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

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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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Items 201–323 of 323

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
Self-citation
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×
“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)).”
BackgroundSelf-citation
DNA Secondary Structure at Chromosomal Fragile Sites in Human Disease
Thys, R. G., Lehman, C. E., Pierce, L., & Wang, Y. (2015) · Current Genomics · doi:10.2174/1389202916666150114223205 · Cited by 59
PKD1 Unusual DNA Conformations Are Recognized by Nucleotide Excision Repair*
Bacolla, A., Jaworski, A., Connors, T. D., & Wells, R. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m100845200 · Cited by 58
Crosstalk between MSH2–MSH3 and polβ promotes trinucleotide repeat expansion during base excision repair
Lai, Y., Budworth, H., Beaver, J. M., Chan, N. L. S., Zhang, Z., McMurray, C. T., & Liu, Y. (2016) · Nature Communications · doi:10.1038/ncomms12465 · Cited by 58
Secondary structure formation and DNA instability at fragile site FRA16B
Burrow, A. A., Marullo, A., Holder, L. R., & Wang, Y. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1245 · Cited by 57
Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: Insights from DNA complex structures
Pike, A., Gomathinayagam, S., Swuec, P., Berti, M., Zhang, Y., Schnecke, C., Marino, F., von Delft, F., Renault, L., Costa, A., et al. (2015) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1417594112 · Cited by 57
Deep learning approach for predicting functional Z-DNA regions using omics data
Beknazarov, N., Jin, S., & Poptsova, M. S. (2020) · Scientific Reports · doi:10.1038/s41598-020-76203-1 · Cited by 57
MutSβ promotes trinucleotide repeat expansion by recruiting DNA polymerase β to nascent (CAG)n or (CTG)n hairpins for error-prone DNA synthesis
Guo, J., Gu, L., Leffak, M., & Li, G. (2016) · Cell Research · doi:10.1038/cr.2016.66 · Cited by 57
Stable G-quadruplexes are found outside nucleosome-bound regions.
Wong, H.-M., & Huppert, J. (2009) · Molecular Biosystems · doi:10.1039/b905848f · Cited by 56
Identification of transcriptionally induced Z-DNA segments in the human c-myc gene.
Wölfl, S., Wittig, B., & Rich, A. (1995) · Biochimica et Biophysica Acta · doi:10.1016/0167-4781(95)00155-7 · Cited by 56
Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation
Guilbaud, G., Murat, P., Wilkes, H. S., Lerner, L. K., Sale, J., & Krude, T. (2021) · bioRxiv · doi:10.1093/nar/gkac555 · Cited by 55
Warsaw Breakage Syndrome associated DDX11 helicase resolves G-quadruplex structures to support sister chromatid cohesion
van Schie, J. J. M., Faramarz, A., Balk, J. A., Stewart, G., Cantelli, E., Oostra, A., Rooimans, M., Parish, J. L., Estéves, C. D. A., Dumic, K., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18066-8 · Cited by 55
Interplay between human high mobility group protein 1 and replication protein A on psoralen-cross-linked DNA.
Reddy, M., Christensen, J., & Vasquez, K. M. (2005) · Biochemistry · doi:10.1021/bi047902n · Cited by 55
Self-citation
Involvement of the Nucleotide Excision Repair Protein UvrA in Instability of CAG·CTG Repeat Sequences in Escherichia coli *
Oussatcheva, E. A., Hashem, V., Zou, Y., Sinden, R., & Potaman, V. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m104697200 · Cited by 55
The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli
Du, X., Wójtowicz, D., Bowers, A., Levens, D., Benham, C., & Przytycka, T. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt308 · Cited by 54
Molecular understanding of aluminum-induced topological changes in (CCG)12 triplet repeats: relevance to neurological disorders.
Latha, K. S., Anitha, S., Rao, K., & Viswamitra, M. A. (2002) · Biochimica et Biophysica Acta · doi:10.1016/s0925-4439(02)00133-3 · Cited by 54
ALU non-B-DNA conformations, flipons, binary codes and evolution
Herbert, A. G. (2020) · Royal Society Open Science · doi:10.1098/rsos.200222 · Cited by 54
DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions
Rocher, V., Genais, M., Nassereddine, E., & Mourad, R. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009308 · Cited by 52
Left-handed Z-DNA and intramolecular triplex formation at the site of an unequal sister chromatid exchange.
Weinreb, A., Collier, D. A., Birshtein, B. K., & Wells, R. D. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)40021-5 · Cited by 51
Human syndromes with genomic instability and multiprotein machines that repair DNA double-strand breaks.
de la Torre, C., Pincheira, J., & López-Sáez, J. F. (2003) · PubMed · doi:10.14670/hh-18.225 · Cited by 50
Altered Replication in Human Cells Promotes DMPK (CTG) n · (CAG) n Repeat Instability
Liu, G., Chen, X., Gao, Y., Lewis, T., Barthelemy, J., & Leffak, M. (2012) · Molecular and Cellular Biology · doi:10.1128/mcb.06727-11 · Cited by 49 · cited 1×
“Expansion of CTG repeats in the 3′-UTR of the DMPK gene leads to long CUG runs in the RNA that can interfere with the developmentally regulated alternative splicing of pre-mRNAs, resulting in toxicity associated with myotonic dystrophy type 1 (ref.(268)).”
Background
Allele-specific analysis of DNA replication origins in mammalian cells
Bartholdy, B., Mukhopadhyay, R., Lajugie, J., Aladjem, M. I., & Bouhassira, E. E. (2015) · Nature Communications · doi:10.1038/ncomms8051 · Cited by 49
TTS Mapping: integrative WEB tool for analysis of triplex formation target DNA Sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome
Jenjaroenpun, P., & Kuznetsov, V. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-s3-s9 · Cited by 46
Left-handed Z-DNA and genetic recombination.
Blaho, J. A., & Wells, R. D. (1989) · Progress in Nucleic Acid Research and Molecular Biology · doi:10.1016/s0079-6603(08)60696-0 · Cited by 46
Modulation of DNA structure formation using small molecules
del Mundo, I. M. A., Vásquez, K. M., & Wang, G. (2019) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2019.118539 · Cited by 45
Self-citation
Mammalian DNA Polymerase Kappa Activity and Specificity
Stern, H. R., Sefcikova, J., Chaparro, V. E., & Beuning, P. J. (2019) · Molecules · doi:10.3390/molecules24152805 · Cited by 45
Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop ‘G4 Kissing’ interaction
Williams, J. D., Houserova, D., Johnson, B. R., Dyniewski, B., Berroyer, A., French, H., Barchie, A. A., Bilbrey, D. D., DeMeis, J. D., Ghee, K. R., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa357 · Cited by 45
Targeting Non-B-Form DNA in Living Cells
Du, Y., & Zhou, X. (2013) · The Chemical Record · doi:10.1002/tcr.201300005 · Cited by 44
DNA polymerase δ stalls on telomeric lagging strand templates independently from G-quadruplex formation
Lormand, J. D., Buncher, N. A., Murphy, C. T., Kaur, P., Lee, M. Y., Burgers, P., Wang, H., Kunkel, T. A., & Opresko, P. L. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt813 · Cited by 44
High-resolution comparative mapping among man, cattle and mouse suggests a role for repeat sequences in mammalian genome evolution
Schibler, L., Roig, A., Mahé, M., Laurent, P., Hayes, H., Rodolphe, F., & Cribiu, E. P. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-194 · Cited by 43
Translesion polymerase eta both facilitates DNA replication and promotes increased human genetic variation at common fragile sites
Twayana, S., Bacolla, A., Barreto-Galvez, A., De-Paula, R. B., Drosopoulos, W. C., Kosiyatrakul, S. T., Bouhassira, E. E., Tainer, J. A., Madireddy, A., & Schildkraut, C. L. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2106477118 · Cited by 43
Evidence for the kinetic partitioning of polymerase activity on G-quadruplex DNA
Eddy, S., Maddukuri, L., Ketkar, A., Zafar, M. K., Henninger, E. E., Pursell, Z., & Eoff, R. (2015) · Biochemistry · doi:10.1021/acs.biochem.5b00060 · Cited by 43
DNA helical instability facilitates initiation at the SV40 replication origin.
Lin, S. D., & Kowalski, D. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1009 · Cited by 43
Human Translesion Polymerase κ Exhibits Enhanced Activity and Reduced Fidelity Two Nucleotides from G-Quadruplex DNA
Eddy, S., Tillman, M., Maddukuri, L., Ketkar, A. D., Zafar, M. K., & Eoff, R. L. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00374 · Cited by 43
Structure-specific endonucleases: guardians of fragile site stability
Minocherhomji, S., & Hickson, I. D. (2013) · Trends in Cell Biology · doi:10.1016/j.tcb.2013.11.007 · Cited by 42
Yeast Genome Maintenance by the Multifunctional PIF1 DNA Helicase Family
Muellner, J., & Schmidt, K. H. (2020) · Genes · doi:10.3390/genes11020224 · Cited by 42
A Comparative Study of G-Quadruplex Unfolding and DNA Reeling Activities of Human RECQ5 Helicase
Budhathoki, J. B., Maleki, P., Roy, W. A., Janščák, P., Yodh, J. G., & Balci, H. (2016) · Biophysical Journal · doi:10.1016/j.bpj.2016.05.016 · Cited by 41
Unwinding of the third strand of a DNA triple helix, a novel activity of the SV40 large T-antigen helicase.
Kopel, V., Pozner, A., Baran, N., & Manor, H. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.2.330 · Cited by 39
Stable G-quadruplex DNA structures promote replication-dependent genome instability
Rider, S. D., Gadgil, R. Y., Hitch, D. C., Damewood, F. J., Zavada, N., Shanahan, M., Alhawach, V., Shrestha, R., Shin‐ya, K., & Leffak, M. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.101947 · Cited by 39
Replication stress at microsatellites causes DNA double-strand breaks and break-induced replication
Gadgil, R. Y., Romer, E. J., Goodman, C. C., Rider, S. D., Damewood, F. J., Barthelemy, J., Shin‐ya, K., Hanenberg, H., & Leffak, M. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.013495 · Cited by 39
Expanded CAG/CTG Repeat DNA Induces a Checkpoint Response That Impacts Cell Proliferation in Saccharomyces cerevisiae
Sundararajan, R., & Freudenreich, C. H. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001339 · Cited by 36
Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA editing enzyme Adar1 is required for fear extinction
Marshall, P. R., Zhao, Q.-Y., Li, X., Wei, W., Periyakaruppiah, A., Zajaczkowski, E., Leighton, L., Madugalle, S. U., Basic, D., Wang, Z.-Q., et al. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-0627-5 · Cited by 36
Altered replication and inverted repeats induce mismatch repair-independent recombination between highly diverged DNAs in yeast
Tran, H., Degtyareva, N., Gordenin, D. A., & Resnick, M. A. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.2.1027 · Cited by 36
Secondary structural choice of DNA and RNA associated with CGG/CCG trinucleotide repeat expansion rationalizes the RNA misprocessing in FXTAS
Ajjugal, Y., Kolimi, N., & Rathinavelan, T. (2021) · Scientific Reports · doi:10.1038/s41598-021-87097-y · Cited by 36
Replication intermediates that escape Dna2 activity are processed by Holliday junction resolvase Yen1
Ölmezer, G., Levikova, M., Klein, D., Falquet, B., Fontana, G., Ćejka, P., & Rass, U. (2016) · Nature Communications · doi:10.1038/ncomms13157 · Cited by 35 · cited 1×
“Cruciform DNA shares some structural similarities with Holliday junctions and, as expected, the Yen1/GEN1 (refs.(252,253)) resolvases, SLX1/ SLX4 (refs.”
Background
Histone Acetylation Induced Transformation of B-DNA to Z-DNA in Cells Probed through FT-IR Spectroscopy.
Zhang, F., Huang, Q., Yan, J., & Chen, Z. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.6b00400 · Cited by 35
The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism
Yangyuoru, P. M., Bradburn, D. A., Liu, Z., Xiao, T., & Russell, R. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.815076 · Cited by 34
G-Quadruplexes and DNA Replication Origins
Prioleau, M. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-981-10-6955-0_13 · Cited by 34
E. coli Rep helicase and RecA recombinase unwind G4 DNA and are important for resistance to G4-stabilizing ligands
Paul, T., Voter, A. F., Cueny, R. R., Gavrilov, M. M., Ha, T., Keck, J. L., & Myong, S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa442 · Cited by 33
A Live-Cell Imaging Approach for Measuring DNA Replication Rates
Dovrat, D., Dahan, D., Sherman, S., Tsirkas, I., Elia, N., & Aharoni, A. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.06.018 · Cited by 32
Sticky DNA: Effect of the Polypurine·Polypyrimidine Sequence*
Vetcher, A., Napierala, M., & Wells, R. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m205210200 · Cited by 32
detectIR: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation
Ye, C.-T., Ji, G.-L., Li, L., & Liang, C. (2014) · PLoS ONE · doi:10.1371/journal.pone.0113349 · Cited by 31
Small inverted repeats drive mitochondrial genome evolution in Lake Baikal sponges.
Lavrov, D., Maikova, O., Pett, W., & Belikov, S. (2012) · Gene · doi:10.1016/j.gene.2012.05.039 · Cited by 31
Activities of human exonuclease 1 that promote cleavage of transcribed immunoglobulin switch regions
Vallur, A. C., & Maizels, N. (2008) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0805327105 · Cited by 31
The Structure of the Cyprinid herpesvirus 3 ORF112-Zα·Z-DNA Complex Reveals a Mechanism of Nucleic Acids Recognition Conserved with E3L, a Poxvirus Inhibitor of Interferon Response*
Kuś, K., Rakus, K., Boutier, M., Tsigkri, T., Gabriel, L., Vanderplasschen, A., & Athanasiadis, A. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.679407 · Cited by 30
Sticky DNA: in vivo formation in E. coli and in vitro association of long GAA*TTC tracts to generate two independent supercoiled domains.
Son, L., Bacolla, A., & Wells, R. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.05.025 · Cited by 30
Most meiotic CAG repeat tract-length alterations in yeast are SPO11 dependent
Jankowski, C., & Nag, D. K. (2002) · Zeitschrift für Induktive Abstammungs- und Vererbungslehre · doi:10.1007/s00438-001-0635-4 · Cited by 30
G-quadruplex recognition activities of E. Coli MutS
Ehrat, E. A., Johnson, B. R., Williams, J. D., Borchert, G., & Larson, E. D. (2012) · BMC Molecular Biology · doi:10.1186/1471-2199-13-23 · Cited by 29
DNA Repair and DNA Triplet Repeat Expansion: The Impact of Abasic Lesions on Triplet Repeat DNA Energetics
Völker, J., Plum, G., KLUMP, H. H., & Breslauer, K. J. (2009) · Journal of the American Chemical Society · doi:10.1021/ja902161e · Cited by 29
SOS Repair and DNA Supercoiling Influence the Genetic Stability of DNA Triplet Repeats in Escherichia coli
Majchrzak, M., Bowater, R. P., Staczek, P., & Parniewski, P. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.08.093 · Cited by 29
Transcription blockage by stable H-DNA analogs in vitro
Pandey, S., Ogloblina, A., Belotserkovskii, B. P., Dolinnaya, N. G., Yakubovskaya, M., Mirkin, S., & Hanawalt, P. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv622 · Cited by 28
The In Vitro Fidelity Of Yeast DNA Polymerase δ And Polymerase ε Holoenzymes During Dinucleotide Microsatellite DNA Synthesis
Abdulovic, A. L., Hile, S., Kunkel, T., & Eckert, K. (2011) · DNA Repair · doi:10.1016/j.dnarep.2011.02.003 · Cited by 28
DNA structure and transcription
Travers, A. (1978) · Nature · doi:10.1038/275089a0 · Cited by 28
Friedreich's Ataxia GAA·TTC Duplex and GAA·GAA·TTC Triplex Structures Exclude Nucleosome Assembly
Ruan, H., & Wang, Y. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.08.053 · Cited by 28
FAN1 exo- not endo-nuclease pausing on disease-associated slipped-DNA repeats: A mechanism of repeat instability
Deshmukh, A. L., Caron, M., Mohiuddin, M., Lanni, S., Panigrahi, G. B., Khan, M., Engchuan, W., Shum, N., Faruqui, A., Wang, P., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110078 · Cited by 27
CGG Repeats in the 5’UTR of FMR1 RNA Regulate Translation of Other RNAs Localized in the Same RNA Granules
Rovozzo, R., Korza, G., Baker, M. W., Li, M., Bhattacharyya, A., Barbarese, E., & Carson, J. H. (2016) · PLoS ONE · doi:10.1371/journal.pone.0168204 · Cited by 26
Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts
Georgakopoulos‐Soares, I., Koh, C. C., Momen, S., Jiricny, J., Hemberg, M., & Nik‐Zainal, S. (2020) · Nature Communications · doi:10.1038/s41467-020-15901-w · Cited by 25
The DEAH helicase DHX36 and its role in G-quadruplex-dependent processes
Schult, P., & Paeschke, K. (2020) · Biological Chemistry · doi:10.1515/hsz-2020-0292 · Cited by 25
XPD-dependent activation of apoptosis in response to triplex-induced DNA damage
Tiwari, M. K., & Rogers, F. A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt670 · Cited by 25
Selective recognition of pyrimidine motif triplexes by a protein encoded by the bacterial transposon Tn7.
Rao, J. E., & Craig, N. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4553 · Cited by 24
Formation of a Combined H-DNA/Open TATA Box Structure in the Promoter Sequence of the Human Na,K-ATPase α2 Gene*
Potaman, V., Ussery, D., & Sinden, R. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.23.13441 · Cited by 24
Competing B-Z and helix-coil conformational transitions in supercoiled plasmid DNA.
Aboul-ela, F., Bowater, R. P., & Lilley, D. M. J. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)46013-9 · Cited by 24
Delineation of the DNA Structural Features of Eukaryotic Core Promoter Classes
Vanaja, A., & Yella, V. R. (2022) · ACS Omega · doi:10.1021/acsomega.1c04603 · Cited by 23
Structure specific DNA recognition by the SLX1–SLX4 endonuclease complex
Xu, X., Wang, M., Sun, J., Yu, Z., Li, G., Yang, N., & Xu, R.-M. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab542 · Cited by 23 · cited 1×
“) resolvases, SLX1/ SLX4 (refs.(254,255)) and Mus81–Eme1 (Mms4 in budding yeast) resolvases(256) were all reported to cleave cruciform structures(257,258).”
Background
Sequence-dependent cost for Z-form shapes the torsion-driven B–Z transition via close interplay of Z-DNA and DNA bubble
Kim, S. H., Jung, H. J., Lee, I.-B., Lee, N., & Hong, S.-C. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab153 · Cited by 23
Conservation and Periodicity of DNA Bend Sites in the Human β-Globin Gene Locus (*)
Wada‐Kiyama, Y., & Kiyama, R. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.21.12439 · Cited by 23
Protection of the C. elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation
Meier, B., Volkova, N. V., Hong, Y., Bertolini, S., González‐Huici, V., Petrova, T., Boulton, S. J., Campbell, P. J., Gerstung, M., & Gartner, A. (2021) · PLoS ONE · doi:10.1371/journal.pone.0250291 · Cited by 23
Replication-independent instability of Friedreich’s ataxia GAA repeats during chronological aging
Neil, A. J., Hisey, J. A., Quasem, I., McGinty, R. J., Hitczenko, M., Khristich, A. N., & Mirkin, S. M. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2013080118 · Cited by 23
Base Excision Repair of Chemotherapeutically-Induced Alkylated DNA Damage Predominantly Causes Contractions of Expanded GAA Repeats Associated with Friedreich's Ataxia
Lai, Y., Beaver, J. M., Lorente, K., Melo, J. A., Ramjagsingh, S., Agoulnik, I. U., Zhang, Z., & Liu, Y. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093464 · Cited by 23
Repair bias of large loop mismatches during recombination in mammalian cells depends on loop length and structure
Bill, C. A., Taghian, D. G., Duran, W., & Nickoloff, J. A. (2001) · Mutation Research/DNA Repair · doi:10.1016/s0921-8777(01)00065-9 · Cited by 22
G4detector: Convolutional Neural Network to Predict DNA G-Quadruplexes
Barshai, M., Aubert, A., & Orenstein, Y. (2021) · IEEE/ACM Transactions on Computational Biology & Bioinformatics · doi:10.1109/tcbb.2021.3073595 · Cited by 22
Escherichia coli DNA polymerase I can disrupt G‐quadruplex structures during DNA replication
Teng, F., Hou, X., Fan, S., Réty, S., Dou, S., & Xi, X. (2017) · FEBS Journal · doi:10.1111/febs.14290 · Cited by 22
Formation of DNA triple helices inhibits DNA unwinding by the SV40 large T-antigen helicase.
Peleg, M., Kopel, V., Borowiec, J., & Manor, H. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.8.1292 · Cited by 22
A Role for Non‐B DNA Forming Sequences in Mediating Microlesions Causing Human Inherited Disease
Kamat, M., Bacolla, A., Cooper, D. N., & Chuzhanova, N. (2016) · Human Mutation · doi:10.1002/humu.22917 · Cited by 21
Triplex-forming oligonucleotides targeting c-MYC potentiate the anti-tumor activity of gemcitabine in a mouse model of human cancer
Boulware, S., Christensen, L. A., Thames, H., Coghlan, L., Vasquez, K. M., & Finch, R. A. (2013) · Molecular Carcinogenesis · doi:10.1002/mc.22026 · Cited by 21
Self-citation
A new peculiar DNA structure: NMR solution structure of a DNA kissing complex
Barbault, F., Huynh-Dinh, T., Paoletti, J., & Lancelot, G. (2002) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2002.10506771 · Cited by 21
Transcription-Replication Collisions—A Series of Unfortunate Events
Germain, C. S., Zhao, H., & Barlow, J. H. (2021) · Biomolecules · doi:10.3390/biom11081249 · Cited by 21
Structural parameters of palindromic repeats determine the specificity of nuclease attack of secondary structures
Saada, A. A., Costa, A. B., Sheng, Z., Guo, W., Haber, J., & Lobachev, K. S. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab168 · Cited by 20
Responses of DNA Mismatch Repair Proteins to a Stable G-Quadruplex Embedded into a DNA Duplex Structure
Pavlova, A., Monakhova, M., Ogloblina, A., Andreeva, N. A., Laptev, G., Polshakov, V., Gromova, E., Zvereva, M. I., Yakubovskaya, M., Oretskaya, T., et al. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21228773 · Cited by 20
Novel roles of an intragenic G-quadruplex in controlling microRNA expression and cardiac function
Zhu, M., Gao, J., Lin, X., Gong, Y., Qi, Y., Ma, Y.-L., Song, Y., Tan, W., Li, F.-Y., Ye, M., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab055 · Cited by 19
Mycobacterium tuberculosis UvrD1 and UvrD2 helicases unwind G‐quadruplex DNA
Saha, T., Shukla, K., Thakur, R., Desingu, A., & Nagaraju, G. (2019) · The FEBS Journal · doi:10.1111/febs.14798 · Cited by 18
Cruciform DNA Sequences in Gene Promoters Can Impact Transcription upon Oxidative Modification of 2′-Deoxyguanosine
Fleming, A. M., Zhu, J., Espejo, M. A. J., & Burrows, C. J. (2020) · Biochemistry · doi:10.1021/acs.biochem.0c00387 · Cited by 18
Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction
Xu, X.-J., & Chen, S.-J. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa463 · Cited by 17
Methods to detect replication-dependent and replication-independent DNA structure-induced genetic instability
Wang, G., Gaddis, S., & Vasquez, K. M. (2013) · Methods · doi:10.1016/j.ymeth.2013.08.004 · Cited by 17
Self-citation
Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements
Cheloshkina, K., & Poptsova, M. S. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008749 · Cited by 17
Human Rev1 relies on insert-2 to promote selective binding and accurate replication of stabilized G-quadruplex motifs
Ketkar, A. D., Smith, L., Johnson, C., Richey, A., Berry, M., Hartman, J. H., Maddukuri, L., Reed, M. R., Gunderson, J. E. C., Leung, J. W. C., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab041 · Cited by 16
Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegansPreprint
Krassovsky, K., Ghosh, R. P., & Meyer, B. J. (2021) · Genome Research · doi:10.1101/gr.270082.120 · Cited by 15
Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats
Fakharzadeh, A., Zhang, J., Roland, C., & Sagui, C. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac339 · Cited by 15
DNA polymerase θ promotes CAG•CTG repeat expansions in Huntington’s disease via insertion sequences of its catalytic domain
Chan, K. Y., Li, X., Ortega, J., Gu, L., & Li, G. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.101144 · Cited by 14
Mechanisms of Genome Instability in the Fragile X-Related Disorders
Hayward, B. E., & Usdin, K. (2021) · Genes · doi:10.3390/genes12101633 · Cited by 14
Distinct mechanisms of mutagenic processing of alternative DNA structures by repair proteins
McKinney, J. A., Wang, G., & Vasquez, K. M. (2020) · Molecular & Cellular Oncology · doi:10.1080/23723556.2020.1743807 · Cited by 13
Self-citation
pH-Responsive DNA Motif: From Rational Design to Analytical Applications
Zheng, L., Li, J.-Z., Li, Y.-X., Gao, J.-B., Dong, J.-X., & Gao, Z.-F. (2021) · Frontiers in Chemistry · doi:10.3389/fchem.2021.732770 · Cited by 12
Insights into the kinetic partitioning folding dynamics of human telomeric G-quadruplex from molecular simulations and machine learning.
Bian, Y.-Q., Song, F., Zhang, J., Yu, J.-F., Wang, J.-H., & Wang, W. (2020) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.0c00340 · Cited by 12
Requirement or exclusion of inverted repeat sequences with cruciform-forming potential in Escherichia coli revealed by genome-wide analyses
Miura, O., Ogake, T., & Ohyama, T. (2018) · Current Genetics · doi:10.1007/s00294-018-0815-y · Cited by 12
Remodeling Chromatin Induces Z-DNA Conformation Detected through Fourier Transform Infrared Spectroscopy.
Li, Y.-L., Huang, Q., Yao, G., Wang, X., Zhang, F., Wang, T., Shao, C.-S., Zheng, X., Jing, X., & Zhou, H.-Y. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c02432 · Cited by 11
Tissue-specific impact of stem-loops and quadruplexes on cancer breakpoints formation
Cheloshkina, K., & Poptsova, M. S. (2019) · BMC Cancer · doi:10.1186/s12885-019-5653-x · Cited by 11
Spectrum of variations in dog-1/FANCJ and mdf-1/MAD1 defective Caenorhabditis elegans strains after long-term propagation
Tarailo‐Graovac, M., Wong, T., Qin, Z., Flibotte, S., Taylor, J. C., Moerman, D. G., Rose, A. M., & Chen, N. (2015) · BMC Genomics · doi:10.1186/s12864-015-1402-y · Cited by 11
Opposite roles of transcription elongation factors Spt4/5 and Elf1 in RNA polymerase II transcription through B-form versus non-B DNA structures
Xu, J., Chong, J. P. C., & Wang, D. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab240 · Cited by 11
Associations between intronic non-B DNA structures and exon skipping
Tsai, Z.-T.-Y., Chu, W., Cheng, J.-H., & Tsai, H.-K. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt939 · Cited by 10
Construction of a G-quadruplex-specific DNA endonuclease.
Dang, D. T., Nguyen, L., Trương, T. T. T., Nguyen, H., & Phan, A. (2021) · Chemical Communications · doi:10.1039/d0cc05890d · Cited by 9
A strong structural correlation between short inverted repeat sequences and the polyadenylation signal in yeast and nucleosome exclusion by these inverted repeats
Miura, O., Ogake, T., Yoneyama, H., Kikuchi, Y., & Ohyama, T. (2018) · Current Genetics · doi:10.1007/s00294-018-0907-8 · Cited by 9
Demystifying the D-loop during DNA recombination
Roy, U., & Greene, E. C. (2020) · Nature · doi:10.1038/d41586-020-02831-2 · Cited by 9
Chromosomal model for analysis of a long CTG/CAG tract stability in wild-type Escherichia coli and its nucleotide excision repair mutants.
Szwarocka, S. T. S. T., Stączek, P., & Parniewski, P. (2007) · Canadian Journal of Microbiology (print) · doi:10.1139/w07-047 · Cited by 8
Sequence-specific functions of the early palindrome domain within the SV40 core origin of replication.
Kim, Y., & Kang, H.-S. (1989) · Nucleic Acids Research · doi:10.1093/nar/17.22.9279 · Cited by 8
A thermodynamic understanding of the salt-induced B-to-Z transition of DNA containing BZ junctions.
Son, H., Bae, S.-D., & Lee, S. (2021) · Biochemical and Biophysical Research Communications - BBRC · doi:10.1016/j.bbrc.2021.10.065 · Cited by 7
Position preference of essential genes in prokaryotic operons
Liu, T., Luo, H., & Gao, F. (2021) · PLoS ONE · doi:10.1371/journal.pone.0250380 · Cited by 7
Cruciform DNA in mouse growing oocytes: Its dynamics and its relationship with DNA transcription
Feng, X., Xie, F.-Y., Ou, X.-H., & Ma, J.-Y. (2020) · PLoS ONE · doi:10.1371/journal.pone.0240844 · Cited by 7
Cooperation between non-essential DNA polymerases contributes to genome stability in Saccharomyces cerevisiae
Meyer, D. H., Fu, B. X. H., Chavez, M., Loeillet, S., Cerqueira, P. G., Nicolas, A. G., & Heyer, W. (2019) · DNA repair · doi:10.1016/j.dnarep.2019.02.004 · Cited by 5
Detection of cis- and trans-acting Factors in DNA Structure-Induced Genetic Instability Using In silico and Cellular Approaches
Wang, G., Zhao, J., & Vásquez, K. M. (2016) · Frontiers in Genetics · doi:10.3389/fgene.2016.00135 · Cited by 5
Self-citation
Multiple G-quadruplex binding ligand induced transcriptomic map of cancer cell lines
Revikumar, A., Kashyap, V. K., Palollathil, A., Aravind, A., Raguraman, R., Kumar, K. M., Vijayakumar, M., Prasad, T. S. K., & Raju, R. (2021) · Journal of cell communication and signaling · doi:10.1007/s12079-021-00637-z · Cited by 4
DNA replication: Pif1 overcomes a quadruplex hurdle
Schuldt, A. (2011) · Nature reviews. Molecular cell biology · doi:10.1038/nrm3142 · Cited by 3
A transposon‐introduced G‐quadruplex motif is selectively retained and constrained to downregulate CYP321A1
Deng, Z.-Y., Zhang, Y., Gao, C., Shen, W., Wang, S., Ni, X., Liu, S.-Y., & Li, X.-C. (2022) · Insect Science · doi:10.1111/1744-7917.13021 · Cited by 2

Flagged first, then by citations

15 of the 338 references couldn’t be matched to a known paper.

Research works printed but not linked: 7

Smith, S. S. Evolutionary expansion of structurally complex DNA sequences. Cancer Genomics Proteomics 7, 207–215 (2010).
Yahyaoui, W., Callejo, M., Price, G. B. & Zannis-Hadjopoulos, M. Deletion of the cruciform binding domain in CBP/14-3-3 displays reduced origin binding and initiation of DNA replication in budding yeast. BMC Mol. Biol. 8, 27 (2007). · DOI
Nag, D. K. & Kurst, A. A 140-bp-long palindromic sequence induces double-strand breaks during meiosis in the yeast Saccharomyces cerevisiae. Genetics 146, 835–847 (1997). · DOI
Palombo, F. et al. hMutSbeta, a heterodimer of hMSH2 and hMSH3, binds to insertion/deletion loops in DNA. Curr. Biol. 6, 1181–1184 (1996). · DOI
Farah, J. A., Hartsuiker, E., Mizuno, K., Ohta, K. & Smith, G. R. A 160-bp palindrome is a Rad50.Rad32-dependent mitotic recombination hotspot in Schizosaccharomyces pombe. Genetics 161, 461–468 (2002). · DOI
Sinden, R. R., Zheng, G. X., Brankamp, R. G. & Allen, K. N. On the deletion of inverted repeated DNA in Escherichia coli: effects of length, thermal stability, and cruciform formation in vivo. Genetics 129, 991–1005 (1991). · DOI
Achaz, G., Coissac, E., Netter, P. & Rocha, E. P. Associations between inverted repeats and the structural evolution of bacterial genomes. Genetics 164, 1279–1289 (2003). · DOI

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
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 118
“…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 66
Unraveling the multifaceted role of extracellular DNA (eDNA) of biofilm in bacterial physiology, biofilm formation, and matrixome architecture
Rath, S., Fatma, S., & Das, S. (2025) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2025.2497270 · Cited by 44
Multifaceted Role of PARP1 in Maintaining Genome Stability Through Its Binding to Alternative DNA Structures
Laspata, N., Muoio, D., & Fouquerel, E. (2023) · Journal of Molecular Biology · doi:10.1016/j.jmb.2023.168207 · Cited by 40

See all 196

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 › Biochemistry, Genetics and Molecular Biology › Genetics › 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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Dynamic alternative DNA structures in biology and disease

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