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Wieruszewska J, Pawłowicz A, Połomska E, Pasternak K, Gdaniec Z, Andrałojć W. The 8-17 DNAzyme can operate in a single active structure regardless of metal ion cofactor. Nat Commun 2024; 15:4218. [PMID: 38760331 PMCID: PMC11101458 DOI: 10.1038/s41467-024-48638-x] [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: 04/13/2023] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
DNAzymes - synthetic enzymes made of DNA - have long attracted attention as RNA-targeting therapeutic agents. Yet, as of now, no DNAzyme-based drug has been approved, partially due to our lacking understanding of their molecular mode of action. In this work we report the solution structure of 8-17 DNAzyme bound to a Zn2+ ion solved through NMR spectroscopy. Surprisingly, it turned out to be very similar to the previously solved Pb2+-bound form (catalytic domain RMSD = 1.28 Å), despite a long-standing literature consensus that Pb2+ recruits a different DNAzyme fold than other metal ion cofactors. Our follow-up NMR investigations in the presence of other ions - Mg2+, Na+, and Pb2+ - suggest that at DNAzyme concentrations used in NMR all these ions induce a similar tertiary fold. Based on these findings, we propose a model for 8-17 DNAzyme interactions with metal ions postulating the existence of only a single catalytically-active structure, yet populated to a different extent depending on the metal ion cofactor. Our results provide structural information on the 8-17 DNAzyme in presence of non-Pb2+ cofactors, including the biologically relevant Mg2+ ion.
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Affiliation(s)
- Julia Wieruszewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Aleksandra Pawłowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Ewa Połomska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Karol Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland
| | - Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Noskowskiego, 12/14, Poland.
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2
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Li J, Xu T, Zheng Y, Liu D, Zhang C, Li J, Wang ZA, Du Y. In Silico Study on a Binding Mechanism of ssDNA Aptamers Targeting Glycosidic Bond-Containing Small Molecules. Anal Chem 2024; 96:5056-5064. [PMID: 38497564 DOI: 10.1021/acs.analchem.4c00927] [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: 03/19/2024]
Abstract
Aptamer-based detection targeting glycoconjugates has attracted significant attention for its remarkable potential in identifying structural changes in saccharides in different stages of various diseases. However, the challenges in screening aptamers for small carbohydrates or glycoconjugates, which contain highly flexible and diverse glycosidic bonds, have hindered their application and commercialization. In this study, we investigated the binding conformations between three glycosidic bond-containing small molecules (GlySMs; glucose, N-acetylneuraminic acid, and neomycin) and their corresponding aptamers in silico, and analyzed factors contributing to their binding affinities. Based on the findings, a novel binding mechanism was proposed, highlighting the central role of the stem structure of the aptamer in binding and recognizing GlySMs and the auxiliary role of the mismatched bases in the adjacent loop. Guided by this binding mechanism, an aptamer with a higher 6'-sialyllactose binding affinity was designed, achieving a KD value of 4.54 ± 0.64 μM in vitro through a single shear and one mutation. The binding mechanism offers crucial guidance for designing high-affinity aptamers, enhancing the virtual screening efficiency for GlySMs. This streamlined workflow filters out ineffective binding sites, accelerating aptamer development and providing novel insights into glycan-nucleic acid interactions.
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Affiliation(s)
- Jiaqing Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Tong Xu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yalan Zheng
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Dongdong Liu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
| | - Chen Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
| | - Jianjun Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
| | - Zhuo A Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
| | - Yuguang Du
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
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3
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Xie TJ, Xie JL, Luo YJ, Mao K, Huang CZ, Li YF, Zhen SJ. CRISPR-Cas12a Coupled with DNA Nanosheet-Amplified Fluorescence Anisotropy for Sensitive Detection of Biomolecules. Anal Chem 2023; 95:7237-7243. [PMID: 37120835 DOI: 10.1021/acs.analchem.3c00156] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
DNA nanosheets (DNSs) have been utilized effectively as a fluorescence anisotropy (FA) amplifier for biosensing. But, their sensitivity needs to be further improved. Herein, CRISPR-Cas12a with strong trans-cleavage activity was utilized to enhance the FA amplification ability of DNSs for the sensitive detection of miRNA-155 (miR-155) as a proof-of-principle target. In this method, the hybrid of the recognition probe of miR-155 (T1) and a blocker sequence (T2) was immobilized on the surface of magnetic beads (MBs). In the presence of miR-155, T2 was released by a strand displacement reaction, which activated the trans-cleavage activity of CRISPR-Cas12a. The single-stranded DNA (ssDNA) probe modified with a carboxytetramethylrhodamine (TAMRA) fluorophore was cleaved in large quantities and could not bind to the handle chain on DNSs, inducing a low FA value. In contrast, in the absence of miR-155, T2 could not be released and the trans-cleavage activity of CRISPR-Cas12a could not be activated. The TAMRA-modified ssDNA probe remained intact and was complementary to the handle chain on the DNSs, and a high FA value was obtained. Thus, miR-155 was detected through the obviously decreased FA value with a low limit of detection (LOD) of 40 pM. Impressively, the sensitivity of this method was greatly improved about 322 times by CRISPR-Cas12a, confirming the amazing signal amplification ability of CRISPR-Cas12a. At the same time, the SARS-CoV-2 nucleocapsid protein was detected by the strategy successfully, indicating that this method was general. Moreover, this method has been applied in the analysis of miR-155 in human serum and the lysates of cells, which provides a new avenue for the sensitive determination of biomarkers in biochemical research and disease diagnosis.
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Affiliation(s)
- Tian Jin Xie
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, P. R. China
| | - Jia Li Xie
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, P. R. China
| | - Yu Jie Luo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, P. R. China
| | - Kai Mao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, P. R. China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, 400715 Chongqing, P. R. China
| | - Yuan Fang Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, P. R. China
| | - Shu Jun Zhen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, P. R. China
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4
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Liu X, Cao S, Gao Y, Luo S, Zhu Y, Wang L. Subcellular localization of DNA nanodevices and their applications. Chem Commun (Camb) 2023; 59:3957-3967. [PMID: 36883516 DOI: 10.1039/d2cc06017e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The application of nanodevices based on DNA self-assembly in the field of cell biology has made significant progress in the past decade. In this study, the development of DNA nanotechnology is briefly reviewed. The subcellular localization of DNA nanodevices, and their new progress and applications in the fields of biological detection, subcellular and organ pathology, biological imaging, and other fields are reviewed. The future of subcellular localization and biological applications of DNA nanodevices is also discussed.
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Affiliation(s)
- Xia Liu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuting Cao
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Gao
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shihua Luo
- Department of Traumatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Ying Zhu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. .,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. .,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Chen L, Lyu Y, Zhang X, Zheng L, Li Q, Ding D, Chen F, Liu Y, Li W, Zhang Y, Huang Q, Wang Z, Xie T, Zhang Q, Sima Y, Li K, Xu S, Ren T, Xiong M, Wu Y, Song J, Yuan L, Yang H, Zhang XB, Tan W. Molecular imaging: design mechanism and bioapplications. Sci China Chem 2023. [DOI: 10.1007/s11426-022-1461-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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6
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Qu H, Zheng M, Ma Q, Wang L, Mao Y, Eisenstein M, Tom Soh H, Zheng L. Allosteric Regulation of Aptamer Affinity through Mechano-Chemical Coupling. Angew Chem Int Ed Engl 2023; 62:e202214045. [PMID: 36646642 DOI: 10.1002/anie.202214045] [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: 09/22/2022] [Revised: 01/06/2023] [Accepted: 01/16/2023] [Indexed: 01/18/2023]
Abstract
The capacity to precisely modulate aptamer affinity is important for a wide variety of applications. However, most such engineering strategies entail laborious trial-and-error testing or require prior knowledge of an aptamer's structure and ligand-binding domain. We describe here a simple and generalizable strategy for allosteric modulation of aptamer affinity by employing a double-stranded molecular clamp that destabilizes aptamer secondary structure through mechanical tension. We demonstrate the effectiveness of the approach with a thrombin-binding aptamer and show that we can alter its affinity by as much as 65-fold. We also show that this modulation can be rendered reversible by introducing a restriction enzyme cleavage site into the molecular clamp domain and describe a design strategy for achieving even more finely-tuned affinity modulation. This strategy requires no prior knowledge of the aptamer's structure and binding mechanism and should thus be generalizable across aptamers.
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Affiliation(s)
- Hao Qu
- School of Food and Biological Engineering and Engineering Research Center of Bioprocess of Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Manyi Zheng
- School of Food and Biological Engineering and Engineering Research Center of Bioprocess of Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Qihui Ma
- School of Food and Biological Engineering and Engineering Research Center of Bioprocess of Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Lu Wang
- School of Food and Biological Engineering and Engineering Research Center of Bioprocess of Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Yu Mao
- School of Food and Biological Engineering and Engineering Research Center of Bioprocess of Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Michael Eisenstein
- Department of Electrical Engineering and Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Hyongsok Tom Soh
- Department of Electrical Engineering and Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Lei Zheng
- School of Food and Biological Engineering and Engineering Research Center of Bioprocess of Ministry of Education, Hefei University of Technology, Hefei, 230009, China
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7
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Wei LN, Luo L, Wang BZ, Lei HT, Guan T, Shen YD, Wang H, Xu ZL. Biosensors for detection of paralytic shellfish toxins: Recognition elements and transduction technologies. Trends Food Sci Technol 2023. [DOI: 10.1016/j.tifs.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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8
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Hu WH, Zhou K, Liu L, Wu HC. Construction of a pH-Mediated Single-Molecule Switch with a Nanopore-DNA Complex. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2201650. [PMID: 35723176 DOI: 10.1002/smll.202201650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/16/2022] [Indexed: 06/15/2023]
Abstract
A molecular switch is one of the simplest examples of artificial molecular machines. Even so, the development of molecular switches is still at its very early stage. Currently, building single-molecule switches mostly rely on the molecular junction technique, but many of their performance characteristics are device-dependent. Here, a pH-mediated single-molecule switch based on the combination of an α-hemolysin (αHL) nanopore and a hexacyclen-modified DNA strand is developed. The single-stranded DNA is suspended inside an αHL through biotin-streptavidin linkage and the hexacyclen-modified nucleobase interacts with amino acid residues at positions 111, 113, and 147 to cause current oscillations. Distinct current transitions are observed when pH is tuned back and forth in the range of 3.0-7.4, with a typical "up" level when pH > 6.5 and a "down" level when pH < 4.5. This nanopore-DNA complex possesses membrane-bound advantages and may find applications in single-cell studies where pH could be readily tuned to control ON-OFF functions.
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Affiliation(s)
- Wei-Hu Hu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ke Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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10
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Billet B, Chovelon B, Fiore E, Faure P, Ravelet C, Peyrin E. Detection of small molecules by fluorescence intensity using single dye labeled aptamers and quencher transition metal ions. Biosens Bioelectron 2022; 205:114091. [PMID: 35217256 DOI: 10.1016/j.bios.2022.114091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 12/29/2022]
Abstract
We describe herein an aptamer-based sensing approach that signal the presence of small-molecule targets when fluorescent DNA probes are challenged with the Ni2+ or Co2+ quencher metal ions. Functional oligonucleotides targeting L-tyrosinamide (L-Tym), adenosine (Ade) or cocaine (Coc) were end-labeled by the Texas-Red fluorophore. A fluorescence quenching occurred upon association of these transition metal ions with the free conjugates. The formation of the target-probe complex, by the way of variations in the overall binding of quencher metal ions along the DNA strands, led to a partial restoration (for the Ade and Coc systems) or a further attenuation (for the L-Tym system) of the fluorescence intensity. The absolute signal gain varied from 40 to 180% depending on the target-probe pair investigated. The approach was also used to detect the compound Ade in a spiked biological matrix in 1 min or less. The transition metal ion-based quenching strategy is characterized by its very simple implementation, low cost, and rapid signaling.
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Affiliation(s)
- Blandine Billet
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Patrice Faure
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France.
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France.
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11
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Qi S, Duan N, Khan IM, Dong X, Zhang Y, Wu S, Wang Z. Strategies to manipulate the performance of aptamers in SELEX, post-SELEX and microenvironment. Biotechnol Adv 2022; 55:107902. [DOI: 10.1016/j.biotechadv.2021.107902] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023]
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12
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Zaccaria F, van der Lubbe SCC, Nieuwland C, Hamlin TA, Fonseca Guerra C. How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes. Chemphyschem 2021; 22:2286-2296. [PMID: 34435425 PMCID: PMC9293024 DOI: 10.1002/cphc.202100529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/24/2021] [Indexed: 11/06/2022]
Abstract
The formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon coordination. In this work, we study the affinity of the internal GQ channel site towards alkaline earth metal (Mg2+, Ca2+, Sr2+, and Ba2+), and (post‐)transition metal (Zn2+, Cd2+, Hg2+, and Pb2+) cations using density functional theory computations. We find that divalent cations generally bind to the GQ cavity with a higher affinity than conventional monovalent cations (e. g. K+). Importantly, we establish the nature of the cation‐GQ interaction and highlight the relationship between ionic and nuclear charge, and the electrostatic and covalent interactions. The covalent interaction strength plays an important role in the cation affinity and can be traced back to the relative stabilization of cations’ unoccupied atomic orbitals. Overall, our findings contribute to a deeper understanding of how pollution metals could induce genomic instability.
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Affiliation(s)
- Francesco Zaccaria
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Stephanie C C van der Lubbe
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Celine Nieuwland
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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