A DNA G-quadruplex/i-motif hybrid

Chu, Betty; Zhang, Daoning; Paukstelis, Paul J.

doi:10.1093/nar/gkz1008

Title: A DNA G-quadruplex/i-motif hybrid

Journal Article · 14 November 2019 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkz1008 · OSTI ID:1607551

Chu, Betty ^[1]; Zhang, Daoning ^[1]; Paukstelis, Paul J. ^[1]

Univ. of Maryland, College Park, MD (United States)

DNA can form many structures beyond the canonical Watson–Crick double helix. It is now clear that noncanonical structures are present in genomic DNA and have biological functions. G-rich G-quadruplexes and C-rich i-motifs are the most well-characterized noncanonical DNA motifs that have been detected in vivo with either proscribed or postulated biological roles. Because of their independent sequence requirements, these structures have largely been considered distinct types of quadruplexes. Here, we describe the crystal structure of the DNA oligonucleotide, d(CCAGGCTGCAA), that self-associates to form a quadruplex structure containing two central antiparallel G-tetrads and six i-motif C–C⁺ base pairs. Solution studies suggest a robust structural motif capable of assembling as a tetramer of individual strands or as a dimer when composed of tandem repeats. This hybrid structure highlights the growing structural diversity of DNA and suggests that biological systems may harbor many functionally important non-duplex structures.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH); USDOE

Grant/Contract Number:: AC02-05CH11231; P30 GM124165; S10RR25528; S10RR02897

OSTI ID:: 1607551

Alternate ID(s):: OSTI ID: 1578242

Journal Information:: Nucleic Acids Research, Vol. 47, Issue (22) ; 12, 2019; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 19 works

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Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere. Kang, C.; Berger, I.; Lockshin, C. Proceedings of the National Academy of Sciences, Vol. 92, Issue 9 https://doi.org/10.1073/pnas.92.9.3874	journal	April 1995
NMR Structure of the Thrombin-Binding DNA Aptamer Stabilized by Sr ²⁺ Mao, Xi-an; Marky, Luis A.; Gmeiner, William H. Journal of Biomolecular Structure and Dynamics, Vol. 22, Issue 1 https://doi.org/10.1080/07391102.2004.10506977	journal	August 2004
A Topological Classification of G-Quadruplex Structures Esposito, V.; Galeone, A.; Mayol, L. Nucleosides, Nucleotides and Nucleic Acids, Vol. 26, Issue 8-9 https://doi.org/10.1080/15257770701527059	journal	November 2007
Functional Mechanisms of Microsatellite DNA in Eukaryotic Genomes Bagshaw, Andrew T. M. Genome Biology and Evolution, Vol. 9, Issue 9 https://doi.org/10.1093/gbe/evx164	journal	August 2017
Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex DNA Marathias, V. M.; Bolton, P. H. Nucleic Acids Research, Vol. 28, Issue 9 https://doi.org/10.1093/nar/28.9.1969	journal	May 2000
i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeats Esmaili, N. Nucleic Acids Research, Vol. 33, Issue 1 https://doi.org/10.1093/nar/gki160	journal	January 2005
Prevalence of quadruplexes in the human genome Huppert, J. L. Nucleic Acids Research, Vol. 33, Issue 9 https://doi.org/10.1093/nar/gki609	journal	May 2005
Quadruplex DNA: sequence, topology and structure Burge, Sarah; Parkinson, Gary N.; Hazel, Pascale Nucleic Acids Research, Vol. 34, Issue 19 https://doi.org/10.1093/nar/gkl655	journal	September 2006
Empirical comparison of ab initio repeat finding programs Saha, S.; Bridges, S.; Magbanua, Z. V. Nucleic Acids Research, Vol. 36, Issue 7 https://doi.org/10.1093/nar/gkn064	journal	February 2008
Sequence variant (CTAGGG)n in the human telomere favors a G-quadruplex structure containing a G·C·G·C tetrad Lim, Kah Wai; Alberti, Patrizia; Guédin, Aurore Nucleic Acids Research, Vol. 37, Issue 18 https://doi.org/10.1093/nar/gkp630	journal	August 2009
Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes Cang, Xiaohui; Šponer, Jiří; Cheatham, Thomas E. Nucleic Acids Research, Vol. 39, Issue 10 https://doi.org/10.1093/nar/gkr031	journal	February 2011
Detection of G-quadruplex DNA in mammalian cells Henderson, A.; Wu, Y.; Huang, Y. C. Nucleic Acids Research, Vol. 42, Issue 2 https://doi.org/10.1093/nar/gkt957	journal	October 2013
Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad Zhang, Diana; Huang, Terry; Lukeman, Philip S. Nucleic Acids Research, Vol. 42, Issue 21 https://doi.org/10.1093/nar/gku1122	journal	November 2014
G-quadruplexes and their regulatory roles in biology Rhodes, Daniela; Lipps, Hans J. Nucleic Acids Research, Vol. 43, Issue 18 https://doi.org/10.1093/nar/gkv862	journal	September 2015
Stabilization of i-motif structures by 2′-β-fluorination of DNA Assi, Hala Abou; Harkness, Robert W.; Martin-Pintado, Nerea Nucleic Acids Research, Vol. 44, Issue 11 https://doi.org/10.1093/nar/gkw402	journal	May 2016
Identification of multiple genomic DNA sequences which form i-motif structures at neutral pH Wright, Elisé P.; Huppert, Julian L.; Waller, Zöe A. E. Nucleic Acids Research, Vol. 45, Issue 22 https://doi.org/10.1093/nar/gkx1178	journal	November 2017
An intercalation-locked parallel-stranded DNA tetraplex Tripathi, Shailesh; Zhang, Daoning; Paukstelis, Paul J. Digital Repository at the University of Maryland https://doi.org/10.13016/m2ww7705n	text	January 2015

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