1
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Alanazi AFR, Parkinson GN, Haider S. Structural Motifs at the Telomeres and Their Role in Regulatory Pathways. Biochemistry 2024; 63:827-842. [PMID: 38481135 PMCID: PMC10993422 DOI: 10.1021/acs.biochem.4c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Telomeres are specialized structures, found at the ends of linear chromosomes in eukaryotic cells, that play a crucial role in maintaining the stability and integrity of genomes. They are composed of repetitive DNA sequences, ssDNA overhangs, and several associated proteins. The length of telomeres is linked to cellular aging in humans, and deficiencies in their maintenance are associated with various diseases. Key structural motifs at the telomeres serve to protect vulnerable chromosomal ends. Telomeric DNA also has the ability to form diverse complex DNA higher-order structures, including T-loops, D-loops, R-loops, G-loops, G-quadruplexes, and i-motifs, in the complementary C-rich strand. While many essential proteins at telomeres have been identified, the intricacies of their interactions and structural details are still not fully understood. This Perspective highlights recent advancements in comprehending the structures associated with human telomeres. It emphasizes the significance of telomeres, explores various telomeric structural motifs, and delves into the structural biology surrounding telomeres and telomerase. Furthermore, telomeric loops, their topologies, and the associated proteins that contribute to the safeguarding of telomeres are discussed.
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Affiliation(s)
- Abeer F R Alanazi
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
- UCL Centre for Advanced Research Computing, University College London, London WC1H 9RN, United Kingdom
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2
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Hou X, Ga L, Zhang X, Ai J. Advances in the application of logic gates in nanozymes. Anal Bioanal Chem 2024:10.1007/s00216-024-05240-w. [PMID: 38488951 DOI: 10.1007/s00216-024-05240-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/17/2024]
Abstract
Nanozymes are a class of nanomaterials with biocatalytic function and enzyme-like activity, whose advantages include high stability, low cost, and mass production. They can catalyze the substrates of natural enzymes based on specific nanostructures and serve as substitutes for natural enzymes. Their applied research involves a wide range of fields such as biomedicine, environmental governance, agriculture, and food. Molecular logic gates are a new cross-disciplinary discipline, which can simulate the function of silicon circuits on a molecular scale, perform single or multiple input logic operations, and generate logic outputs. A molecular logic gate is a binary operation that converts an input signal into an output signal according to the rules of Boolean logic, generating two signals, a high level, and a low level. The high and low levels represent the "true" and "false" values of the logic gates, and their outputs correspond to "l" and "0" of the molecular logic gates, respectively. The combination of nanozymes and logic gates is a novel and attractive research direction, and the cross-application of the two brings new opportunities and ideas for various fields, such as the construction of efficient biocomputers, intelligent drug delivery systems, and the precise diagnosis of diseases. This review describes the application of logic gates based on nanozymes, which is expected to provide a certain theoretical foundation for researchers' subsequent studies.
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Affiliation(s)
- Xiangru Hou
- College of Chemistry and Enviromental Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, 81 zhaowudalu, Hohhot, 010022, China
| | - Lu Ga
- College of Pharmacy, Inner Mongolia Medical University, Jinchuankaifaqu, Hohhot, 010110, China
| | - Xin Zhang
- College of Chemical Engineering, Inner Mongolia University of Technology, 49 Aimin Road, Hohhot, 010051, China.
| | - Jun Ai
- College of Chemistry and Enviromental Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, 81 zhaowudalu, Hohhot, 010022, China.
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3
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Mehra K, Khurana S, Kukreti S, Kaushik M. Nanomaterials and DNA multistranded structures: a treasure hunt for targeting specific biomedical applications. J Biomol Struct Dyn 2023; 41:11324-11340. [PMID: 36546729 DOI: 10.1080/07391102.2022.2159878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
The advent in nanoscience and nanotechnology has enabled the successful synthesis and characterization of different nanomaterials with unique electrical, optical, magnetic and catalytic activities. However, with respect to sensing applications, nanomaterials intrinsically lack target recognition ability to selectively bind with the analyte. DNA, an important genetic material carrying biopolymer is polymorphic in nature and shows structural polymorphism, forming secondary/multistranded structures like hairpin, cruciform, pseudoknot, duplex, triplex, G-quadruplex and i-motif. Studies reported so far have suggested that these polymorphic structures have been targeted specifically for the treatment or diagnosis of various diseases. DNA is widely used in conjugation with nanomaterials for the development of nanoarchitectures due to its rigidity, sequence programmability and specific molecular recognition, which makes this biomolecule a treasure for designing of DNA based frameworks. These two entities (DNA and nanomaterials) can be used in association with each other, as their alliance can result into creation of novel assay platforms for different purposes, ranging from imaging, sensing and diagnostics to targeted delivery. In this review, we have discussed about the recent reports on association of various mutistranded/ polymorphic forms of DNA with nanomaterials. Furthermore, different applications using this versatile DNA-nanomaterial assembly has also been elaborated at length. This review aims to target the interests of scientists from various interdisciplinary fields, including biologists, chemists and nanotechnologists, who wish to gain an understanding of nano-fabrications using a plethora of DNA polymorphic forms.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Komal Mehra
- Nano-bioconjugate chemistry lab, Cluster Innovation Centre, University of Delhi, Delhi, India
- Nucleic acids research lab, Department of Chemistry, University of Delhi, Delhi, India
| | - Sonia Khurana
- Nano-bioconjugate chemistry lab, Cluster Innovation Centre, University of Delhi, Delhi, India
- Nucleic acids research lab, Department of Chemistry, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic acids research lab, Department of Chemistry, University of Delhi, Delhi, India
| | - Mahima Kaushik
- Nano-bioconjugate chemistry lab, Cluster Innovation Centre, University of Delhi, Delhi, India
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4
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Ghezzo M, Trajkovski M, Plavec J, Sissi C. A Screening Protocol for Exploring Loop Length Requirements for the Formation of a Three Cytosine-Cytosine + Base-Paired i-Motif. Angew Chem Int Ed Engl 2023; 62:e202309327. [PMID: 37611164 DOI: 10.1002/anie.202309327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 08/25/2023]
Abstract
DNA sequences containing at least four runs of repetitive cytosines can fold into tetra-helical structures called i-Motifs (iMs). The interest in these DNA secondary structures is increasing due to their therapeutical and technological applications. Still, limited knowledge of their folding requirements is currently available. We developed a novel step-by-step pipeline for the systematic screening of putative iM-forming model sequences. Focusing on structures comprising only three cytosine-cytosine+ base pairs, we investigated what the minimal lengths of the loops required for formation of an intra-molecular iM are. Our data indicate that two and three nucleotides are required to connect the strands through the minor and majorgrooves of the iM, respectively. Additionally, they highlight an asymmetric behavior according to the distribution of the cytosines. Specifically, no sequence containing a single cytosine in the first and third run was able to fold into intra-molecular iMs with the same stability of those formed when the first and the third run comprise two cytosines. This knowledge represents a step forward toward the development of prediction tools for the proper identification of biologically functional iMs, as well as for the rational design of these secondary structures as technological devices.
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Affiliation(s)
- Michele Ghezzo
- Department of Pharmaceutical and Pharmacological Science, University of Padua, Via Marzolo 5, 35131, Padua, Italy
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Science, University of Padua, Via Marzolo 5, 35131, Padua, Italy
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5
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Zanin I, Ruggiero E, Nicoletto G, Lago S, Maurizio I, Gallina I, Richter SN. Genome-wide mapping of i-motifs reveals their association with transcription regulation in live human cells. Nucleic Acids Res 2023; 51:8309-8321. [PMID: 37528048 PMCID: PMC10484731 DOI: 10.1093/nar/gkad626] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 07/07/2023] [Accepted: 07/23/2023] [Indexed: 08/03/2023] Open
Abstract
i-Motifs (iMs) are four-stranded DNA structures that form at cytosine (C)-rich sequences in acidic conditions in vitro. Their formation in cells is still under debate. We performed CUT&Tag sequencing using the anti-iM antibody iMab and showed that iMs form within the human genome in live cells. We mapped iMs in two human cell lines and recovered C-rich sequences that were confirmed to fold into iMs in vitro. We found that iMs in cells are mainly present at actively transcribing gene promoters, in open chromatin regions, they overlap with R-loops, and their abundance and distribution are specific to each cell type. iMs with both long and short C-tracts were recovered, further extending the relevance of iMs. By simultaneously mapping G-quadruplexes (G4s), which form at guanine-rich regions, and comparing the results with iMs, we proved that the two structures can form in independent regions; however, when both iMs and G4s are present in the same genomic tract, their formation is enhanced. iMs and G4s were mainly found at genes with low and high transcription rates, respectively. Our findings support the in vivo formation of iM structures and provide new insights into their interplay with G4s as new regulatory elements in the human genome.
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Affiliation(s)
- Irene Zanin
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Emanuela Ruggiero
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Giulia Nicoletto
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Sara Lago
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Ilaria Maurizio
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Irene Gallina
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
- Microbiology and Virology Unit, Padua University Hospital, 35121 Padua, Italy
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6
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Ji H, Zhu Q. Application of intelligent responsive DNA self-assembling nanomaterials in drug delivery. J Control Release 2023; 361:803-818. [PMID: 37597810 DOI: 10.1016/j.jconrel.2023.08.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Smart nanomaterials are nano-scaled materials that respond in a controllable and reversible way to external physical or chemical stimuli. DNA self-assembly is an effective way to construct smart nanomaterials with precise structure, diverse functions and wide applications. Among them, static structures such as DNA polyhedron, DNA nanocages and DNA hydrogels, as well as dynamic reactions such as catalytic hairpin reaction, hybridization chain reaction and rolling circle amplification, can serve as the basis for building smart nanomaterials. Due to the advantages of DNA, such as good biocompatibility, simple synthesis, rational design, and good stability, these materials have attracted increasing attention in the fields of pharmaceuticals and biology. Based on their specific response design, DNA self-assembled smart nanomaterials can deliver a variety of drugs, including small molecules, nucleic acids, proteins and other drugs; and they play important roles in enhancing cellular uptake, resisting enzymatic degradation, controlling drug release, and so on. This review focuses on different assembly methods of DNA self-assembled smart nanomaterials, therapeutic strategies based on various intelligent responses, and their applications in drug delivery. Finally, the opportunities and challenges of smart nanomaterials based on DNA self-assembly are summarized.
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Affiliation(s)
- Haofei Ji
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha 410013, Hunan, China.
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7
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Pandey A, Roy S, Srivatsan SG. Probing the Competition between Duplex, G-Quadruplex and i-Motif Structures of the Oncogenic c-Myc DNA Promoter Region. Chem Asian J 2023; 18:e202300510. [PMID: 37541298 DOI: 10.1002/asia.202300510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/09/2023] [Indexed: 08/06/2023]
Abstract
Development of probe systems that provide unique spectral signatures for duplex, G-quadruplex (GQ) and i-motif (iM) structures is very important to understand the relative propensity of a G-rich-C-rich promoter region to form these structures. Here, we devise a platform using a combination of two environment-sensitive nucleoside analogs namely, 5-fluorobenzofuran-modified 2'-deoxyuridine (FBF-dU) and 5-fluoro-2'-deoxyuridine (F-dU) to study the structures adopted by a promoter region of the c-Myc oncogene. FBF-dU serves as a dual-purpose probe containing a fluorescent and 19 F NMR label. When incorporated into the C-rich sequence, it reports the formation of different iMs via changes in its fluorescence properties and 19 F signal. F-dU incorporated into the G-rich ON reports the formation of a GQ structure whose 19 F signal is clearly different from the signals obtained for iMs. Rewardingly, the labeled ONs when mixed with respective complementary strands allows us to determine the relative population of different structures formed by the c-Myc promoter by the virtue of the probe's ability to produce distinct and resolved 19 F signatures for different structures. Our results indicate that at physiological pH and temperature the c-Myc promoter forms duplex, random coil and GQ structures, and does not form an iM. Whereas at acidic pH, the mixture largely forms iM and GQ structures. Taken together, our system will complement existing tools and provide unprecedented insights on the population equilibrium and dynamics of nucleic acid structures under different conditions.
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Affiliation(s)
- Akanksha Pandey
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Sarupa Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
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8
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Li KS, Jordan D, Lin LY, McCarthy SE, Schneekloth JS, Yatsunyk LA. Crystal Structure of an i-Motif from the HRAS Oncogene Promoter. Angew Chem Int Ed Engl 2023; 62:e202301666. [PMID: 36995904 PMCID: PMC10330059 DOI: 10.1002/anie.202301666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/22/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023]
Abstract
An i-motif is a non-canonical DNA structure implicated in gene regulation and linked to cancers. The C-rich strand of the HRAS oncogene, 5'-CGCCCGTGCCCTGCGCCCGCAACCCGA-3' (herein referred to as iHRAS), forms an i-motif in vitro but its exact structure was unknown. HRAS is a member of the RAS proto-oncogene family. About 19 % of US cancer patients carry mutations in RAS genes. We solved the structure of iHRAS at 1.77 Å resolution. The structure reveals that iHRAS folds into a double hairpin. The two double hairpins associate in an antiparallel fashion, forming an i-motif dimer capped by two loops on each end and linked by a connecting region. Six C-C+ base pairs form each i-motif core, and the core regions are extended by a G-G base pair and a cytosine stacking. Extensive canonical and non-canonical base pairing and stacking stabilizes the connecting region and loops. The iHRAS structure is the first atomic resolution structure of an i-motif from a human oncogene. This structure sheds light on i-motifs folding and function in the cell.
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Affiliation(s)
- Kevin S Li
- Department Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Deondre Jordan
- Department Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Linda Y Lin
- Department Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Sawyer E McCarthy
- Department Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, National Institute of Health, Frederick, MD 21702, USA
| | - Liliya A Yatsunyk
- Department Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
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9
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Zare I, Taheri-Ledari R, Esmailzadeh F, Salehi MM, Mohammadi A, Maleki A, Mostafavi E. DNA hydrogels and nanogels for diagnostics, therapeutics, and theragnostics of various cancers. NANOSCALE 2023. [PMID: 37337663 DOI: 10.1039/d3nr00425b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
As an efficient class of hydrogel-based therapeutic drug delivery systems, deoxyribonucleic acid (DNA) hydrogels (particularly DNA nanogels) have attracted massive attention in the last five years. The main contributor to this is the programmability of these 3-dimensional (3D) scaffolds that creates fundamental effects, especially in treating cancer diseases. Like other active biological ingredients (ABIs), DNA hydrogels can be functionalized with other active agents that play a role in targeting drug delivery and modifying the half-life of the therapeutic cargoes in the body's internal environment. Considering the brilliant advantages of DNA hydrogels, in this survey, we intend to submit an informative collection of feasible methods for the design and preparation of DNA hydrogels and nanogels, and the responsivity of the immune system to these therapeutic cargoes. Moreover, the interactions of DNA hydrogels with cancer biomarkers are discussed in this account. Theragnostic DNA nanogels as an advanced species for both detection and therapeutic purposes are also briefly reviewed.
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Affiliation(s)
- Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz 7178795844, Iran
| | - Reza Taheri-Ledari
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran
| | - Farhad Esmailzadeh
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran
| | - Mohammad Mehdi Salehi
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran
| | - Adibeh Mohammadi
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran
| | - Ali Maleki
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran
| | - Ebrahim Mostafavi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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10
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Kim SE, Hong SC. Two Opposing Effects of Monovalent Cations on the Stability of i-Motif Structure. J Phys Chem B 2023; 127:1932-1939. [PMID: 36811958 DOI: 10.1021/acs.jpcb.2c07069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
At acidic pH, cytosine-rich single-stranded DNA can be folded into a tetraplex structure called i-motif (iM). In recent studies, the effect of monovalent cations on the stability of iM structure has been addressed, but a consensus about the issue has not been reached yet. Thus, we investigated the effects of various factors on the stability of iM structure using fluorescence resonance energy transfer (FRET)-based analysis for three types of iM derived from human telomere sequences. We confirmed that the protonated cytosine-cytosine (C:C+) base pair is destabilized as the concentration of monovalent cations (Li+, Na+, K+) increases and that Li+ has the greatest tendency of destabilization. Intriguingly, monovalent cations would play an ambivalent role in iM formation by making single-stranded DNA flexible and pliant for an iM structure. In particular, we found that Li+ has a notably greater flexibilizing effect than Na+ and K+. All taken together, we conclude that the stability of iM structure is controlled by the subtle balance of the two counteractive effects of monovalent cations: electrostatic screening and disruption of cytosine base pairing.
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Affiliation(s)
- Sung Eun Kim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul, Korea, Department of Physics, Korea University, Seoul 02841, Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul, Korea, Department of Physics, Korea University, Seoul 02841, Korea
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11
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Petrunina NA, Shtork AS, Lukina MM, Tsvetkov VB, Khodarovich YM, Feofanov AV, Moysenovich AM, Maksimov EG, Shipunova VO, Zatsepin TS, Bogomazova AN, Shender VO, Aralov AV, Lagarkova MA, Varizhuk AM. Ratiometric i-Motif-Based Sensor for Precise Long-Term Monitoring of pH Micro Alterations in the Nucleoplasm and Interchromatin Granules. ACS Sens 2023; 8:619-629. [PMID: 36662613 DOI: 10.1021/acssensors.2c01813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
DNA-intercalated motifs (iMs) are facile scaffolds for the design of various pH-responsive nanomachines, including biocompatible pH sensors. First, DNA pH sensors relied on complex intermolecular scaffolds. Here, we used a simple unimolecular dual-labeled iM scaffold and minimized it by replacing the redundant loop nucleosides with abasic or alkyl linkers. These modifications improved the thermal stability of the iM and increased the rates of its pH-induced conformational transitions. The best effects were obtained upon the replacement of all three native loops with short and flexible linkers, such as the propyl one. The resulting sensor showed a pH transition value equal to 6.9 ± 0.1 and responded rapidly to minor acidification (tau1/2 <1 s for 7.2 → 6.6 pH jump). We demonstrated the applicability of this sensor for pH measurements in the nuclei of human lung adenocarcinoma cells (pH = 7.4 ± 0.2) and immortalized embryonic kidney cells (pH = 7.0 ± 0.2). The sensor stained diffusely the nucleoplasm and piled up in interchromatin granules. These findings highlight the prospects of iMs in the studies of normal and pathological pH-dependent processes in the nucleus, including the formation of biomolecular condensates.
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Affiliation(s)
- Nataliia A Petrunina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow119435, Russia
| | - Alina S Shtork
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow119435, Russia
| | - Maria M Lukina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow119435, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow119435, Russia
| | - Vladimir B Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow119435, Russia.,Institute of Biodesign and Complex System Modeling, I.M. Sechenov First Moscow State Medical University, Moscow119991, Russia.,A.V. Topchiev Institute of Petrochemical Synthesis RAS, Leninsky Prospect Str. 29, Moscow119991, Russia
| | - Yuri M Khodarovich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow117997, Russia.,The Peoples' Friendship University of Russia, 117198Moscow, Russia
| | - Alexey V Feofanov
- Biological Faculty, Lomonosov Moscow State University, Moscow119992, Russia.,Institute of Gene Biology RAS, Russian Academy of Sciences, Moscow119334, Russia
| | | | - Eugene G Maksimov
- Biological Faculty, Lomonosov Moscow State University, Moscow119992, Russia
| | - Victoria O Shipunova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow117997, Russia
| | - Timofei S Zatsepin
- Department of Chemistry, Lomonosov Moscow State University, Moscow119992, Russia
| | - Alexandra N Bogomazova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow119435, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow119435, Russia
| | - Victoria O Shender
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow119435, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow119435, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow117997, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow117997, Russia
| | - Maria A Lagarkova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow119435, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow119435, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow119435, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow119435, Russia.,G4_Interact, USERN, University of Pavia, 27100Pavia, Italy
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12
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Miranda-Quintana RA, Smiatek J. Electronic properties of amino acids and nucleobases: similarity classes and pairing principles from chemical reactivity indices. Phys Chem Chem Phys 2022; 24:22477-22486. [PMID: 36106477 DOI: 10.1039/d2cp02767d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a new classification scheme for amino acids and nucleobases based on the electronic properties of the individual molecules. Using chemical reactivity indices such as electronegativity, electrophilicity, and chemical hardness, we can identify similarities and differences between each class of amino acids and nucleobases. Notable differences emerge in particular with regard to high, neutral or low electronegativity as well as different combinations of chemical hardness. Our approach allows us to relate these insights to the properties of the side groups in terms of a unique reference scheme. We further show that hydrophobic differences between amino acids are rather negligible in the context of electronic properties. Our classification scheme also rationalizes the occurrence of distinct stable nucleobase pairs and clearly emphasizes certain differences between individual molecules. The stability and abundant occurrence of Watson-Crick nucleobase pairs is further discussed in the context of the minimum electrophilicity principle.
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Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany.
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13
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Greco F, Marzano M, Falanga AP, Terracciano M, Piccialli G, Roviello GN, D'Errico S, Borbone N, Oliviero G. Cytosine-rich oligonucleotides incorporating a non-nucleotide loop: A further step towards the obtainment of physiologically stable i-motif DNA. Int J Biol Macromol 2022; 219:626-636. [PMID: 35952813 DOI: 10.1016/j.ijbiomac.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 08/02/2022] [Indexed: 11/05/2022]
Abstract
i-Motifs, also known as i-tetraplexes, are secondary structures of DNA occurring in cytosine-rich oligonucleotides (CROs) that recall increasing interest in the scientific community for their relevance in various biological processes and DNA nanotechnology. This study reports the design of new structurally modified CROs, named Double-Ended-Linker-CROs (DEL-CROs), capable of forming stable i-motif structures. Here, two C-rich strands having sequences d(AC4A) and d(C6) have been attached, in a parallel fashion, to the two linker's edges by their 3' or 5' ends. The resulting DEL-CROs have been investigated for their capability to form i-motif structures by circular dichroism, poly-acrylamide gel electrophoresis, HPLC-size-exclusion chromatography, and NMR studies. This investigation established that DEL-CROs could form more stable i-motif structures than the corresponding unmodified CROs. In particular, the i-motif formed by DEL-5'-d(C6)2 resulted stable enough to be detected even at near physiological conditions (37 °C, pH 7.0). The results open the way to developing pH-switchable nanocarriers and aptamers based on suitably functionalized DEL-CROs.
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Affiliation(s)
- Francesca Greco
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Maria Marzano
- Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Andrea Patrizia Falanga
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Monica Terracciano
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy
| | - Giovanni Nicola Roviello
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy; ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy.
| | - Giorgia Oliviero
- ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via Sergio Pansini 5, 80131 Napoli, Italy
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14
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Khatik SY, Srivatsan SG. Environment-Sensitive Nucleoside Probe Unravels the Complex Structural Dynamics of i-Motif DNAs. Bioconjug Chem 2022; 33:1515-1526. [PMID: 35819865 DOI: 10.1021/acs.bioconjchem.2c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although evidence for the existence and biological role of i-motif (iM) DNA structures in cells is emerging, probing their structural polymorphism and identifying physiologically active conformations using currently available tools remain a major challenge. Here, we describe the development of an innovative device to investigate the conformation equilibrium of different iMs formed by C-rich telomeric repeat and oncogenic B-raf promoter sequences using a new conformation-sensitive dual-purpose nucleoside probe. The nucleoside is composed of a trifluoromethyl-benzofuran-2-yl moiety at the C5 position of 2'-deoxyuridine, which functions as a responsive fluorescent and 19F NMR probe. While the fluorescent component is useful in monitoring and estimating the folding process, the 19F label provides spectral signatures for various iMs, thereby enabling a systematic analysis of their complex population equilibrium under different conditions (e.g., pH, temperature, metal ions, and cell lysate). Distinct 19F signals exhibited by the iMs formed by the human telomeric repeat helped in calculating their relative population. A battery of fluorescence and 19F NMR studies using native and mutated B-raf oligonucleotides gave valuable insights into the iM structure landscape and its dependence on environmental conditions and also helped in predicting the structure of the major iM conformation. Overall, our findings indicate that the probe is highly suitable for studying complex nucleic acid systems.
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Affiliation(s)
- Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
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15
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Bao Y, Zhang X, Xiang X, Zhang Y, Zhao B, Guo X. Revealing the effect of intramolecular interactions on DNA SERS detection: SERS capability for structural analysis. Phys Chem Chem Phys 2022; 24:10311-10317. [PMID: 35437563 DOI: 10.1039/d1cp05607g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Intramolecular interactions are key factors for constructing the secondary conformations of biomolecules and they are also vital for biomolecular functions. Their effect on the surface-enhanced Raman spectroscopy (SERS) spectra is also important for reliable label-free detection. The current work focuses on three GCGC-quadruplexes as model molecules for SERS studies, which contain both the G-quartet and the GCGC-quartet. Their spectra are compared with the ones of the G-quadruplex and the duplex. The present work presents the specific effect of intramolecular interactions, including various Watson-Crick and Hoogsteen hydrogen bonds as well as base stacking, on the SERS signals of closely-related secondary conformations. The overall results indicated a significant influence on the direct label-free detection of DNA molecules and the SERS capability for secondary structural analysis.
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Affiliation(s)
- Ying Bao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China.
| | - Xiaonong Zhang
- Key Laboratory of Polymer Ecomaterials Jilin Biomedical Polymers Engineering Laboratory Changchun Institute of Applied Chemistry Chinese Academy of Sciences, Changchun 130022, P. R. China.
| | - Xiaoxuan Xiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China.
| | - Yujing Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China.
| | - Bing Zhao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China.
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China. .,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, P. R. China
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16
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Stability and context of intercalated motifs (i-motifs) for biological applications. Biochimie 2022; 198:33-47. [PMID: 35259471 DOI: 10.1016/j.biochi.2022.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/21/2022] [Accepted: 03/03/2022] [Indexed: 11/24/2022]
Abstract
DNA is naturally dynamic and can self-assemble into alternative secondary structures including the intercalated motif (i-motif), a four-stranded structure formed in cytosine-rich DNA sequences. Until recently, i-motifs were thought to be unstable in physiological cellular environments. Studies demonstrating their existence in the human genome and role in gene regulation are now shining light on their biological relevance. Herein, we review the effects of epigenetic modifications on i-motif structure and stability, and biological factors that affect i-motif formation within cells. Furthermore, we highlight recent progress in targeting i-motifs with structure-specific ligands for biotechnology and therapeutic purposes.
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17
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Ding Y, Xie L, Li D, Shen H, Li C, Xu W. Interconversion between guanine quartets and triads on the Au(111) surface. Chem Commun (Camb) 2022; 58:3198-3201. [PMID: 35174832 DOI: 10.1039/d2cc00060a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on STM imaging and DFT calculations, we show the real-space experimental evidence of the interconversion between G-quartets and G-triads on the Au(111) surface, and further reveal the relative stabilities of these two elementary motifs, which helps to increase the fundamental understanding of the relationship between G-triplex and G-quadruplex DNA structures.
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Affiliation(s)
- Yuanqi Ding
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China.
| | - Lei Xie
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China.
| | - Donglin Li
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China.
| | - Hanlin Shen
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China.
| | - Cuiyu Li
- Advanced Computing East China Sub-Center, Suma Technology Co., Ltd., Kunshan 215300, P. R. China
| | - Wei Xu
- Interdisciplinary Materials Research Center, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China.
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18
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The Dynamic Regulation of G-Quadruplex DNA Structures by Cytosine Methylation. Int J Mol Sci 2022; 23:ijms23052407. [PMID: 35269551 PMCID: PMC8910436 DOI: 10.3390/ijms23052407] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 02/01/2023] Open
Abstract
It is well known that certain non B-DNA structures, including G-quadruplexes, are key elements that can regulate gene expression. Here, we explore the theory that DNA modifications, such as methylation of cytosine, could act as a dynamic switch by promoting or alleviating the structural formation of G-quadruplex structures in DNA or RNA. The interaction between epigenetic DNA modifications, G4 formation, and the 3D architecture of the genome is a complex and developing area of research. Although there is growing evidence for such interactions, a great deal still remains to be discovered. In vivo, the potential effect that cytosine methylation may have on the formation of DNA structures has remained largely unresearched, despite this being a potential mechanism through which epigenetic factors could regulate gene activity. Such interactions could represent novel mechanisms for important biological functions, including altering nucleosome positioning or regulation of gene expression. Furthermore, promotion of strand-specific G-quadruplex formation in differentially methylated genes could have a dynamic role in directing X-inactivation or the control of imprinting, and would be a worthwhile focus for future research.
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19
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Kretzmann JA, Irving KL, Smith NM, Evans CW. Modulating gene expression in breast cancer via DNA secondary structure and the CRISPR toolbox. NAR Cancer 2022; 3:zcab048. [PMID: 34988459 PMCID: PMC8693572 DOI: 10.1093/narcan/zcab048] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is the most commonly diagnosed malignancy in women, and while the survival prognosis of patients with early-stage, non-metastatic disease is ∼75%, recurrence poses a significant risk and advanced and/or metastatic breast cancer is incurable. A distinctive feature of advanced breast cancer is an unstable genome and altered gene expression patterns that result in disease heterogeneity. Transcription factors represent a unique therapeutic opportunity in breast cancer, since they are known regulators of gene expression, including gene expression involved in differentiation and cell death, which are themselves often mutated or dysregulated in cancer. While transcription factors have traditionally been viewed as 'undruggable', progress has been made in the development of small-molecule therapeutics to target relevant protein-protein, protein-DNA and enzymatic active sites, with varying levels of success. However, non-traditional approaches such as epigenetic editing, transcriptional control via CRISPR/dCas9 systems, and gene regulation through non-canonical nucleic acid secondary structures represent new directions yet to be fully explored. Here, we discuss these new approaches and current limitations in light of new therapeutic opportunities for breast cancers.
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Affiliation(s)
- Jessica A Kretzmann
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, Germany
| | - Kelly L Irving
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
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20
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Liu J, Yan L, He S, Hu J. Engineering DNA quadruplexes in DNA nanostructures for biosensor construction. NANO RESEARCH 2021; 15:3504-3513. [PMID: 35401944 PMCID: PMC8983328 DOI: 10.1007/s12274-021-3869-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/28/2021] [Accepted: 09/04/2021] [Indexed: 06/14/2023]
Abstract
DNA quadruplexes are nucleic acid conformations comprised of four strands. They are prevalent in human genomes and increasing efforts are being directed toward their engineering. Taking advantage of the programmability of Watson-Crick base-pairing and conjugation methodology of DNA with other molecules, DNA nanostructures of increasing complexity and diversified geometries have been artificially constructed since 1980s. In this review, we investigate the interweaving of natural DNA quadruplexes and artificial DNA nanostructures in the development of the ever-prosperous field of biosensing, highlighting their specific roles in the construction of biosensor, including recognition probe, signal probe, signal amplifier and support platform. Their implementation in various sensing scenes was surveyed. And finally, general conclusion and future perspective are discussed for further developments.
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Affiliation(s)
- Jingxin Liu
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118 China
| | - Li Yan
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118 China
| | - Shiliang He
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118 China
| | - Junqing Hu
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518118 China
- Shenzhen Bey Laboratory, Shenzhen, 518132 China
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21
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Novotný A, Novotný J, Kejnovská I, Vorlíčková M, Fiala R, Marek R. Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip. Nucleic Acids Res 2021; 49:11425-11437. [PMID: 34718718 PMCID: PMC8599794 DOI: 10.1093/nar/gkab915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 09/17/2021] [Accepted: 09/27/2021] [Indexed: 11/12/2022] Open
Abstract
Non-canonical forms of nucleic acids represent challenging objects for both structure-determination and investigation of their potential role in living systems. In this work, we uncover a structure adopted by GA repetition locked in a parallel homoduplex by an i-motif. A series of DNA oligonucleotides comprising GAGA segment and C3 clip is analyzed by NMR and CD spectroscopies to understand the sequence-structure-stability relationships. We demonstrate how the relative position of the homopurine GAGA segment and the C3 clip as well as single-base mutations (guanine deamination and cytosine methylation) affect base pairing arrangement of purines, i-motif topology and overall stability. We focus on oligonucleotides C3GAGA and methylated GAGAC3 exhibiting the highest stability and structural uniformity which allowed determination of high-resolution structures further analyzed by unbiased molecular dynamics simulation. We describe sequence-specific supramolecular interactions on the junction between homoduplex and i-motif blocks that contribute to the overall stability of the structures. The results show that the distinct structural motifs can not only coexist in the tight neighborhood within the same molecule but even mutually support their formation. Our findings are expected to have general validity and could serve as guides in future structure and stability investigations of nucleic acids.
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Affiliation(s)
- Aleš Novotný
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia
| | - Jan Novotný
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia
| | - Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65 Brno, Czechia
| | - Michaela Vorlíčková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65 Brno, Czechia
| | - Radovan Fiala
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia
| | - Radek Marek
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia
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22
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Balasubramaniyam T, Oh KI, Jin HS, Ahn HB, Kim BS, Lee JH. Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides. Int J Mol Sci 2021; 22:9552. [PMID: 34502459 PMCID: PMC8430589 DOI: 10.3390/ijms22179552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.
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Affiliation(s)
- Thananjeyan Balasubramaniyam
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Kwnag-Im Oh
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Ho-Seong Jin
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Hye-Bin Ahn
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Byeong-Seon Kim
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
- Department of Chemistry Education, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Joon-Hwa Lee
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
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23
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Hong SW, Oh GJ, Hwang GT. 2‐Dimethylaminofluorene‐Labeled 2'‐Deoxyuridine as a Turn‐On Fluorescent Probe for i‐Motif DNA. ChemistrySelect 2021. [DOI: 10.1002/slct.202102658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Seung Woo Hong
- Department of Chemistry and Green-Nano Materials Research Center Kyungpook National University Daegu 41566 Republic of Korea
| | - Gon Ji Oh
- Department of Chemistry and Green-Nano Materials Research Center Kyungpook National University Daegu 41566 Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center Kyungpook National University Daegu 41566 Republic of Korea
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24
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Lu S, Shen J, Fan C, Li Q, Yang X. DNA Assembly-Based Stimuli-Responsive Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100328. [PMID: 34258165 PMCID: PMC8261508 DOI: 10.1002/advs.202100328] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Indexed: 05/06/2023]
Abstract
Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.
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Affiliation(s)
- Shasha Lu
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Jianlei Shen
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Chunhai Fan
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineDepartment of UrologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Qian Li
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Xiurong Yang
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
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25
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Chaudhuri R, Fatma K, Dash J. Regulation of gene expression by targeting DNA secondary structures. J CHEM SCI 2021. [DOI: 10.1007/s12039-021-01898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Iaccarino N, Cheng M, Qiu D, Pagano B, Amato J, Di Porzio A, Zhou J, Randazzo A, Mergny J. Effects of Sequence and Base Composition on the CD and TDS Profiles of i‐DNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nunzia Iaccarino
- Department of Pharmacy University of Naples Federico II Via D. Montesano 49 80131 Naples Italy
| | - 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 U 1212, CNRS UMR5320 IECB 33607 Pessac France
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry & Chemical Engineering Nanjing University Nanjing 210023 China
| | - Bruno Pagano
- Department of Pharmacy University of Naples Federico II Via D. Montesano 49 80131 Naples Italy
| | - Jussara Amato
- Department of Pharmacy University of Naples Federico II Via D. Montesano 49 80131 Naples Italy
| | - Anna Di Porzio
- Department of Pharmacy University of Naples Federico II Via D. Montesano 49 80131 Naples Italy
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry & Chemical Engineering Nanjing University Nanjing 210023 China
| | - Antonio Randazzo
- Department of Pharmacy University of Naples Federico II Via D. Montesano 49 80131 Naples Italy
| | - 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 U 1212, CNRS UMR5320 IECB 33607 Pessac France
- Laboratoire d'Optique et Biosciences Ecole Polytechnique CNRS INSERM Institut Polytechnique de Paris 91128 Palaiseau France
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27
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Iaccarino N, Cheng M, Qiu D, Pagano B, Amato J, Di Porzio A, Zhou J, Randazzo A, Mergny J. Effects of Sequence and Base Composition on the CD and TDS Profiles of i-DNA. Angew Chem Int Ed Engl 2021; 60:10295-10303. [PMID: 33617090 PMCID: PMC8251954 DOI: 10.1002/anie.202016822] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 12/19/2022]
Abstract
The i-motif DNA, also known as i-DNA, is a non-canonical DNA secondary structure formed by cytosine-rich sequences, consisting of two intercalated parallel-stranded duplexes held together by hemi-protonated cytosine-cytosine+ (C:C+ ) base pairs. The growing interest in the i-DNA structure as a target in anticancer therapy increases the need for tools for a rapid and meaningful interpretation of the spectroscopic data of i-DNA samples. Herein, we analyzed the circular dichroism (CD) and thermal difference UV-absorbance spectra (TDS) of 255 DNA sequences by means of multivariate data analysis, aiming at unveiling peculiar spectral regions that could be used as diagnostic features during the analysis of i-DNA-forming sequences.
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Affiliation(s)
- Nunzia Iaccarino
- Department of PharmacyUniversity of Naples Federico IIVia D. Montesano 4980131NaplesItaly
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry & Chemical EngineeringNanjing UniversityNanjing210023China
- ARNA LaboratoryUniversité de BordeauxInserm U 1212, CNRS UMR5320IECB33607PessacFrance
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry & Chemical EngineeringNanjing UniversityNanjing210023China
| | - Bruno Pagano
- Department of PharmacyUniversity of Naples Federico IIVia D. Montesano 4980131NaplesItaly
| | - Jussara Amato
- Department of PharmacyUniversity of Naples Federico IIVia D. Montesano 4980131NaplesItaly
| | - Anna Di Porzio
- Department of PharmacyUniversity of Naples Federico IIVia D. Montesano 4980131NaplesItaly
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry & Chemical EngineeringNanjing UniversityNanjing210023China
| | - Antonio Randazzo
- Department of PharmacyUniversity of Naples Federico IIVia D. Montesano 4980131NaplesItaly
| | - Jean‐Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry & Chemical EngineeringNanjing UniversityNanjing210023China
- ARNA LaboratoryUniversité de BordeauxInserm U 1212, CNRS UMR5320IECB33607PessacFrance
- Laboratoire d'Optique et BiosciencesEcole PolytechniqueCNRSINSERMInstitut Polytechnique de Paris91128PalaiseauFrance
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28
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Fantoni NZ, Brown T, Kellett A. DNA-Targeted Metallodrugs: An Untapped Source of Artificial Gene Editing Technology. Chembiochem 2021; 22:2184-2205. [PMID: 33570813 DOI: 10.1002/cbic.202000838] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/09/2021] [Indexed: 12/20/2022]
Abstract
DNA binding metal complexes are synonymous with anticancer drug discovery. Given the array of structural and chemical reactivity properties available through careful design, metal complexes have been directed to bind nucleic acid structures through covalent or noncovalent binding modes. Several recognition modes - including crosslinking, intercalation, and oxidation - are central to the clinical success of broad-spectrum anticancer metallodrugs. However, recent progress in nucleic acid click chemistry coupled with advancement in our understanding of metal complex-nucleic acid interactions has opened up new avenues in genetic engineering and targeted therapies. Several of these applications are enabled by the hybridisation of oligonucleotide or polyamine probes to discrete metal complexes, which facilitate site-specific reactivity at the nucleic acid interface under the guidance of the probe. This Review focuses on recent advancements in hybrid design and, by way of an introduction to this topic, we provide a detailed overview of nucleic acid structures and metal complex-nucleic acid interactions. Our aim is to provide readers with an insight on the rational design of metal complexes with DNA recognition properties and an understanding of how the sequence-specific targeting of these interactions can be achieved for gene engineering applications.
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Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for, Cellular Biotechnology and Nano Research Facility, Dublin City University, Glasnevin, Dublin, 9, Ireland
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29
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Gao B, Hou XM. Opposite Effects of Potassium Ions on the Thermal Stability of i-Motif DNA in Different Buffer Systems. ACS OMEGA 2021; 6:8976-8985. [PMID: 33842768 PMCID: PMC8028132 DOI: 10.1021/acsomega.0c06350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/11/2021] [Indexed: 05/12/2023]
Abstract
i-motifs are noncanonical DNA structures formed via the stack of intercalating hemi-protonated C+: C base pairs in C-rich DNA strands and play essential roles in the regulation of gene expression. Here, we systematically investigated the impacts of K+ on i-motif DNA folding using different buffer systems. We found that i-motif structures display very different T m values at the same pH and ion strength in different buffer systems. More importantly, K+ disrupts the i-motif formed in the MES and Bis-Tris buffer; however, K+ stabilizes the i-motif in phosphate, citrate, and sodium cacodylate buffers. Next, we selected phosphate buffer and confirmed by single-molecule fluorescence resonance energy transfer that K+ indeed has the stabilizing effect on the folding of i-motif DNA from pH 5.8 to 8.0. Nonetheless, circular dichroism spectra further indicate that the structures formed by i-motif sequences at high K+ concentrations at neutral and alkaline pH are not i-motif but other types of higher-order structures and most likely C-hairpins. We finally proposed the mechanisms of how K+ plays the opposite roles in different buffer systems. The present study may provide new insights into our understanding of the formation and stability of i-motif DNA.
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Affiliation(s)
| | - Xi-Miao Hou
- . Phone: +86 29 8708 1664. Fax: +86 29 8708 1664
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30
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Winogradoff D, Li P, Joshi H, Quednau L, Maffeo C, Aksimentiev A. Chiral Systems Made from DNA. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003113. [PMID: 33717850 PMCID: PMC7927625 DOI: 10.1002/advs.202003113] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/13/2020] [Indexed: 05/05/2023]
Abstract
The very chemical structure of DNA that enables biological heredity and evolution has non-trivial implications for the self-organization of DNA molecules into larger assemblies and provides limitless opportunities for building functional nanostructures. This progress report discusses the natural organization of DNA into chiral structures and recent advances in creating synthetic chiral systems using DNA as a building material. How nucleic acid chirality naturally comes into play in a diverse array of situations is considered first, at length scales ranging from an individual nucleotide to entire chromosomes. Thereafter, chiral liquid crystal phases formed by dense DNA mixtures are discussed, including the ongoing efforts to understand their origins. The report then summarizes recent efforts directed toward building chiral structures, and other structures of complex topology, using the principle of DNA self-assembly. Discussed last are existing and proposed functional man-made nanostructures designed to either probe or harness DNA's chirality, from plasmonics and spintronics to biosensing.
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Affiliation(s)
- David Winogradoff
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Pin‐Yi Li
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Himanshu Joshi
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Lauren Quednau
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Christopher Maffeo
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Aleksei Aksimentiev
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
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31
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Xing L, Zhao Y, Gong M, Liu X, Zhang Y, Li D, He Z, Yan P, Yang J. Graphene oxide and Lambda exonuclease assisted screening of L-carnitine aptamers and the site-directed mutagenesis design of C-rich structure aptamer. Biochem Biophys Res Commun 2021; 545:171-176. [PMID: 33556657 DOI: 10.1016/j.bbrc.2021.01.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/09/2021] [Accepted: 01/13/2021] [Indexed: 01/03/2023]
Abstract
In this study, Graphene Oxide (GO) was used to screen the binding with the aptamers of L-carnitine chiral enantiomers. The ssDNA library was prepared by the method of Lambda exonuclease. In addition, a simple casing device was designed to improve the purification and recovery efficiency of the small ssDNA fragments in the process of screening. Finally, more than 160,000 aptamer sequences were obtained by high-throughput sequencing. We determined the strongest affinity aptamer sequence, CA04, by the Resonance Rayleigh scattering (RRS) technology. We also analyzed the key binding sites (in the 16th position case) of the truncated aptamer sequence CAD10. Interestingly, we found that aptamer CA10 and CA06 were both C-rich bases through sequence alignment and analysis, and the aptamer CA10 was confirmed that the CA10 and CA06 were formed under acidic conditions (pH 4.5) by CD spectrum and ESI-MS analysis. The interaction between gold nanoparticles (AuNPs) and functionalized aptamer CA10 was analyzed. We used Site-directed mutagenesis design and QGRS Mapper to optimize aptamer CA10, where an optimal aptamer CA10-03 were obtained after affinity analysis. It is also proved to be an effective method to obtain stronger affinity aptamer. Meanwhile, Native-PAGE and UV spectrum analysis were performed on the mutation sequences, and the interaction with ThT was analyzed. Finally, it is hoped that my study can provide help for later identification and detection of L-carnitine.
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Affiliation(s)
- Ligang Xing
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China; Department of Life Science and Technology, Yangtze Normal University, Chongqing, 408100, China
| | - Yanmei Zhao
- Guangyuan China Nuclear Vocational and Technical College, Sichuan, 628000, China
| | - Mingzhu Gong
- Department of Life Science and Technology, Yangtze Normal University, Chongqing, 408100, China
| | - Xia Liu
- Department of Life Science and Technology, Yangtze Normal University, Chongqing, 408100, China
| | - Yuhui Zhang
- School of Chemistry and Environmental Engineering, Chongqing Three Gorges University, Chongqing, 404000, China
| | - Dan Li
- Department of Life Science and Technology, Yangtze Normal University, Chongqing, 408100, China
| | - Zefeng He
- Department of Life Science and Technology, Yangtze Normal University, Chongqing, 408100, China
| | - Ping Yan
- Department of Life Science and Technology, Yangtze Normal University, Chongqing, 408100, China
| | - Jidong Yang
- School of Chemistry and Environmental Engineering, Chongqing Three Gorges University, Chongqing, 404000, China.
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32
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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33
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Cambré A, Aertsen A. Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria. Microbiol Mol Biol Rev 2020; 84:e00008-20. [PMID: 33115939 PMCID: PMC7599038 DOI: 10.1128/mmbr.00008-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rise in fluorescence-based imaging techniques over the past 3 decades has improved the ability of researchers to scrutinize live cell biology at increased spatial and temporal resolution. In microbiology, these real-time vivisections structurally changed the view on the bacterial cell away from the "watery bag of enzymes" paradigm toward the perspective that these organisms are as complex as their eukaryotic counterparts. Capitalizing on the enormous potential of (time-lapse) fluorescence microscopy and the ever-extending pallet of corresponding probes, initial breakthroughs were made in unraveling the localization of proteins and monitoring real-time gene expression. However, later it became clear that the potential of this technique extends much further, paving the way for a focus-shift from observing single events within bacterial cells or populations to obtaining a more global picture at the intra- and intercellular level. In this review, we outline the current state of the art in fluorescence-based vivisection of bacteria and provide an overview of important case studies to exemplify how to use or combine different strategies to gain detailed information on the cell's physiology. The manuscript therefore consists of two separate (but interconnected) parts that can be read and consulted individually. The first part focuses on the fluorescent probe pallet and provides a perspective on modern methodologies for microscopy using these tools. The second section of the review takes the reader on a tour through the bacterial cell from cytoplasm to outer shell, describing strategies and methods to highlight architectural features and overall dynamics within cells.
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Affiliation(s)
- Alexander Cambré
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
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34
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Cruz‐Ortiz AF, Taccone MI, Maitre P, Rossa M, Pino GA. On the Interaction between Deprotonated Cytosine [C
(−H)
]
−
and Ba
2+
: Infrared Multiphoton Spectroscopy and Dynamics. Chemphyschem 2020; 21:2571-2582. [DOI: 10.1002/cphc.202000696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/21/2020] [Indexed: 01/11/2023]
Affiliation(s)
- Andrés F. Cruz‐Ortiz
- INFIQC (CONICET-UNC) Ciudad Universitaria Pabellón Argentina 5000 Córdoba Argentina
- Departamento de Fisicoquímica Fac. de Ciencias Químicas Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
- Centro Láser de Ciencias Moleculares Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
| | - Martín I. Taccone
- INFIQC (CONICET-UNC) Ciudad Universitaria Pabellón Argentina 5000 Córdoba Argentina
- Departamento de Fisicoquímica Fac. de Ciencias Químicas Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
- Centro Láser de Ciencias Moleculares Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
| | - Philippe Maitre
- Université Paris-Saclay CNRS, Institut de Chimie Physique 91405 Orsay France
| | - Maximiliano Rossa
- INFIQC (CONICET-UNC) Ciudad Universitaria Pabellón Argentina 5000 Córdoba Argentina
- Departamento de Fisicoquímica Fac. de Ciencias Químicas Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
- Centro Láser de Ciencias Moleculares Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
| | - Gustavo A. Pino
- INFIQC (CONICET-UNC) Ciudad Universitaria Pabellón Argentina 5000 Córdoba Argentina
- Departamento de Fisicoquímica Fac. de Ciencias Químicas Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
- Centro Láser de Ciencias Moleculares Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
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35
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Chalikian TV, Liu L, Macgregor RB. Duplex-tetraplex equilibria in guanine- and cytosine-rich DNA. Biophys Chem 2020; 267:106473. [PMID: 33031980 DOI: 10.1016/j.bpc.2020.106473] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Noncanonical four-stranded DNA structures, including G-quadruplexes and i-motifs, have been discovered in the cell and are implicated in a variety of genomic regulatory functions. The tendency of a specific guanine- and cytosine-rich region of genomic DNA to adopt a four-stranded conformation depends on its ability to overcome the constraints of duplex base-pairing by undergoing consecutive duplex-to-coil and coil-to-tetraplex transitions. The latter ability is determined by the balance between the free energies of participating ordered and disordered structures. In this review, we present an overview of the literature on the stability of G-quadruplex and i-motif structures and discuss the extent of duplex-tetraplex competition as a function of the sequence context of the DNA and environmental conditions including temperature, pH, salt, molecular crowding, and the presence of G-quadruplex-binding ligands. We outline how the results of in vitro studies can be expanded to understanding duplex-tetraplex equilibria in vivo.
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Affiliation(s)
- Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.
| | - Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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36
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He F, Wen N, Xiao D, Yan J, Xiong H, Cai S, Liu Z, Liu Y. Aptamer-Based Targeted Drug Delivery Systems: Current Potential and Challenges. Curr Med Chem 2020; 27:2189-2219. [PMID: 30295183 DOI: 10.2174/0929867325666181008142831] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/04/2018] [Accepted: 08/15/2018] [Indexed: 02/06/2023]
Abstract
Aptamers are single-stranded DNA or RNA with 20-100 nucleotides in length that can specifically bind to target molecules via formed three-dimensional structures. These innovative targeting molecules have attracted an increasing interest in the biomedical field. Compared to traditional protein antibodies, aptamers have several advantages, such as small size, high binding affinity, specificity, good biocompatibility, high stability and low immunogenicity, which all contribute to their wide application in the biomedical field. Aptamers can bind to the receptors on the cell membrane and mediate themselves or conjugated nanoparticles to enter into cells. Therefore, aptamers can be served as ideal targeting ligands for drug delivery. Since their excellent properties, different aptamer-mediated drug delivery systems had been developed for cancer therapy. This review provides a brief overview of recent advances in drug delivery systems based on aptamers. The advantages, challenges and future prospectives are also discussed.
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Affiliation(s)
- Fen He
- School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Nachuan Wen
- School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Daipeng Xiao
- School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Jianhua Yan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Hongjie Xiong
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Shundong Cai
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Zhenbao Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Yanfei Liu
- School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
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37
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Chu B, Zhang D, Paukstelis PJ. A DNA G-quadruplex/i-motif hybrid. Nucleic Acids Res 2020; 47:11921-11930. [PMID: 31724696 PMCID: PMC7145706 DOI: 10.1093/nar/gkz1008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/08/2019] [Accepted: 11/08/2019] [Indexed: 01/23/2023] Open
Abstract
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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Affiliation(s)
- Betty Chu
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Daoning Zhang
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Paul J Paukstelis
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
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38
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Duan J, Wang X, Kizer ME. Biotechnological and Therapeutic Applications of Natural Nucleic Acid Structural Motifs. Top Curr Chem (Cham) 2020; 378:26. [PMID: 32067108 DOI: 10.1007/s41061-020-0290-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/11/2020] [Indexed: 11/28/2022]
Abstract
Genetic information and the blueprint of life are stored in the form of nucleic acids. The primary sequence of DNA, read from the canonical double helix, provides the code for RNA and protein synthesis. Yet these already-information-rich molecules have higher-order structures which play critical roles in transcription and translation. Uncovering the sequences, parameters, and conditions which govern the formation of these structural motifs has allowed researchers to study them and to utilize them in biotechnological and therapeutic applications in vitro and in vivo. This review covers both DNA and RNA structural motifs found naturally in biological systems including catalytic nucleic acids, non-coding RNA, aptamers, G-quadruplexes, i-motifs, and Holliday junctions. For each category, an overview of the structural characteristics, biological prevalence, and function will be discussed. The biotechnological and therapeutic applications of these structural motifs are highlighted. Future perspectives focus on the addition of proteins and unnatural modifications to enhance structural stability for greater applicability.
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Affiliation(s)
- Jinwei Duan
- Department of Chemistry and Materials Science, College of Sciences, Chang'an University, Xi'an, 710064, Shaanxi, People's Republic of China.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Xing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Megan E Kizer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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39
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Gao T, Luo Y, Li W, Cao Y, Pei R. Progress in the isolation of aptamers to light-up the dyes and the applications. Analyst 2020; 145:701-718. [DOI: 10.1039/c9an01825e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The progress in the selection of aptamers to light-up the dyes and the related applications are reviewed.
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Affiliation(s)
- Tian Gao
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Yu Luo
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
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40
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Abdelaziz A, Zaitsau DH, Buzyurov AV, Verevkin SP, Schick C. Sublimation thermodynamics of nucleobases derived from fast scanning calorimetry. Phys Chem Chem Phys 2020; 22:838-853. [DOI: 10.1039/c9cp04761a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Fast scanning calorimetry was utilized to measure the sublimation thermodynamics of nucleobases. The results were rationalized at the molecular level.
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Affiliation(s)
- A. Abdelaziz
- University of Rostock
- Institute of Physics
- 18059 Rostock
- Germany
- University of Rostock
| | - D. H. Zaitsau
- University of Rostock
- Faculty of Interdisciplinary Research
- Competence Centre CALOR
- 18059 Rostock
- Germany
| | | | - S. P. Verevkin
- University of Rostock
- Faculty of Interdisciplinary Research
- Competence Centre CALOR
- 18059 Rostock
- Germany
| | - C. Schick
- University of Rostock
- Institute of Physics
- 18059 Rostock
- Germany
- University of Rostock
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41
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Niu K, Xiang L, Jin Y, Peng Y, Wu F, Tang W, Zhang X, Deng H, Xiang H, Li S, Wang J, Song Q, Feng Q. Identification of LARK as a novel and conserved G-quadruplex binding protein in invertebrates and vertebrates. Nucleic Acids Res 2019; 47:7306-7320. [PMID: 31165881 PMCID: PMC6698653 DOI: 10.1093/nar/gkz484] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 05/14/2019] [Accepted: 05/29/2019] [Indexed: 12/30/2022] Open
Abstract
Double-stranded DNAs are usually present in the form of linear B-form double-helix with the base pairs of adenine (A) and thymine (T) or cytosine (C) and guanine (G), but G-rich DNA can form four-stranded G-quadruplex (G4) structures, which plays important roles in transcription, replication, translation and protection of telomeres. In this study, a RNA recognition motif (RRM)-containing protein, BmLARK, was identified and demonstrated to bind G4 structures in the promoters of a transcription factor BmPOUM2 and other three unidentified genes of Bombyx mori, as well as three well-defined G4 structures in the human genes. Homologous LARKs from Bombyx mori, Drosophila melanogaster, Mus musculus and Homo sapiens bound G4 structures in BmPOUM2 and other genes in B. mori and H. sapiens. Upon binding, LARK facilitated the formation and stability of the G4 structure, enhancing the transcription of target genes. The G4 structure was visualized in vivo in cells and testis from invertebrate B. mori and vertebrate Chinese hamster ovary (CHO) cells. The results of this study strongly suggest that LARK is a novel and conserved G4-binding protein and that the G4 structure may have developed into an elaborate epigenetic mechanism of gene transcription regulation during evolution.
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Affiliation(s)
- Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Lijun Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Ying Jin
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yuling Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Feng Wu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wenhuan Tang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaojuan Zhang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Huimin Deng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Hui Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jian Wang
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
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42
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43
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Kitamura Y, Nagai K, Furuzono T, Katsuda Y, Ihara T. Cooperative recognition of a repetitive sequence through consecutive formation of triplex and duplex structures. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:97-108. [PMID: 31638471 DOI: 10.1080/15257770.2019.1679833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Cooperative recognition of a repetitive sequence was performed with a short single DNA strand consisting of duplex- and triplex-forming regions modified with a ligand (benzoquinoquinoxaline) to stabilize a triplex structure. The former region was complementary with one unit of a repetitive sequence and the latter had a sequence that can bind with a cognate duplex formed by another DNA molecule bound on an adjacent site. The DNA binding to one unit of the repetitive sequence is expected to facilitate the second binding to an adjacent unit through cooperative triplex formation. The cooperativity was confirmed by evaluation of thermal stabilities of the complexes with a series of model repetitive sequences.
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Affiliation(s)
- Yusuke Kitamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Koki Nagai
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Tomohiro Furuzono
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Yousuke Katsuda
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Toshihiro Ihara
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
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44
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Školáková P, Renčiuk D, Palacký J, Krafčík D, Dvořáková Z, Kejnovská I, Bednářová K, Vorlíčková M. Systematic investigation of sequence requirements for DNA i-motif formation. Nucleic Acids Res 2019; 47:2177-2189. [PMID: 30715498 PMCID: PMC6412112 DOI: 10.1093/nar/gkz046] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
The formation of intercalated motifs (iMs) - secondary DNA structures based on hemiprotonated C.C+ pairs in suitable cytosine-rich DNA sequences, is reflected by typical changes in CD and UV absorption spectra. By means of spectroscopic methods, electrophoresis, chemical modifications and other procedures, we characterized iM formation and stability in sequences with different cytosine block lengths interrupted by various numbers and types of nucleotides. Particular attention was paid to the formation of iMs at pH conditions close to neutral. We identified the optimal conditions and minimal requirements for iM formation in DNA sequences, and addressed gaps and inaccurate data interpretations in existing studies to specify principles of iM formation and modes of their folding.
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Affiliation(s)
- Petra Školáková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Renčiuk
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Jan Palacký
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Krafčík
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Zuzana Dvořáková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Klára Bednářová
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
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45
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Bhavsar-Jog YP, Van Dornshuld E, Brooks TA, Tschumper GS, Wadkins RM. Co-Localization of DNA i-Motif-Forming Sequences and 5-Hydroxymethyl-cytosines in Human Embryonic Stem Cells. Molecules 2019; 24:molecules24193619. [PMID: 31597270 PMCID: PMC6804057 DOI: 10.3390/molecules24193619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/01/2019] [Accepted: 10/04/2019] [Indexed: 12/25/2022] Open
Abstract
G-quadruplexes (G4s) and i-motifs (iMs) are tetraplex DNA structures. Sequences capable of forming G4/iMs are abundant near the transcription start sites (TSS) of several genes. G4/iMs affect gene expression in vitro. Depending on the gene, the presence of G4/iMs can enhance or suppress expression, making it challenging to discern the underlying mechanism by which they operate. Factors affecting G4/iM structures can provide additional insight into their mechanism of regulation. One such factor is epigenetic modification. The 5-hydroxymethylated cytosines (5hmCs) are epigenetic modifications that occur abundantly in human embryonic stem cells (hESC). The 5hmCs, like G4/iMs, are known to participate in gene regulation and are also enriched near the TSS. We investigated genomic co-localization to assess the possibility that these two elements may play an interdependent role in regulating genes in hESC. Our results indicate that amongst 15,760 G4/iM-forming locations, only 15% have 5hmCs associated with them. A detailed analysis of G4/iM-forming locations enriched in 5hmC indicates that most of these locations are in genes that are associated with cell differentiation, proliferation, apoptosis and embryogenesis. The library generated from our analysis is an important resource for investigators exploring the interdependence of these DNA features in regulating expression of selected genes in hESC.
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Affiliation(s)
- Yogini P Bhavsar-Jog
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA.
| | - Eric Van Dornshuld
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Tracy A Brooks
- Department of Pharmaceutical Sciences, Binghamton University, Binghamton, NY 13902, USA.
| | - Gregory S Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA.
| | - Randy M Wadkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA.
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46
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Trnkova L, Triskova I, Vorlickova M, Kejnovska I, Dvorakova Z, Pivonkova H, Fiala R. Comparative Electrochemical and Spectroscopic Studies of I‐Motif‐forming DNA Nonamers. ELECTROANAL 2019. [DOI: 10.1002/elan.201900323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Libuse Trnkova
- Department of Chemistry, Faculty of ScienceMasaryk University, Kamenice 5 CZ-625 00 Brno Czech Republic
| | - Iveta Triskova
- Department of Chemistry, Faculty of ScienceMasaryk University, Kamenice 5 CZ-625 00 Brno Czech Republic
| | - Michaela Vorlickova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135 CZ-612 65 Brno Czech Republic
| | - Iva Kejnovska
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135 CZ-612 65 Brno Czech Republic
| | - Zuzana Dvorakova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135 CZ-612 65 Brno Czech Republic
| | - Hana Pivonkova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135 CZ-612 65 Brno Czech Republic
| | - Radovan Fiala
- CEITEC MU – Central European Institute of Technology, Faculty of ScienceMasaryk University, Kamenice 5 CZ-625 00 Brno Czech Republic
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47
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Assessing the influence of pH and cationic strength on i-motif DNA structure. Anal Bioanal Chem 2019; 411:7473-7479. [PMID: 31529141 DOI: 10.1007/s00216-019-02120-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/02/2019] [Indexed: 10/26/2022]
Abstract
The i-motif is a biologically relevant non-canonical DNA structure formed by cytosine-rich sequences. Despite the importance of the factors affecting the formation/stability of such a structure, like pH, cation type and concentration, no systematic study that simultaneously analysed their effect on the i-motif in vitro has been carried out so far. Therefore, here we report a systematic study that aims to evaluate the effect of these factors, and their possible interaction, on the formation of an i-motif structure. Our results confirm that pH plays the main role in i-motif formation. However, we demonstrate that the effect of the cation concentration on the i-motif is strictly dependent on the pH, while no significant differences are observed among the investigated cation types. Graphical abstract.
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48
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Kim SH, Lim SH, Lee AR, Kwon DH, Song HK, Lee JH, Cho M, Johner A, Lee NK, Hong SC. Unveiling the pathway to Z-DNA in the protein-induced B-Z transition. Nucleic Acids Res 2019; 46:4129-4137. [PMID: 29584891 PMCID: PMC5934635 DOI: 10.1093/nar/gky200] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/13/2018] [Indexed: 12/31/2022] Open
Abstract
Left-handed Z-DNA is an extraordinary conformation of DNA, which can form by special sequences under specific biological, chemical or physical conditions. Human ADAR1, prototypic Z-DNA binding protein (ZBP), binds to Z-DNA with high affinity. Utilizing single-molecule FRET assays for Z-DNA forming sequences embedded in a long inactive DNA, we measure thermodynamic populations of ADAR1-bound DNA conformations in both GC and TG repeat sequences. Based on a statistical physics model, we determined quantitatively the affinities of ADAR1 to both Z-form and B-form of these sequences. We also reported what pathways it takes to induce the B–Z transition in those sequences. Due to the high junction energy, an intermediate B* state has to accumulate prior to the B–Z transition. Our study showing the stable B* state supports the active picture for the protein-induced B–Z transition that occurs under a physiological setting.
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Affiliation(s)
- Sook Ho Kim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, South Korea.,Department of Physics, Korea University, Seoul 02841, South Korea
| | - So-Hee Lim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, South Korea.,Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju 52828, South Korea
| | - Do Hoon Kwon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, South Korea.,Department of Life Sciences, Korea University, Seoul 02841, South Korea
| | - Hyun Kyu Song
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, South Korea.,Department of Life Sciences, Korea University, Seoul 02841, South Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju 52828, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, South Korea.,Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Albert Johner
- Institute Charles Sadron, CNRS 23 rue du Loess 67034, Strasbourg cedex 2, France.,Department of Physics, Sejong University, Seoul 05006, South Korea
| | - Nam-Kyung Lee
- Institute Charles Sadron, CNRS 23 rue du Loess 67034, Strasbourg cedex 2, France.,Department of Physics, Sejong University, Seoul 05006, South Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, South Korea.,Department of Physics, Korea University, Seoul 02841, South Korea
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49
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Freidhoff P, Bruist MF. In silico survey of the central conserved regions in viroids of the Pospiviroidae family for conserved asymmetric loop structures. RNA (NEW YORK, N.Y.) 2019; 25:985-1003. [PMID: 31123078 PMCID: PMC6633198 DOI: 10.1261/rna.070409.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/14/2019] [Indexed: 06/01/2023]
Abstract
Viroids are the smallest replicative pathogens, consisting of RNA circles (∼300 nucleotides) that require host machinery to replicate. Structural RNA elements recruit these host factors. Currently, many of these structural elements and the nature of their interactions are unknown. All Pospiviroidae have homology in the central conserved region (CCR). The CCR of potato spindle tuber viroid (PSTVd) contains a sarcin/ricin domain (SRD), the only viroid structural element with an unequivocal replication role. We assumed that every member of this family uses this region to recruit host factors, and that each CCR has an SRD-like asymmetric loop within it. Potential SRD or SRD-like motifs were sought in the CCR of each Pospiviroidae member as follows. Motif location in each CCR was predicted with MUSCLE alignment and Vienna RNAfold. Viroid-specific models of SRD-like motifs were built by superimposing noncanonical base pairs and nucleotides on a model of an SRD. The RNA geometry search engine FR3D was then used to find nucleotide groups close to the geometry suggested by this superimposition. Atomic resolution structures were assembled using the molecular visualization program Chimera, and the stability of each motif was assessed with molecular dynamics (MD). Some models required a protonated cytosine. To be stable within a cell, the pKa of that cytosine must be shifted up. Constant pH-replica exchange MD analysis showed such a shift in the proposed structures. These data show that every Pospiviroidae member could form a motif that resembles an SRD in its CCR, and imply there could be undiscovered mimics of other RNA domains.
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Affiliation(s)
- Paul Freidhoff
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, USA
| | - Michael F Bruist
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, USA
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50
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Kumar V, Nguyen TJD, Palmfeldt J, Gothelf KV. Formation of i-motifs from acyclic (l)-threoninol nucleic acids. Org Biomol Chem 2019; 17:7655-7659. [PMID: 31360984 DOI: 10.1039/c9ob01220f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Acyclic (l)-threoninol nucleic acids ((l)-aTNA) containing poly-cytosines are prepared and investigated at various pH values, revealing the formation of a highly stable structure at lower pH that have the characteristics of an i-motif. Depending on the sequence, the aTNA forms inter-, bi- and intra-molecular i-motif structures. Pyrene was conjugated to aTNA sequences and both monomeric and excimer fluorescence were efficiently quenched by the i-motif structures and thus demonstrated that the aTNA i-motif can serve as a pH switch.
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Affiliation(s)
- Vipin Kumar
- Center for Multifunctional Biomolecular Drug Design (CEMBID), iNANO and Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark.
| | - Thuy J D Nguyen
- Center for Multifunctional Biomolecular Drug Design (CEMBID), iNANO and Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark.
| | - Johan Palmfeldt
- Department of Clinical Medicine - Research Unit for Molecular Medicine Aarhus University, 8200 Aarhus N, Denmark
| | - Kurt V Gothelf
- Center for Multifunctional Biomolecular Drug Design (CEMBID), iNANO and Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark.
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