1
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Trajkovski M, Pastore A, Plavec J. Dimeric structures of DNA ATTTC repeats promoted by divalent cations. Nucleic Acids Res 2024; 52:1591-1601. [PMID: 38296828 PMCID: PMC10899783 DOI: 10.1093/nar/gkae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 02/02/2024] Open
Abstract
Structural studies of repetitive DNA sequences may provide insights why and how certain repeat instabilities in their number and nucleotide sequence are managed or even required for normal cell physiology, while genomic variability associated with repeat expansions may also be disease-causing. The pentanucleotide ATTTC repeats occur in hundreds of genes important for various cellular processes, while their insertion and expansion in noncoding regions are associated with neurodegeneration, particularly with subtypes of spinocerebellar ataxia and familial adult myoclonic epilepsy. We describe a new striking domain-swapped DNA-DNA interaction triggered by the addition of divalent cations, including Mg2+ and Ca2+. The results of NMR characterization of d(ATTTC)3 in solution show that the oligonucleotide folds into a novel 3D architecture with two central C:C+ base pairs sandwiched between a couple of T:T base pairs. This structural element, referred to here as the TCCTzip, is characterized by intercalative hydrogen-bonding, while the nucleobase moieties are poorly stacked. The 5'- and 3'-ends of TCCTzip motif are connected by stem-loop segments characterized by A:T base pairs and stacking interactions. Insights embodied in the non-canonical DNA structure are expected to advance our understanding of why only certain pyrimidine-rich DNA repeats appear to be pathogenic, while others can occur in the human genome without any harmful consequences.
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Affiliation(s)
- Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Annalisa Pastore
- King's College London, the Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
- EN-FIST, Center of Excellence, 1000 Ljubljana, Slovenia
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2
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Yang T, Xu Q, Chen J, Jia PK, Xie BB, Wang D, Zhou X, Shao Y. Selectively Identifying Exposed-over-Unexposed C-C + Pairs in Human Telomeric i-Motif Structures with Length-Dependent Polymorphism. Anal Chem 2022; 94:14994-15001. [PMID: 36263663 DOI: 10.1021/acs.analchem.2c02875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The i-motif structure (iM) has attracted much attention, because of its in vivo bioactivity and wide in vitro applications such as DNA-based switches. Herein, the length-dependent folding of cytosine-rich repeats of the human telomeric 5'-(CCCTAA)n-1CCC-3' (iM-n, where n = 2-8) was fully explored. We found that iM-4, iM-5, and iM-8 mainly form the intramolecular monomer iM structures, while a tetramolecular structure populates only for iM-3. However, iM-6 and iM-7 have the potential to fold as well into the dimeric iM structures besides the monomer ones. The natural hypericin (Hyp) was used as the polymorphism-selective probe to recognize the iM structures. Interestingly, only iM-3, iM-6, and iM-7 can efficiently switch on the Hyp fluorescence by specifically binding with the outmost C-C+ base pairs that are exposed directly to solution. However, other iM structures that fold in a way with a coverage of the outmost C-C+ pairs by loop sequences are totally unavailable for the Hyp binding. Theoretical modeling indicates that adaptive π-π and cation-π interactions contribute to the Hyp recognition toward the exposed C-C+ pairs. This specific iM recognition can be boosted by a photocatalytic DNAzyme construct. Our work provides a reliable fluorescence method to selectively explore the polymorphism of iM structures.
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Affiliation(s)
- Tong Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Qiuda Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Jiahui Chen
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Pei-Ke Jia
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, People's Republic of China
| | - Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, People's Republic of China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
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3
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Cheng M, Chen J, Ju H, Zhou J, Mergny JL. Drivers of i-DNA Formation in a Variety of Environments Revealed by Four-Dimensional UV Melting and Annealing. J Am Chem Soc 2021; 143:7792-7807. [PMID: 33988990 DOI: 10.1021/jacs.1c02209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
i-DNA is a four-stranded, pH-sensitive structure formed by cytosine-rich DNA sequences. Previous reports have addressed the conditions for formation of this motif in DNA in vitro and validated its existence in human cells. Unfortunately, these in vitro studies have often been performed under different experimental conditions, making comparisons difficult. To overcome this, we developed a four-dimensional UV melting and annealing (4DUVMA) approach to analyze i-DNA formation under a variety of conditions (e.g., pH, temperature, salt, crowding). Analysis of 25 sequences provided a global understanding of i-DNA formation under disparate conditions, which should ultimately allow the design of accurate prediction tools. For example, we found reliable linear correlations between the midpoint of pH transition and temperature (-0.04 ± 0.003 pH unit per 1.0 °C temperature increment) and between the melting temperature and pH (-23.8 ± 1.1 °C per pH unit increment). In addition, by analyzing the hysteresis between denaturing and renaturing profiles in both pH and thermal transitions, we found that loop length, nature of the C-tracts, pH, temperature, and crowding agents all play roles in i-DNA folding kinetics. Interestingly, our data indicate which conformer is more favorable for the sequences with an odd number of cytosine base pairs. Then the thermal and pH stabilities of "native" i-DNAs from human promoter genes were measured under near physiological conditions (pH 7.0, 37 °C). The 4DUVMA method can become a universal resource to analyze the properties of any i-DNA-prone sequence.
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Affiliation(s)
- Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR5320, IECB, Pessac 33607, France
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR5320, IECB, Pessac 33607, France.,Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau Cedex 91128, France
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4
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He S, Liu M, Yin F, Liu J, Ge Z, Li F, Li M, Shi J, Wang L, Mao X, Zuo X, Li Q. Programming folding cooperativity of the dimeric i-motif with DNA frameworks for sensing small pH variations. Chem Commun (Camb) 2021; 57:3247-3250. [PMID: 33646233 DOI: 10.1039/d1cc00266j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The response sensitivity of a molecular sensor is determined by the folding cooperativity of its responsive module. Using an H+-responsive dimeric DNA i-motif as a model, we demonstrate the enhancement of its folding cooperativity through preorganization by a DNA framework, and with it we fabricate robust intracellular pH sensors with high response sensitivity.
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Affiliation(s)
- Shiliang He
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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5
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Oh KI, Kim J, Park CJ, Lee JH. Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy. Int J Mol Sci 2020; 21:E2673. [PMID: 32290457 PMCID: PMC7216225 DOI: 10.3390/ijms21082673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
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6
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Dvoráková Z, Renciuk D, Kejnovská I, Školáková P, Bednárová K, Sagi J, Vorlícková M. i-Motif of cytosine-rich human telomere DNA fragments containing natural base lesions. Nucleic Acids Res 2019; 46:1624-1634. [PMID: 29378012 PMCID: PMC5829569 DOI: 10.1093/nar/gky035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/15/2018] [Indexed: 12/01/2022] Open
Abstract
i-Motif (iM) is a four stranded DNA structure formed by cytosine-rich sequences, which are often present in functionally important parts of the genome such as promoters of genes and telomeres. Using electronic circular dichroism and UV absorption spectroscopies and electrophoretic methods, we examined the effect of four naturally occurring DNA base lesions on the folding and stability of the iM formed by the human telomere DNA sequence (C3TAA)3C3T. The results demonstrate that the TAA loop lesions, the apurinic site and 8-oxoadenine substituting for adenine, and the 5-hydroxymethyluracil substituting for thymine only marginally disturb the formation of iM. The presence of uracil, which is formed by enzymatic or spontaneous deamination of cytosine, shifts iM formation towards substantially more acidic pH values and simultaneously distinctly reduces iM stability. This effect depends on the position of the damage sites in the sequence. The results have enabled us to formulate additional rules for iM formation.
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Affiliation(s)
- Zuzana Dvoráková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Renciuk
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petra Školáková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Klára Bednárová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
| | - Michaela Vorlícková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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7
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Abou Assi H, Garavís M, González C, Damha MJ. i-Motif DNA: structural features and significance to cell biology. Nucleic Acids Res 2019; 46:8038-8056. [PMID: 30124962 PMCID: PMC6144788 DOI: 10.1093/nar/gky735] [Citation(s) in RCA: 239] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/13/2018] [Indexed: 12/20/2022] Open
Abstract
The i-motif represents a paradigmatic example of the wide structural versatility of nucleic acids. In remarkable contrast to duplex DNA, i-motifs are four-stranded DNA structures held together by hemi- protonated and intercalated cytosine base pairs (C:C+). First observed 25 years ago, and considered by many as a mere structural oddity, interest in and discussion on the biological role of i-motifs have grown dramatically in recent years. In this review we focus on structural aspects of i-motif formation, the factors leading to its stabilization and recent studies describing the possible role of i-motifs in fundamental biological processes.
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Affiliation(s)
- Hala Abou Assi
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Miguel Garavís
- Instituto de Química Física 'Rocasolano', CSIC, C/Serrano 119, 28006 Madrid, Spain
| | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, C/Serrano 119, 28006 Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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8
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Base-pair Opening Dynamics of Nucleic Acids in Relation to Their Biological Function. Comput Struct Biotechnol J 2019; 17:797-804. [PMID: 31312417 PMCID: PMC6607312 DOI: 10.1016/j.csbj.2019.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/20/2019] [Indexed: 12/12/2022] Open
Abstract
Base-pair opening is a conformational transition that is required for proper biological function of nucleic acids. Hydrogen exchange, observed by NMR spectroscopic experiments, is a widely used method to study the thermodynamics and kinetics of base-pair opening in nucleic acids. The hydrogen exchange data of imino protons are analyzed based on a two-state (open/closed) model for the base-pair, where hydrogen exchange only occurs from the open state. In this review, we discuss examples of how hydrogen exchange data provide insight into several interesting biological processes involving functional interactions of nucleic acids: i) selective recognition of DNA by proteins; ii) regulation of RNA cleavage by site-specific mutations; iii) intermolecular interaction of proteins with their target DNA or RNA; iv) formation of PNA:DNA hybrid duplexes. This review systematically summarizes hydrogen exchange theory for base-paired imino protons of nucleic acids. Base-pair opening kinetics explain how the DNA can be selectively recognized by its target proteins. Base-pair opening kinetics explain the mechanisms by which site-specific mutations regulate RNA cleavage. Hydrogen exchange studies can elucidate the intermolecular interaction of proteins with their target DNA or RNA.
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9
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Tsvetkov VB, Zatsepin TS, Turaev AV, Farzan VM, Pozmogova GE, Aralov AV, Varizhuk AM. DNA i-Motifs With Guanidino- i-Clamp Residues: The Counterplay Between Kinetics and Thermodynamics and Implications for the Design of pH Sensors. Comput Struct Biotechnol J 2019; 17:527-536. [PMID: 31049164 PMCID: PMC6479070 DOI: 10.1016/j.csbj.2019.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/08/2019] [Accepted: 04/10/2019] [Indexed: 11/12/2022] Open
Abstract
I-motif structures, adopted by cytosine-rich DNA strands, have attracted considerable interest as possible regulatory elements in genomes. Applied science exploits the advantages of i-motif stabilization under acidic conditions: i-motif-based pH sensors and other biocompatible nanodevices are being developed. Two key characteristics of i-motifs as core elements of nanodevices, i.e., their stability under physiological conditions and folding/unfolding rates, still need to be improved. We have previously reported a phenoxazine derivative (i-clamp) that enhances the thermal stability of the i-motif and shifts the pH transition point closer to physiological values. Here, we performed i-clamp guanidinylation to further explore the prospects of clamp-like modifications in i-motif fine-tuning. Based on molecular modeling data, we concluded that clamp guanidinylation facilitated interstrand interactions in an i-motif core and ultimately stabilized the i-motif structure. We tested the effects of guanidino-i-clamp insertions on the thermal stabilities of genomic and model i-motifs. We also investigated the folding/unfolding kinetics of native and modified i-motifs under moderate, physiologically relevant pH alterations. We demonstrated fast folding/unfolding of native genomic and model i-motifs in response to pH stimuli. This finding supports the concept of i-motifs as possible genomic regulatory elements and encourages the future design of rapid-response pH probes based on such structures. Incorporation of guanidino-i-clamp residues at/near the 5′-terminus of i-motifs dramatically decreased the apparent unfolding rates and increased the thermal stabilities of the structures. This counterplay between the effects of modifications on i-motif stability and their effects on kinetics should be taken into account in the design of pH sensors.
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Affiliation(s)
- Vladimir B Tsvetkov
- Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.,I.M. Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, 119991 Moscow, Russia.,Research Institute of Influenza, Professora Popova str., 15/17, Sankt-Peterburg 197376, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, 143026 Moscow, Russia.,Lomonosov Moscow State University, Department of Chemistry, Leninskie Gory Str. 1-3, 119992 Moscow, Russia
| | - Anton V Turaev
- Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.,Moscow Institute of Physics and Technology, Institutsky lane 9, Dolgoprudny 141700, Russia
| | - Valentina M Farzan
- Skolkovo Institute of Science and Technology, Skolkovo, 143026 Moscow, Russia
| | - Galina E Pozmogova
- Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.,Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospect, 33, build. 2, Moscow 119071, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str. 16/10, Moscow 117997, Russia
| | - Anna M Varizhuk
- Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia
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10
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Shi L, Peng P, Du Y, Li T. Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device. Nucleic Acids Res 2017; 45:4306-4314. [PMID: 28369541 PMCID: PMC5416763 DOI: 10.1093/nar/gkx202] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/18/2017] [Indexed: 01/24/2023] Open
Abstract
Four-stranded DNAs including G-quadruplexes and i-motifs are formed from four stretches of identical bases (G or C). A challenge remains in controlling the intermolecular folding of different G-rich or C-rich strands due to the self-association of each component. Here, we introduce a well-designed bimolecular i-motif that does not allow the dimerization of the same strand, and illustrate its usefulness in a pH-switched ATP-sensing DNA molecular device. We analyze two groups of i-motif DNAs containing two stretches of different C-residues (Cn-1TmCn and CnTmCn-1; n = 3−6, m = 1, 3) and show that their bimolecular folding patterns (L- and H-form) noticeably differs in the thermal stability. The L-form structures generally display a relatively low stability, with a bigger difference from that of conventional i-motifs formed by CnTmCn. It inspires us to at utmost improving the structural stability by extending the core of L-form bimolecular i-motifs with a few flanking noncanonical base pairs, and therefore to avoid the dimeric association of each component. This meaningful bimolecular i-motif is then incorporated into a three-way junction (3WJ) and a four-way junction (4WJ) functionalized with two components of a ATP-binding split DNA aptamer, allowing the pH-triggered directional assembly of 3WJ and 4WJ into the desired (3+4)WJ structure that is verified by gel electrophoresis. It therefore enables the ATP-induced association of the split aptamer within the (3+4)WJ structure, as monitored by fluorescence quenching. In this way, the designed DNA system behaves as a pH-switched reversible molecular device, showing a high sensitivity and selectivity for fluorescent ATP analysis. The i-motif folding topology-programmed DNA nanoassembly may find more applications in the context of larger 2D/3D DNA nanostructures like lattices and polyhedra.
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Affiliation(s)
- Lili Shi
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Pai Peng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Yi Du
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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11
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Benabou S, Aviñó A, Lyonnais S, González C, Eritja R, De Juan A, Gargallo R. i-motif structures in long cytosine-rich sequences found upstream of the promoter region of the SMARCA4 gene. Biochimie 2017; 140:20-33. [DOI: 10.1016/j.biochi.2017.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/06/2017] [Indexed: 12/27/2022]
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12
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Alba JJ, Sadurní A, Gargallo R. Nucleic Acid i-Motif Structures in Analytical Chemistry. Crit Rev Anal Chem 2016; 46:443-54. [DOI: 10.1080/10408347.2016.1143347] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joan Josep Alba
- Department of Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Anna Sadurní
- Department of Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Raimundo Gargallo
- Department of Analytical Chemistry, University of Barcelona, Barcelona, Spain
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13
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Benabou S, Garavís M, Lyonnais S, Eritja R, González C, Gargallo R. Understanding the effect of the nature of the nucleobase in the loops on the stability of the i-motif structure. Phys Chem Chem Phys 2016; 18:7997-8004. [DOI: 10.1039/c5cp07428b] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The nature of bases in the loops affects the acid–base and thermal stability of i-motif structures.
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Affiliation(s)
- Sanae Benabou
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona
- Spain
| | - Miguel Garavís
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid
- Spain
| | - Sébastien Lyonnais
- Institute of Molecular Biology of Barcelona (IBMB-CSIC)
- 08028 Barcelona
- Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN
- E-08034 Barcelona
- Spain
| | - Carlos González
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid
- Spain
- BIOESTRAN
| | - Raimundo Gargallo
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona
- Spain
- BIOESTRAN
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14
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Ding Y, Fleming AM, He L, Burrows CJ. Unfolding Kinetics of the Human Telomere i-Motif Under a 10 pN Force Imposed by the α-Hemolysin Nanopore Identify Transient Folded-State Lifetimes at Physiological pH. J Am Chem Soc 2015; 137:9053-60. [PMID: 26110559 PMCID: PMC4513840 DOI: 10.1021/jacs.5b03912] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
Cytosine
(C)-rich DNA can adopt i-motif folds under acidic conditions,
with the human telomere i-motif providing a well-studied example.
The dimensions of this i-motif are appropriate for capture in the
nanocavity of the α-hemolysin (α-HL) protein pore under
an electrophoretic force. Interrogation of the current vs time (i–t) traces when the i-motif interacts
with α-HL identified characteristic signals that were pH dependent.
These features were evaluated from pH 5.0 to 7.2, a region surrounding
the transition pH of the i-motif (6.1). When the i-motif without polynucleotide
tails was studied at pH 5.0, the folded structure entered the nanocavity
of α-HL from either the top or bottom face to yield characteristic
current patterns. Addition of a 5′ 25-mer poly-2′-deoxyadensosine
tail allowed capture of the i-motif from the unfolded terminus, and
this was used to analyze the pH dependency of unfolding. At pH values
below the transition point, only folded strands were observed, and
when the pH was increased above the transition pH, the number of folded
events decreased, while the unfolded events increased. At pH 6.8 and
7.2 4% and 2% of the strands were still folded, respectively. The
lifetimes for the folded states at pH 6.8 and 7.2 were 21 and 9 ms,
respectively, at 160 mV electrophoretic force. These lifetimes are
sufficiently long to affect enzymes operating on DNA. Furthermore,
these transient lifetimes are readily obtained using the α-HL
nanopore, a feature that is not easily achievable by other methods.
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Affiliation(s)
- Yun Ding
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Lidong He
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
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15
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Reilly SM, Lyons DF, Wingate SE, Wright RT, Correia JJ, Jameson DM, Wadkins RM. Folding and hydrodynamics of a DNA i-motif from the c-MYC promoter determined by fluorescent cytidine analogs. Biophys J 2015; 107:1703-11. [PMID: 25296324 DOI: 10.1016/j.bpj.2014.08.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 08/05/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022] Open
Abstract
The four-stranded i-motif (iM) conformation of cytosine-rich DNA has importance to a wide variety of biochemical systems that range from their use in nanomaterials to potential roles in oncogene regulation. The iM structure is formed at slightly acidic pH, where hemiprotonation of cytosine results in a stable C-C(+) basepair. Here, we performed fundamental studies to examine iM formation from a C-rich strand from the promoter of the human c-MYC gene. We used a number of biophysical techniques to characterize both the hydrodynamic properties and folding kinetics of a folded iM. Our hydrodynamic studies using fluorescence anisotropy decay and analytical ultracentrifugation show that the iM structure has a compact size in solution and displays the rigidity of a double strand. By studying the rates of circular dichroism spectral changes and quenching of fluorescent cytidine analogs, we also established a mechanism for the folding of a random coil oligo into the iM. In the course of determining this folding pathway, we established that the fluorescent dC analogs tC° and PdC can be used to monitor individual residues of an iM structure and to determine the pKa of an iM. We established that the C-C(+) hydrogen bonding of certain bases initiates the folding of the iM structure. We also showed that substitutions in the loop regions of iMs give a distinctly different kinetic signature during folding compared with bases that are intercalated. Our data reveal that the iM passes through a distinct intermediate form between the unfolded and folded forms. Taken together, our results lay the foundation for using fluorescent dC analogs to follow structural changes during iM formation. Our technique may also be useful for examining folding and structural changes in more complex iMs.
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Affiliation(s)
- Samantha M Reilly
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi
| | - Daniel F Lyons
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi
| | - Sara E Wingate
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi
| | - Robert T Wright
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi
| | - John J Correia
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi
| | - David M Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Randy M Wadkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi.
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16
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Garavís M, Escaja N, Gabelica V, Villasante A, González C. Centromeric Alpha-Satellite DNA Adopts Dimeric i-Motif Structures Capped by AT Hoogsteen Base Pairs. Chemistry 2015; 21:9816-24. [PMID: 26013031 DOI: 10.1002/chem.201500448] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 11/11/2022]
Abstract
Human centromeric alpha-satellite DNA is composed of tandem arrays of two types of 171 bp monomers; type A and type B. The differences between these types are concentrated in a 17 bp region of the monomer called the A/B box. Here, we have determined the solution structure of the C-rich strand of the two main variants of the human alpha-satellite A box. We show that, under acidic conditions, the C-rich strands of two A boxes self-recognize and form a head-to-tail dimeric i-motif stabilized by four intercalated hemi-protonated C:C(+) base pairs. Interestingly, the stack of C:C(+) base pairs is capped by T:T and Hoogsteen A:T base pairs. The two main variants of the A box adopt a similar three-dimensional structure, although the residues involved in the formation of the i-motif core are different in each case. Together with previous studies showing that the B box (known as the CENP-B box) also forms dimeric i-motif structures, our finding of this non-canonical structure in the A box shows that centromeric alpha satellites in all human chromosomes are able to form i-motifs, which consequently raises the possibility that these structures may play a role in the structural organization of the centromere.
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Affiliation(s)
- Miguel Garavís
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain).,Centro de Biología Molecular, "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid (Spain)
| | - Núria Escaja
- Departament de Química Orgànica and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona (Spain)
| | - Valérie Gabelica
- Univ. Bordeaux, ARNA Laboratory, IECB, 2 rue Robert Escarpit 33600 Pessac (France).,Inserm, ARNA Laboratory, 146 Rue Leo Saignat, 33000 Bordeaux (France)
| | - Alfredo Villasante
- Centro de Biología Molecular, "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid (Spain)
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain).
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17
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Benabou S, Aviñó A, Eritja R, González C, Gargallo R. Fundamental aspects of the nucleic acid i-motif structures. RSC Adv 2014. [DOI: 10.1039/c4ra02129k] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.
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Affiliation(s)
- S. Benabou
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
| | - A. Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - R. Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - C. González
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid, Spain
| | - R. Gargallo
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
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18
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Dembska A, Rzepecka P, Juskowiak B. Spectroscopic characterization of i-motif forming c-myc derived sequences double-labeled with pyrene. J Fluoresc 2013; 23:807-12. [PMID: 23519528 PMCID: PMC3696180 DOI: 10.1007/s10895-013-1184-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 02/24/2013] [Indexed: 11/25/2022]
Abstract
In current studies we use the oligonucleotides based on c-myc sequence: CCC CAC CCT CCC CAC CCT CCC C (cmyc22) and CCC CAC CCT CCC CAC CCT CCC CA (cmyc22A) functionalized by pyrene moieties at both termini. Results of the circular dichroism (CD), UV absorption melting experiments, and steady-state fluorescence measurements of pyrene-modified i-motifs as well as their unlabeled precursors are presented and discussed here. The pyrene labels have a remarkable influence on i-motif stability which was deduced from CD spectra and confirmed by UV melting experiments. Both probes emit fluorescence band of pyrene monomer with intensity decreasing upon pH lowering.
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Affiliation(s)
- Anna Dembska
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznań, Poland.
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19
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Escaja N, Viladoms J, Garavís M, Villasante A, Pedroso E, González C. A minimal i-motif stabilized by minor groove G:T:G:T tetrads. Nucleic Acids Res 2012; 40:11737-47. [PMID: 23042679 PMCID: PMC3526289 DOI: 10.1093/nar/gks911] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The repetitive DNA sequences found at telomeres and centromeres play a crucial role in the structure and function of eukaryotic chromosomes. This role may be related to the tendency observed in many repetitive DNAs to adopt non-canonical structures. Although there is an increasing recognition of the importance of DNA quadruplexes in chromosome biology, the co-existence of different quadruplex-forming elements in the same DNA structure is still a matter of debate. Here we report the structural study of the oligonucleotide d(TCGTTTCGT) and its cyclic analog d<pTCGTTTCGTT>. Both sequences form dimeric quadruplex structures consisting of a minimal i-motif capped, at both ends, by a slipped minor groove-aligned G:T:G:T tetrad. These mini i-motifs, which do not exhibit the characteristic CD spectra of other i-motif structures, can be observed at neutral pH, although they are more stable under acidic conditions. This finding is particularly relevant since these oligonucleotide sequences do not contain contiguous cytosines. Importantly, these structures resemble the loop moiety adopted by an 11-nucleotide fragment of the conserved centromeric protein B (CENP-B) box motif, which is the binding site for the CENP-B.
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Affiliation(s)
- Núria Escaja
- Departament de Química Orgànica and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
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20
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Guittet E, Renciuk D, Leroy JL. Junctions between i-motif tetramers in supramolecular structures. Nucleic Acids Res 2012; 40:5162-70. [PMID: 22362739 PMCID: PMC3367196 DOI: 10.1093/nar/gks161] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The symmetry of i-motif tetramers gives to cytidine-rich oligonucleotides the capacity to associate into supramolecular structures (sms). In order to determine how the tetramers are linked together in such structures, we have measured by gel filtration chromatography and NMR the formation and dissociation kinetics of sms built by oligonucleotides containing two short C stretches separated by a non-cytidine-base. We show that a stretch of only two cytidines either at the 3'- or 5'-end is long enough to link the tetramers into sms. The analysis of the properties of sms formed by oligonucleotides differing by the length of the oligo-C stretches, the sequence orientation and the nature of the non-C base provides a model of the junction connecting the tetramers in sms.
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Affiliation(s)
- Eric Guittet
- Laboratoire de Chimie et Biologie Structurales, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
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21
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Laisné A, Pompon D, Leroy JL. [C7GC4]4 association into supra molecular i-motif structures. Nucleic Acids Res 2010; 38:3817-26. [PMID: 20185569 PMCID: PMC2887966 DOI: 10.1093/nar/gkq102] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The self-associative properties of cytidine-rich oligonucleotides into symmetrical i-motif tetramers give to these oligonucleotides the capacity of forming supramolecular structures (sms) that have potential applications in the nanotechnology domain. In order to facilitate sms formation, oligonucleotides containing two cytidine stretches of unequal length (CnXCm) separated by a non-cytidine spacer were synthesized. They were designed to associate into a tetramer including an i-motif core built by intercalation of the C·C+ pairs of the longer C stretch with the two dangling non-intercalated strands of the shorter C stretch at each end. Gel filtration chromatography shows that the non-intercalated C-rich ends give to this structure the capacity of forming extremely stable sms. Using C7GC4 as a model, we find that the sms formation rate varies as the oligonucleotide concentration and increases at high temperature. Competitively with the tetramer involved in sms elongation, CnXCm oligonucleotides form i-motif dimers that compete with sms elongation. The dimer stability is strongly reduced when the pH is moved away from the cytidine pK. This results in an equilibrium shift towards the tetramer and in the acceleration of the sms formation rate. The chromatograms of the sms formed by C7GC4 indicate a broad distribution. In a 1.5 mM solution incubated at 37°C, the equilibrium distribution is centered on a molecular weight corresponding to the assembly of nine tetramers and the upper limit corresponds to 80 tetramers. The lifetime of this structure is about 4 days at 40°C, pH 4.6.
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Affiliation(s)
- Aude Laisné
- Laboratoire d'Ingénerie des Proteines Membranaires, Centre de Génétique Moléculaire, CNRS FRE3144, Unité associé à l'Université Pierre et Marie Curie, Gif-sur-Yvette, 91190, France
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22
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Canalia M, Leroy JL. [5mCCTCTCTCC]4: an i-motif tetramer with intercalated T*T pairs. J Am Chem Soc 2010; 131:12870-1. [PMID: 19702299 DOI: 10.1021/ja903210t] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The i-motif is a four-stranded structure built by intercalation in a head-to-tail orientation of two parallel duplexes associated by hemiprotonated C(*)C(+) pairs. T*T pairs are nearly isomorphic of C*C(+) pairs; however the structural investigations of i-motif tetramers containing thymidines suggest that the i-motif cannot accommodate T*T pairs in a face-to-face orientation. The tetramer of 5mCCTCTCTCC make an exception. It includes two symmetry related open/closed T3/T7 groups, but the central thymidines form two long-lived T5*T5 pairs that are intercalated in a face-to-face orientation. This observation provides indications of the origin of the conflict that usually hinders T*T intercalation into i-motif structures and more generally of the constraints influencing i-motif formation.
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Affiliation(s)
- Muriel Canalia
- Laboratoire de Chimie et Biologie Structurale, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France 91190
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23
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Zhou J, Wei C, Jia G, Wang X, Feng Z, Li C. Formation of i-motif structure at neutral and slightly alkaline pH. MOLECULAR BIOSYSTEMS 2009; 6:580-6. [PMID: 20174686 DOI: 10.1039/b919600e] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
It is well known that oligonucleotides containing tracts cytosines can form i-motif structures under acidic conditions (pH < 7). However, whether i-motif can be formed under normal physiological cellular conditions (pH 7.0-7.5) is yet no conclusive proof. In the present work, using circular dichroism (CD), UV absorption spectroscopies and native polyacrylamide gel electrophoresis (PAGE), we provided the compelling evidence for the formation of i-motif structures by four cytosine clusters, [C(3)TA(2)](3)C(3) (HT), [C(4)G](3)C(4)TA (RET), C(2)T(3)C(2)T(4)C(2)T(3)C(2) (CTC) and GC(2)GC(3)A(4)C(6)G (Rb), at neutral and slightly alkaline pH at 4 degrees C. Furthermore, for HT, we also supplied the evidence for the formation of i-motif structure by fluorescence resonance energy transfer (FRET) and investigated its folding kinetics. The formation time constants obtained by CD and fluorescence experiments are 214 and 493 s, respectively, indicating that HT can slowly form i-motif structure at pH 7.0 and 4 degrees C. This work implies that i-motif structures may possible form in vivo.
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Affiliation(s)
- Jun Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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24
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Abstract
The i-motif is a four-stranded structure formed by two intercalated parallel duplexes containing hemiprotonated C•C+ pairs. In order to describe the sequence of reactions by which four C-rich strands associate, we measured the formation and dissociation rates of three [TCn]4 tetramers (n = 3, 4 and 5), their dissociation constant and the reaction order for tetramer formation by NMR. We find that TCn association results in the formation of several tetramers differing by the number of intercalated C•C+ pairs. The formation rates of the fully and partially intercalated species are comparable but their lifetimes increase strongly with the number of intercalated C•C+ pairs, and for this reason the single tetramer detected at equilibrium is that with optimal intercalation. The tetramer half formation times vary as the power −2 of the oligonucleotide concentration indicating that the reaction order for i-motif formation is 3. This observation is inconsistent with a model supposing association of two preformed duplex and suggests that quadruplex formation proceeds via sequential strand association into duplex and triplex intermediate species and that triplex formation is rate limiting.
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Affiliation(s)
- Jean-Louis Leroy
- Laboratoire de Chimie et Biologie Structurale, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette 91190, France.
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25
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Abstract
Oligonucleotides containing guanosine stretches associate into tetrameric structures stabilized by monovalent ions. In order to describe the sequence of reactions leading to association of four identical strands, we measured by NMR the formation and dissociation rates of (TGnT)4 quadruplexes (n = 3-6), their dissociation constants and the reaction orders for quadruplex formation. The quadruplex formation rates increase with the salt concentration but weakly depend on the nature (K+, Na+ or Li+) of the counter ions. The activation energies for quadruplex formation are negative. The quadruplex lifetimes strongly increase with the G-tract length and are much more longer in K+ solution than in Na+ or Li+ solutions. The reaction order for quadruplex formation is 3 in 0.125 M KCl and 4 in LiCl solutions. The kinetics measurements suggest that quadruplex formation proceeds step by step via sequential strand association into duplex and triplex intermediate species. Triplex formation is rate limiting in 0.125 M KCl solution. In LiCl, each step of the association process depends on the strand concentration. Parallel reactions to formation of the fully matched canonical quadruplex may result in kinetically trapped mismatched quadruplexes making the canonical quadruplex practically inaccessible in particular at low temperature in KCl solution.
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Affiliation(s)
- Caroline Bardin
- Laboratoire de Chimie et Biologie Structurale, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, 91190, France
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26
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Völker J, Klump HH, Breslauer KJ. The energetics of i-DNA tetraplex structures formed intermolecularly by d(TC5) and intramolecularly by d[(C5T3)3C5]. Biopolymers 2007; 86:136-47. [PMID: 17330895 DOI: 10.1002/bip.20712] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cytosine-rich DNA at low pH adopts an antiparallel tetraplex structure via the intercalation of two partially protonated, parallel stranded duplexes. This intriguing structural motif has been named i-DNA. We have used a combination of spectroscopic and calorimetric techniques to characterize the properties of an intermolecular i-DNA formed by d(TC(5)) and an intramolecular i-DNA formed by d[(C(5)T(3))(3)C(5)]. Our measurements reveal that both i-DNA complexes are enthalpically stabilized by 6.5-7.0 kcal/mol(base) and entropically destabilized by 20 cal/mol(base)/K. These values are about 50% larger than the corresponding enthalpy and entropy values per base for Watson and Crick duplexes and for Hoogsteen triplexes, while being similar to per base enthalpy and entropy values reported for G-quadruplexes. Our data also reveal a positive heat capacity change between 20 and 30 cal/mol(base)/K, values similar to that reported for polymeric Watson & Crick DNA duplexes. Solution-dependent studies reveal the overall thermal and thermodynamic stability of i-DNA complexes to be dictated by an interplay between pH and ionic strength. Based on the thermodynamic data measured, we discuss the feasibility of i-DNA formation in the context of conventional DNA sequences, while commenting on potential roles for this structural motif in biological regulatory mechanisms.
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Affiliation(s)
- Jens Völker
- Department of Chemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Dai J, Chen D, Jones RA, Hurley LH, Yang D. NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region. Nucleic Acids Res 2006; 34:5133-44. [PMID: 16998187 PMCID: PMC1636422 DOI: 10.1093/nar/gkl610] [Citation(s) in RCA: 287] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Revised: 08/03/2006] [Accepted: 08/03/2006] [Indexed: 01/22/2023] Open
Abstract
BCL2 protein functions as an inhibitor of cell apoptosis and has been found to be aberrantly expressed in a wide range of human diseases. A highly GC-rich region upstream of the P1 promoter plays an important role in the transcriptional regulation of BCL2. Here we report the NMR solution structure of the major intramolecular G-quadruplex formed on the G-rich strand of this region in K+ solution. This well-defined mixed parallel/antiparallel-stranded G-quadruplex structure contains three G-tetrads of mixed G-arrangements, which are connected with two lateral loops and one side loop, and four grooves of different widths. The three loops interact with the core G-tetrads in a specific way that defines and stabilizes the overall G-quadruplex structure. The loop conformations are in accord with the experimental mutation and footprinting data. The first 3-nt loop adopts a lateral loop conformation and appears to determine the overall folding of the BCL2 G-quadruplex. The third 1-nt double-chain-reversal loop defines another example of a stable parallel-stranded structural motif using the G3NG3 sequence. Significantly, the distinct major BCL2 promoter G-quadruplex structure suggests that it can be specifically involved in gene modulation and can be an attractive target for pathway-specific drug design.
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Affiliation(s)
- Jixun Dai
- College of Pharmacy, The University of Arizona1703 E. Mabel Street, Tucson, AZ 85721, USA
| | - Ding Chen
- College of Pharmacy, The University of Arizona1703 E. Mabel Street, Tucson, AZ 85721, USA
| | - Roger A. Jones
- Department of Chemistry and Chemical Biology, Rutgers University610 Taylor Road, Piscataway, NJ 08854, USA
| | - Laurence H. Hurley
- College of Pharmacy, The University of Arizona1703 E. Mabel Street, Tucson, AZ 85721, USA
- Arizona Cancer Center1515 N. Campbell Avenue, Tucson, AZ 85724, USA
- BIO5 Institute, The University of Arizona1140 E. South Campus Dr, Tucson, AZ 85721, USA
| | - Danzhou Yang
- College of Pharmacy, The University of Arizona1703 E. Mabel Street, Tucson, AZ 85721, USA
- Arizona Cancer Center1515 N. Campbell Avenue, Tucson, AZ 85724, USA
- BIO5 Institute, The University of Arizona1140 E. South Campus Dr, Tucson, AZ 85721, USA
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