindrome formation in yeast: implications for gene amplification and genome stability in eukaryotes.
Butler, D., Yasuda, L. E., & Yao, M. (1996) · Cell · doi:10.1016/s0092-8674(00)81805-x · Cited by 91
Palindromic but not G-rich sequences are targets of class switch recombination.
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Nucleosome Assembly on Methylated CGG Triplet Repeats in the Fragile X Mental Retardation Gene 1 Promoter*
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The in-vivo occurrence of Z DNA.
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Effects of Replication and Transcription on DNA Structure-Related Genetic Instability
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Self-citation
Nucleotide excision repair affects the stability of long transcribed (CTG*CAG) tracts in an orientation-dependent manner in Escherichia coli
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Rare fragile sites
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Analysis of the CTG repeat in skeletal muscle of young and adult myotonic dystrophy patients: when does the expansion occur?
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G4-quadruplex-binding proteins: review and insights into selectivity
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“Many proteins are known to interact with G4 DNA, such as POT1, RPA and BRCA1 (reviewed in ref.(78)).”
Background
Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp
Yuan, J.-B., Zhang, X.-J., Wang, M., Sun, Y.-M., Liu, C.-Z., Li, S.-H., Yu, Y., Gao, Y., Liu, F., Zhang, X., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-01716-y · Cited by 83 · see citing works
Mouse tissue culture models of unstable triplet repeats: in vitro selection for larger alleles, mutational expansion bias and tissue specificity, but no association with cell division rates.
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Double-Strand Break Formation by the RAG Complex at the Bcl-2 Major Breakpoint Region and at Other Non-B DNA Structures In Vitro
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DNA structure and the Werner protein modulate human DNA polymerase delta-dependent replication dynamics within the common fragile site FRA16D
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The intrinsically disordered amino-terminal region of human RecQL4: multiple DNA-binding domains confer annealing, strand exchange and G4 DNA binding
Keller, H., Kiosze, K., Sachsenweger, J., Haumann, S., Ohlenschläger, O., Nuutinen, T., Syväoja, J., Görlach, M., Grosse, F., & Pospiech, H. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku993 · Cited by 77 · see citing works
DHX9 helicase is involved in preventing genomic instability induced by alternatively structured DNA in human cells
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Self-citation
Distinct DNA repair pathways cause genomic instability at alternative DNA structures
McKinney, J. A., Wang, G., Mukherjee, A., Christensen, L. A., Subramanian, S. H. S., Zhao, J., & Vásquez, K. M. (2020) · Nature Communications · doi:10.1038/s41467-019-13878-9 · Cited by 77 · see citing works
Self-citation
Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error ratePreprint
Guiblet, W. M., Cremona, M. A., Čechová, M., Harris, R. S., Kejnovská, I., Kejnovský, E., Eckert, K. A., Chiaromonte, F., & Makova, K. D. (2018) · Genome Research · doi:10.1101/gr.241257.118 · Cited by 76 · see citing works
Reconstitution experiments show that sequence-specific histone-DNA interactions are the basis for nucleosome phasing on mouse satellite DNA.
Linzweiler, W., & Hörz, W. (1985) · Cell · doi:10.1016/s0092-8674(85)80123-9 · Cited by 75 · cited 1×
“Some repetitive satellites serve as signalling sequences for nucleosome assembly, whereas other repeats, such as Z-DNA-forming CG or CGG repeats(59) or H-DNA-forming GA repeats, are resistant to placement within the nucleosome structure(91) (reviewed in ref.(92)).”
Background
DNA unwinding mechanism of a eukaryotic replicative CMG helicase
Yuan, Z.-N., Georgescu, R., Bai, L., Zhang, D., Li, H.-L., & O'Donnell, M. E. (2019) · Nature Communications · doi:10.1038/s41467-020-14577-6 · Cited by 74 · see citing works
Synergistic Coordination of Chromatin Torsional Mechanics and Topoisomerase Activity
Le, T. T., Gao, X., Park, S. H., Lee, J., Inman, J. T., Lee, J. H., Killian, J. L., Badman, R., Berger, J., & Wang, M. D. (2019) · Cell · doi:10.1016/j.cell.2019.09.034 · Cited by 73
Pathways for Holliday Junction Processing during Homologous Recombination in Saccharomyces cerevisiae
Ashton, T. M., Mankouri, H. W., Heidenblut, A., McHugh, P., & Hickson, I. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.01130-10 · Cited by 71 · see citing works
dUTP incorporation into genomic DNA is linked to transcription in yeast
Kim, N., & Jinks-Robertson, S. (2009) · Nature · doi:10.1038/nature08033 · Cited by 71 · see citing works
Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation.
Schneider, T. D. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.23.4881 · Cited by 69
Mechanism of Replicative DNA Polymerase Delta Pausing and a Potential Role for DNA Polymerase Kappa in Common Fragile Site Replication
Walsh, E. M., Wang, X., Lee, M. Y., & Eckert, K. A. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2012.11.016 · Cited by 68 · see citing works
Role of DNA Polymerases in Repeat-Mediated Genome Instability
Shah, K., Shishkin, A. A., Voineagu, I., Pavlov, Y. I., Shcherbakova, P. V., & Mirkin, S. M. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.10.006 · Cited by 68 · see citing works
Expanded CAG Repeats Activate the DNA Damage Checkpoint Pathway
Lahiri, M., Gustafson, T. L., Majors, E. R., & Freudenreich, C. H. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.06.034 · Cited by 68 · see citing works
Human XPC-hHR23B interacts with XPA-RPA in the recognition of triplex-directed psoralen DNA interstrand crosslinks
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In the Sense of Transcription Regulation by G-Quadruplexes: Asymmetric Effects in Sense and Antisense Strands
Agarwal, T., Roy, S., Kumar, S., Chakraborty, T. K., & Maiti, S. (2014) · Biochemistry · doi:10.1021/bi401451q · Cited by 68 · see citing works
FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington’s disease
Goold, R., Hamilton, J., Menneteau, T., Flower, M., Bunting, E. L., Aldous, S. G., Porro, A., Vicente, J. R., Allen, N., Wilkinson, H., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109649 · Cited by 67 · see citing works
Mus81-dependent double-strand DNA breaks at in vivo-generated cruciform structures in S. cerevisiae.
Coté, A. G., & Lewis, S. (2008) · Molecules and Cells · doi:10.1016/j.molcel.2008.08.025 · Cited by 67
Modulation of ADAR1 editing activity by Z-RNA in vitro
Koeris, M., Funke, L., Shrestha, J., Rich, A., & Maas, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki849 · Cited by 67 · see citing works
Brain regional differences in the expansion of a CAG repeat in the spinocerebellar ataxias: Dentatorubral‐pallidoluysian atrophy, machado‐joseph disease, and spinocerebellar ataxia type 1
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Positive correlation between DNA polymerase alpha-primase pausing and mutagenesis within polypyrimidine/polypurine microsatellite sequences.
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Instability at chromosomal fragile sites.
Glover, T. (1998) · Recent results in cancer research. Fortschritte der Krebsforschung. Progres dans les recherches sur le cancer · doi:10.1007/978-3-642-46870-4_11 · Cited by 65 · see citing works
The Human Specialized DNA Polymerases and Non-B DNA: Vital Relationships to Preserve Genome Integrity
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Inhibitory effect of a short Z-DNA forming sequence on transcription elongation by T7 RNA polymerase
Ditlevson, J. V., Tornaletti, S., Belotserkovskii, B. P., Teijeiro, V., Wang, G., Vásquez, K. M., & Hanawalt, P. C. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn136 · Cited by 65 · see citing works
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Saccharomyces cerevisiae Mre11 is a high-affinity G4 DNA-binding protein and a G-rich DNA-specific endonuclease: implications for replication of telomeric DNA
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Holliday junction-containing DNA structures persist in cells lacking Sgs1 or Top3 following exposure to DNA damage
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Negative supercoiling of DNA facilitates an interaction between transcription factor IID and the fibroin gene promoter.
Mizutani, M., Ohta, T., Watanabe, H., Handa, H., & Hirose, S. (1991) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.88.3.718 · Cited by 64
Secondary structure formation and DNA instability at fragile site FRA16B
Burrow, A. A., Marullo, A., Holder, L. R., & Wang, Y.-H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1245 · Cited by 62 · see citing works
A Novel Recombination Pathway Initiated by the Mre11/Rad50/Nbs1 Complex Eliminates Palindromes During Meiosis in Schizosaccharomyces pombe
Farah, J. A., Cromie, G., Steiner, W., & Smith, G. R. (2005) · Genetics · doi:10.1534/genetics.104.037515 · Cited by 61 · see citing works
DNA Polymerase III Proofreading Mutants Enhance the Expansion and Deletion of Triplet Repeat Sequences in Escherichia coli *
Iyer, R. R., Pluciennik, A., Rosche, W. A., Sinden, R., & Wells, R. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.3.2174 · Cited by 61 · see citing works
Targeting oncogenes to improve breast cancer chemotherapy.
Christensen, L. A., Finch, R., Booker, A. J., & Vasquez, K. M. (2006) · Cancer Research · doi:10.1158/0008-5472.can-05-4288 · Cited by 59
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Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes
Zhao, J., Wang, G., del Mundo, I. M. A., McKinney, J. A., Lu, X., Bacolla, A., Boulware, S. B., Zhang, C., Zhang, H., Ren, P. Y., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.01.014 · Cited by 59 · cited 1× · see citing works
“In addition to disorders caused by repetitive DNA itself, many types of non-B DNA structure are involved in human diseases associated with genetic instability, such as cancer (reviewed in ref.(32)).”
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Flagged first, then by citations

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Sorted by citations

Chromosomal fragile site breakage by EBV-encoded EBNA1 at clustered repeats
Li, J. S. Z., Abbasi, A., Kim, D. H., Lippman, S. M., Alexandrov, L. B., & Cleveland, D. W. (2023) · Nature · doi:10.1038/s41586-023-05923-x · Cited by 81 · see citing works
The complete sequence and comparative analysis of ape sex chromosomes
Makova, K. D., Pickett, B. D., Harris, R. S., Hartley, G. A., Čechová, M., Pál, K., Nurk, S., Yoo, D., Li, Q., Hebbar, P., et al. (2024) · Nature · doi:10.1038/s41586-024-07473-2 · Cited by 122 · see citing works
“…us to explore the distribution of motifs able to form non-B-DNA structures—A-phased repeats, direct repeats, G-quadruplexes, inverted repeats, mirror repeats, short tandem repeats and Z-DNA 31 —which have been implicated in numerous cellular processes, including replication and transcription 32 .”
Detection of alternative DNA structures and its implications for human disease
Matos-Rodrigues, G. E., Hisey, J. A., Nussenzweig, A., & Mirkin, S. M. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.08.018 · Cited by 65 · see citing works
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Multifaceted Role of PARP1 in Maintaining Genome Stability Through Its Binding to Alternative DNA Structures
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i-Motif DNA: identification, formation, and cellular functions.
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Analysing protein complexes in plant science: insights and limitation with AlphaFold 3
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Chromatin damage generated by DNA intercalators leads to degradation of RNA Polymerase II
Espinoza, J. A., Kanellis, D. C., Saproo, S., Leal, K., Martínez, J. F., Bartek, J., & Lindström, M. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae069 · Cited by 28 · see citing works
HLTF resolves G4s and promotes G4-induced replication fork slowing to maintain genome stability
Bai, G., Endres, T., Kühbacher, U., Mengoli, V., Greer, B. H., Peacock, E. M., Newton, M. D., Stanage, T. H., Stritto, M. R. D., Lungu, R., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.07.018 · Cited by 34 · see citing works
Molecular bioengineering of functional nucleic acids
Du, Z., Wu, X., Dang, Y., Wu, Q., Fu, T., He, L., Wang, X., Mou, S., Fang, X., Qu, F., et al. (2025) · Nature Reviews Bioengineering · doi:10.1038/s44222-025-00361-y · Cited by 31 · see citing works
“secondary structures such as hairpins, stem-loops, G-quadruplexes and pseudoknots 5,6 .”
Massively parallel analysis of single-molecule dynamics on next-generation sequencing chips
Rivera, J. A., Mao, G., Владимирович, С. А., Panfilov, M., Hou, Q., Lindell, M., Chanez, C., Ritort, F., Jínek, M., & Deindl, S. (2024) · Science · doi:10.1126/science.adn5371 · Cited by 38 · see citing works
Template-Assembled Synthetic G-Quartets (TASQs): multiTASQing Molecular Tools for Investigating DNA and RNA G-Quadruplex Biology
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Structural investigation of pathogenic RFC1 AAGGG pentanucleotide repeats reveals a role of G-quadruplex in dysregulated gene expression in CANVAS
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EndoQuad: a comprehensive genome-wide experimentally validated endogenous G-quadruplex database
Qian, S. H., Shi, M., Xiong, Y.-L., Zhang, Y., Zhang, Z.-H., Song, X., Deng, X.-Y., & Chen, Z. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad966 · Cited by 22 · see citing works
Methods and applications of genome-wide profiling of DNA damage and rare mutations
Pfeifer, G. P., & Jin, S. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00748-4 · Cited by 25 · see citing works
“They can also result from replication stress at chromosome fragile sites, breakage of alternative DNA structures or exposure of cells to ionizing radiation or oxidizing agents 51–54 .”
Formation and biological implications of Z-DNA
Run, Y., Tavakoli, M., Zhang, Y., Vasquez, K. M., & Zhang, W.-L. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.07.006 · Cited by 21 · see citing works
Self-citation
A Phenotypic Approach to the Discovery of Potent G-Quadruplex Targeted Drugs
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“G4s appear to have multiple functions [53] in addition to their involvement in transcriptional initiation, de-Molecules pending on their location in the human genome and in individual genes.”
Background
G-quadruplex-mediated genomic instability drives SNVs in cancer
Richl, T., Kuper, J., & Kisker, C. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae098 · Cited by 20 · see citing works
DNA supercoiling-mediated G4/R-loop formation tunes transcription by controlling the access of RNA polymerase
Hwang, J., Lee, C.-Y., Brahmachari, S., Tripathi, S., Paul, T., Lee, H., Craig, A., Ha, T., & Myong, S. (2025) · Nature Communications · doi:10.1038/s41467-025-58479-x · Cited by 25 · see citing works
“Therefore, negative super-coiling facilitates both RNAP binding and R-loop/G4 formation 2,10,11 .”
Distinguishing G-Quadruplexes Stabilizer and Chaperone for c-MYC Promoter G-Quadruplexes through Single-Molecule Manipulation.
Zhang, Y.-S., Cheng, Y., Luo, Q., Wu, T.-B., Huo, J.-F., Yin, M., Peng, H., Xiao, Y., Tong, Q.-Y., & You, H. (2024) · Journal of the American Chemical Society · doi:10.1021/jacs.3c09074 · Cited by 17 · see citing works
The unusual structural properties and potential biological relevance of switchback DNA
Madhanagopal, B. R., Talbot, H., Rodriguez, A., Louis, J. M., Zeghal, H., Vangaveti, S., Reddy, K., & Chandrasekaran, A. R. (2024) · Nature Communications · doi:10.1038/s41467-024-50348-3 · Cited by 14 · see citing works
“Our hypothesis that switchback DNA could be an alternate secondary structure in repeat sequences is based on the fact that long tracts of repeat sequences are known to adopt several alternate structures 71 .”
Background
Evolutionary dynamics of predicted G-quadruplexes in human and other great apes
Mohanty, S. K., Chiaromonte, F., & Makova, K. D. (2025) · Genome biology · doi:10.1186/s13059-025-03635-1 · Cited by 18 · see citing works
“These alternative DNA structures—such as Z-DNA [5], cruciforms [6], H-DNA [7], bent DNA [8], and G-quadruplexes (G4s) [9]—are involved in various biological processes (reviewed in [10]).”
G-quadruplexes from non-coding RNAs
Li, F., & Zhou, J. (2023) · Journal of molecular medicine · doi:10.1007/s00109-023-02314-7 · Cited by 14 · see citing works
Kolmogorov-Arnold Networks for Genomic Tasks
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Chemoproteomic profiling unveils binding and functional diversity of endogenous proteins that interact with endogenous triplex DNA
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“2f), consistent with the established roles of triplex DNA structures in transcriptional regulation and genome instability 29,33,47,48 .”
High-complexity of DNA double-strand breaks is key for alternative end-joining choice
Hou, Z., Yu, T., Yi, Q.-Y., Du, Y., Zhou, L., Zhao, Y., Wu, Y., Wu, L., Wang, T., & Bian, P. (2024) · Communications Biology · doi:10.1038/s42003-024-06640-5 · Cited by 13 · see citing works
“Endogenous non-B DNA structures such as cruciform DNA can also lead to the formation of complex DSBs 20 .”
DNA at the center of mammalian innate immune recognition of bacterial biofilms.
Gallucci, S. (2024) · Trends in immunology · doi:10.1016/j.it.2023.12.004 · Cited by 13
In vivo detection of DNA secondary structures using Permanganate/S1 Footprinting with Direct Adapter Ligation and Sequencing (PDAL-Seq)Preprint
Lahnsteiner, A., Craig, S. J. C., Kamali, K., Weissensteiner, B., McGrath, B., Risch, A., & Makova, K. D. (2023) · bioRxiv · doi:10.1101/2023.11.28.569002 · Cited by 12 · see citing works
“This long list of biological processes reflects the importance of these structures in living cells (Wang & Vasquez, 2023), as well as in evolution (Makova & Weissensteiner, 2023), and highlights the need of reliable methods for their identification to facilitate our understanding of the underlying…”
Background
Advanced glycation end products (AGEs) and their role in diabetes mellitus and related complications: mechanisms and therapeutic insights
Qaed, E., Aldahmash, W., & Mahyoub, M. A. (2025) · Glycoconjugate Journal · doi:10.1007/s10719-025-10194-x · Cited by 11 · see citing works
“In DM, this increased net efflux demonstrates density dependence, notably absent in individuals not classified as overt DM but with elevated glycated hemoglobin, who exhibit a higher threshold for endothelial reactive oxygen species compared to those with normal glycemia [ 36].”
SLE: a cognitive step forward—a synthesis of rethinking theories, causality, and ignored DNA structures
Rekvig, O. P. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1393814 · Cited by 11 · see citing works
“The dynamic transformation of intricate DNA structures, associated with their involvement in gene regulation, gene expression, DNA replication, and DNA repair (11), has not been considered important in contemporary studies on DNA immunogenicity (2).”
Background
Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure.
Šariċ, A., Rajić, J., Tolić, A., Dučić, T., & Vidaković, M. (2023) · Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy · doi:10.1016/j.saa.2023.123090 · Cited by 11
Untargeted CUT&Tag reads are enriched at accessible chromatin and restrict identification of potential G4-forming sequences in G4-targeted CUT&Tag experiments
Thompson, M. D., & Byrd, A. K. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf678 · Cited by 11 · see citing works
“Formation of non-B DNA secondary structures is both a driver and a consequence of myriad biological processes (reviewed in [ 1 ]).”
Exploring triplex DNA nanostructures: A comprehensive review from fundamentals to applications
Tang, S., He, B.-S., Xie, L.-L., Cao, X.-Y., Ren, W.-J., & Xu, Y.-W. (2025) · Chemical Engineering Journal · doi:10.1016/j.cej.2025.159425 · Cited by 10
The repertoire of short tandem repeats across the tree of life
Chantzi, N., & Georgakopoulos‐Soares, I. (2025) · Genome biology · doi:10.1186/s13059-025-03893-z · Cited by 7 · see citing works
“Furthermore, STRs can form non-canonical DNA structures such as Z-DNA, G-qua-druplexes and hairpins, which are also associated with a higher mutation rate and have a plethora of functional roles [22–26].”
Non-canonical DNA structures in the human ribosomal DNA
Smirnov, E., Molínová, P., Chmúrčiaková, N., Vacík, T., & Cmarko, D. (2023) · Histochemistry and Cell Biology · doi:10.1007/s00418-023-02233-1 · Cited by 10 · see citing works
Single‐Molecule Nanopore Detection of Non‐Canonical Thymine‐Melamine Hydrogen Bonding Base Pair in DNA Abasic Site
Liu, S.-L., Li, J., Wang, Y.-J., Zhang, Z.-R., Wang, Y., Wang, L.-B., & Wang, L. (2025) · Small Methods · doi:10.1002/smtd.202501445 · Cited by 9 · see citing works
Z-form DNA-RNA hybrid blocks DNA replication
Wang, S., & Xu, Y. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf135 · Cited by 9
“…left-handed Z-form double helix structure, including Z-RNA and Z-DNA, has been shown to have an important role in multiple physiological events [ 1–5 ], including the regulation of gene expression [ 6 ], nucleosome positioning [ 7 , 8 ], and genetic instability associated with nucleic acid damage…”
APOBEC3A deaminates CTG hairpin loops to promote fragility and instability of expanded CAG/CTG repeats
Brown, R. E., Coxon, M., Larsen, B. B., Allison, M. J., Chadha, A., Mittelstadt, I., Mertz, T. M., Roberts, S. A., & Freudenreich, C. (2025) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.2408179122 · Cited by 9 · see citing works
“B - form DNA secondary structures, which are drivers of repeat instability; contractions (loss of repeat units), or expansions (gain of repeat units) ( 1 , 2 ).”
How DNA secondary structures drive replication fork instability
Sethi, A., Fernández-Casañas, M., Delpino, B., & Coster, G. (2025) · DNA repair · doi:10.1016/j.dnarep.2025.103913 · Cited by 7 · see citing works
Molecular dynamics of DNA repair and carcinogen interaction: Implications for cancer initiation, progression, and therapeutic strategies
Alyafeai, E., Qaed, E., Al-mashriqi, H. S., Al‐Maamari, A., Almansory, A. H., Futini, F. A., Sultan, M., & Tang, Z. (2024) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2024.111883 · Cited by 8 · see citing works
Unfolding rates of 1:1 and 2:1 complex of CX-5461 and c-MYC promoter G-quadruplexes revealed by single-molecule force spectroscopy
Peng, H., Zhang, Y.-S., Luo, Q., Wang, X., & You, H.-J. (2024) · Biophysics Reports · doi:10.52601/bpr.2024.240018 · Cited by 8 · see citing works
Pathogenic CANVAS (AAGGG)n repeats stall DNA replication due to the formation of alternative DNA structures
Hisey, J. A., Radchenko, E. A., Mandel, N. H., McGinty, R., Matos-Rodrigues, G., Rastokina, A., Masnovo, C., Ceschi, S., Hernandez, A. J., Nussenzweig, A., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae124 · Cited by 8 · see citing works
mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome
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Authors: Wang, G., & Vasquez, K. M.
Affiliations: The University of Texas at Austin (US)
ORCID: Wang, Guliang
Vasquez, Karen M.
Venue: Nature Reviews Genetics
Publisher: Springer Science and Business Media LLC
Published: 2022-10-31
Volume: 24
Issue: 4
Pages: 211-234
ISSN: 1471-0056 (ISSN-L)
1471-0064
DOI: 10.1038/s41576-022-00539-9
PMC: PMC11634456
OpenAlex: W4307744067
Cited by: 196
References: 338
Citations by year: 2026: 52 · 2025: 68 · 2024: 57 · 2023: 18 · 2022: 1
FWCI: 3.83
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Nature Reviews Genetics (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: National Cancer Institute (R01CA093729)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords: non-B DNA structures, Z-DNA, H-DNA, triplex DNA, G-quadruplex, repetitive elements, genome stability, mutagenesis, DNA repair, DNA replication, transcription, chromatin organization, genomic instability, etiology, evolution
MeSH terms: Biology, DNA, DNA Replication, Humans, Genome, Human, G-Quadruplexes

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