1
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Ibrahim N, Gan KB, Mohd Yusof NY, Goh CT, Krupa B N, Tan LL. Electrochemical genosensor based on RNA-responsive human telomeric G-quadruplex DNA: A proof-of-concept with SARS-CoV-2 RNA. Talanta 2024; 274:125916. [PMID: 38547835 DOI: 10.1016/j.talanta.2024.125916] [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: 09/10/2023] [Revised: 01/07/2024] [Accepted: 03/11/2024] [Indexed: 05/04/2024]
Abstract
In this report, a facile and label-free electrochemical RNA biosensor is developed by exploiting methylene blue (MB) as an electroactive positive ligand of G-quadruplex. The electrochemical response mechanism of the nucleic acid assay was based on the change in differential pulse voltammetry (DPV) signal of adsorbed MB on the immobilized human telomeric G-quadruplex DNA with a loop that is complementary to the target RNA. Hybridization between synthetic positive control RNA and G-quadruplex DNA probe on the transducer platform rendered a conformational change of G-quadruplex to double-stranded DNA (dsDNA), and increased the redox current of cationic MB π planar ligand at the sensing interface, thereby the electrochemical signal of the MB-adsorbed duplex is proportional to the concentration of target RNA, with SARS-CoV-2 (COVID-19) RNA as the model. Under optimal conditions, the target RNA can be detected in a linear range from 1 zM to 1 μM with a limit of detection (LOD) obtained at 0.59 zM for synthetic target RNA and as low as 1.4 copy number for positive control plasmid. This genosensor exhibited high selectivity towards SARS-CoV-2 RNA over other RNA nucleotides, such as SARS-CoV and MERS-CoV. The electrochemical RNA biosensor showed DPV signal, which was proportional to the 2019-nCoV_N_positive control plasmid from 2 to 200000 copies (R2 = 0.978). A good correlation between the genosensor and qRT-PCR gold standard was attained for the detection of SARS-CoV-2 RNA in terms of viral copy number in clinical samples from upper respiratory specimens.
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Affiliation(s)
- Nadiah Ibrahim
- Southeast Asia Disaster Prevention Research Initiative (SEADPRI), Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor Darul Ehsan, Malaysia.
| | - Kok Beng Gan
- Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor Darul Ehsan, Malaysia.
| | - Nurul Yuziana Mohd Yusof
- Department of Earth Sciences and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor Darul Ehsan, Malaysia.
| | - Choo Ta Goh
- Southeast Asia Disaster Prevention Research Initiative (SEADPRI), Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor Darul Ehsan, Malaysia.
| | - Niranjana Krupa B
- Department of Electronics and Communication Engineering, PES University, Bengaluru-85, Karnataka, India.
| | - Ling Ling Tan
- Southeast Asia Disaster Prevention Research Initiative (SEADPRI), Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor Darul Ehsan, Malaysia.
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2
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Lacen A, Symasek A, Gunter A, Lee HT. Slow G-Quadruplex Conformation Rearrangement and Accessibility Change Induced by Potassium in Human Telomeric Single-Stranded DNA. J Phys Chem B 2024; 128:5950-5965. [PMID: 38875355 PMCID: PMC11216195 DOI: 10.1021/acs.jpcb.4c00719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024]
Abstract
The guanine-rich telomeric repeats can form G-quadruplexes (G4s) that alter the accessibility of the single-stranded telomeric overhang. In this study, we investigated the effects of Na+ and K+ on G4 folding and accessibility through cation introduction and exchange. We combined differential scanning calorimetry (DSC), circular dichroism (CD), and single molecule Förster resonance energy transfer (smFRET) to monitor the stability, conformational dynamics, and complementary strand binding accessibility of G4 formed by single-stranded telomeric DNA. Our data showed that G4 formed through heating and slow cooling in K+ solution exhibited fewer conformational dynamics than G4 formed in Na+ solution, which is consistent with the higher thermal stability of G4 in K+. Monitoring cation exchange with real time smFRET at room temperature shows that Na+ and K+ can replace each other in G4. When encountering high K+ at room or body temperature, G4 undergoes a slow conformational rearrangement process which is mostly complete by 2 h. The slow conformational rearrangement ends with a stable G4 that is unable to be unfolded by a complementary strand. This study provides new insights into the accessibility of G4 forming sequences at different time points after introduction to a high K+ environment in cells, which may affect how the nascent telomeric overhang interacts with proteins and telomerase.
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Affiliation(s)
- Arianna
N. Lacen
- Department of Chemistry, University
of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United
States
| | - Andrew Symasek
- Department of Chemistry, University
of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United
States
| | - Alan Gunter
- Department of Chemistry, University
of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United
States
| | - Hui-Ting Lee
- Department of Chemistry, University
of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United
States
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3
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Kumar S, Biswas A, Sudhakar S, Kumari D, Pradeepkumar PI. Estrone-Based Derivatives Stabilize the c-MYC and c-KIT G-Quadruplex DNA Structures. ACS OMEGA 2024; 9:6616-6626. [PMID: 38371752 PMCID: PMC10870291 DOI: 10.1021/acsomega.3c07574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 02/20/2024]
Abstract
G-rich sequences are present across the genome and can fold to form dynamic secondary structures, namely, G-quadruplexes (G4). These structures play a pivotal role in regulating numerous biological processes including replication, transcription, and translation. Therefore, targeting these structures using molecular scaffolds is an attractive approach to modulating their functions. Herein, we report the synthesis of three estrone-based derivatives (Est-1, Est-2, and Est-3) with a nonplanar core and a cationic alkyl side chain as G4 stabilizers. CD melting and polymerase stop assay results indicate that these ligands preferentially stabilize parallel c-MYC and c-KIT1 G4s over the other G4s and duplex DNAs. The ligand Est-3 shows cytotoxicity against cancer cell lines and effectively downregulates the c-KIT gene in HepG2 cell lines. Molecular modeling and dynamics studies showed that the ligand prefers stacking over the 5'-quartet of c-MYC G4 using the aromatic ring of the ligand. Overall, the findings of this study demonstrate that even G4 ligands can accommodate nonplanar scaffolds, which opens up new avenues for ligand design.
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Affiliation(s)
- Satendra Kumar
- Department of Chemistry, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Annyesha Biswas
- Department of Chemistry, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Divya Kumari
- Department of Chemistry, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
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4
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Zheng YY, Dartawan R, Wu Y, Wu C, Zhang H, Lu J, Hu A, Vangaveti S, Sheng J. Structural effects of inosine substitution in telomeric DNA quadruplex. Front Chem 2024; 12:1330378. [PMID: 38312345 PMCID: PMC10834636 DOI: 10.3389/fchem.2024.1330378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
The telomeric DNA, a distal region of eukaryotic chromosome containing guanine-rich repetitive sequence of (TTAGGG)n, has been shown to adopt higher-order structures, specifically G-quadruplexes (G4s). Previous studies have demonstrated the implication of G4 in tumor inhibition through chromosome maintenance and manipulation of oncogene expression featuring their G-rich promoter regions. Besides higher order structures, several regulatory roles are attributed to DNA epigenetic markers. In this work, we investigated how the structural dynamics of a G-quadruplex, formed by the telomeric sequence, is affected by inosine, a prevalent modified nucleotide. We used the standard (TTAGGG)n telomere repeats with guanosine mutated to inosine at each G position. Sequences (GGG)4, (IGG)4, (GIG)4, (GGI)4, (IGI)4, (IIG)4, (GII)4, and (III)4, bridged by TTA linker, are studied using biophysical experiments and molecular modeling. The effects of metal cations in quadruplex folding were explored in both Na+ and K+ containing buffers using CD and UV-melting studies. Our results show that antiparallel quadruplex topology forms with the native sequence (GGG)4 and the terminal modified DNAs (IGG)4 and (GGI)4 in both Na+ and K+ containing buffers. Specifically, quadruplex hybrid was observed for (GGG)4 in K+ buffer. Among the other modified sequences, (GIG)4, (IGI)4 and (GII)4 show parallel features, while (IIG)4 and (III)4 show no detectable conformation in the presence of either Na+ or K+. Our studies indicate that terminal lesions (IGG)4 and (GGI)4 may induce certain unknown conformations. The folding dynamics become undetectable in the presence of more than one inosine substitution except (IGI)4 in both buffer ions. In addition, both UV melting and CD melting studies implied that in most cases the K+ cation confers more thermodynamic stability compared to Na+. Collectively, our conformational studies revealed the diverse structural polymorphisms of G4 with position dependent G-to-I mutations in different ion conditions.
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Affiliation(s)
- Ya Ying Zheng
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Ricky Dartawan
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Yuhan Wu
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Chengze Wu
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Hope Zhang
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Jeanne Lu
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Ashley Hu
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Jia Sheng
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
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5
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Sengupta P, Dutta A, Suseela YV, Roychowdhury T, Banerjee N, Dutta A, Halder S, Jana K, Mukherjee G, Chattopadhyay S, Govindaraju T, Chatterjee S. G-quadruplex structural dynamics at MAPK12 promoter dictates transcriptional switch to determine stemness in breast cancer. Cell Mol Life Sci 2024; 81:33. [PMID: 38214819 PMCID: PMC11073236 DOI: 10.1007/s00018-023-05046-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/26/2023] [Accepted: 11/09/2023] [Indexed: 01/13/2024]
Abstract
P38γ (MAPK12) is predominantly expressed in triple negative breast cancer cells (TNBC) and induces stem cell (CSC) expansion resulting in decreased survival of the patients due to metastasis. Abundance of G-rich sequences at MAPK12 promoter implied the functional probability to reverse tumorigenesis, though the formation of G-Quadruplex (G4) structures at MAPK12 promoter is elusive. Here, we identified two evolutionary consensus adjacent G4 motifs upstream of the MAPK12 promoter, forming parallel G4 structures. They exist in an equilibria between G4 and duplex, regulated by the binding turnover of Sp1 and Nucleolin that bind to these G4 motifs and regulate MAPK12 transcriptional homeostasis. To underscore the gene-regulatory functions of G4 motifs, we employed CRISPR-Cas9 system to eliminate G4s from TNBC cells and synthesized a naphthalene diimide (NDI) derivative (TGS24) which shows high-affinity binding to MAPK12-G4 and inhibits MAPK12 transcription. Deletion of G4 motifs and NDI compound interfere with the recruitment of the transcription factors, inhibiting MAPK12 expression in cancer cells. The molecular basis of NDI-induced G4 transcriptional regulation was analysed by RNA-seq analyses, which revealed that MAPK12-G4 inhibits oncogenic RAS transformation and trans-activation of NANOG. MAPK12-G4 also reduces CD44High/CD24Low population in TNBC cells and downregulates internal stem cell markers, arresting the stemness properties of cancer cells.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Anindya Dutta
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Y V Suseela
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, Karnataka, 560064, India
| | - Tanaya Roychowdhury
- Department of Cancer Biology and Inflammatory Disorder, IICB, Kolkata, West Bengal, India
| | - Nilanjan Banerjee
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Ananya Dutta
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Satyajit Halder
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Kuladip Jana
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Gopeswar Mukherjee
- Barasat Cancer Research and Welfare Centre, Barasat, Kolkata, West Bengal, India
| | - Samit Chattopadhyay
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, K. K. Birla Goa Campus, Goa, 403726, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, Karnataka, 560064, India.
| | - Subhrangsu Chatterjee
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India.
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6
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Ling X, Yao Y, Ding L, Ma J. The mechanism of UP1 binding and unfolding of human telomeric DNA G-quadruplex. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194985. [PMID: 37717939 DOI: 10.1016/j.bbagrm.2023.194985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
The human telomere contains multiple copies of the DNA sequence d(TTAGGG) which can fold into higher order intramolecular G-quadruplexes and regulate the maintenance of telomere length and chromosomal integrity. The nucleic acid binding protein heteronuclear ribonucleoprotein A1 (hnRNP A1) and its N-terminus proteolytic product UP1 have been shown to efficiently bind and unfold telomeric DNA G-quadruplex. However, the understanding of the molecular mechanism of the UP1 binding and unfolding telomeric G-quadruplexes is still limited. Here, we performed biochemical and biophysical characterizations of UP1 binding and unfolding of human telomeric DNA G-quadruplex d[AGGG(TTAGGG)3], and in combination of systematic site-direct mutagenesis of two tandem RNA recognition motifs (RRMs) in UP1, revealed that RRM1 is responsible for initial binding and unfolding, whereas RRM2 assists RRM1 to complete the unfolding of G-quadruplex. Isothermal titration calorimetry (ITC) and circular dichroism (CD) studies of the interactions between UP1 and DNA G-quadruplex variants indicate that the "TAG" binding motif in Loop2 of telomeric G-quadruplex is critical for UP1 recognition and G-quadruplex unfolding initiation. Together we depict a model for molecular mechanism of hnRNP A1 (UP1) binding and unfolding of the human telomeric DNA G-quadruplex.
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Affiliation(s)
- Xiaobin Ling
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuqi Yao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lei Ding
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States of America
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China.
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7
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Biswas S, Basak S, Samui S, Pasadi S, Muniyappa K, Naskar J. Co‐Assembly of Peptide with G‐Quadruplex DNA: A Strategic Approach to Develop Anticancer Therapeutics. ChemistrySelect 2023. [DOI: 10.1002/slct.202203563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Soumi Biswas
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
| | - Shubhanwita Basak
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
| | - Satyabrata Samui
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
| | - Sanjeev Pasadi
- Department of Biochemistry Indian Institute of Science Bangalore Karnataka 560 012 India
| | - K. Muniyappa
- Department of Biochemistry Indian Institute of Science Bangalore Karnataka 560 012 India
| | - Jishu Naskar
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
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8
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Verma S, Patidar RK, Tiwari K, Tiwari R, Baranwal J, Velayutham R, Ranjan N. Preferential Recognition of Human Telomeric G-Quadruplex DNA by a Red-Emissive Molecular Rotor. J Phys Chem B 2022; 126:7298-7309. [DOI: 10.1021/acs.jpcb.2c04418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Smita Verma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Rajesh K. Patidar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
| | - Khushboo Tiwari
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
| | - Ratnesh Tiwari
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
| | - Jaya Baranwal
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
| | - Ravichandiran Velayutham
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
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9
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Pal R, Deb I, Sarzynska J, Lahiri A. LNA-induced dynamic stability in a therapeutic aptamer: insights from molecular dynamics simulations. J Biomol Struct Dyn 2022; 41:2221-2230. [PMID: 35100936 DOI: 10.1080/07391102.2022.2029567] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Modulation of structural and thermodynamic properties of nucleic acids with synthetic modifications is a promising area of research with possible applications in nanotechnology and nanotherapeutics. Locked nucleic acid (LNA) is one such modification in which the C4' and O2' atoms of the sugar moiety are connected through a methylene bridge. The LNA modified DNA aptamer RNV66, and its unmodified counterpart V7t1, both of which target the vascular endothelial growth factor (VEGF) implicated in oncogenic angiogenesis, have a G-rich tract that can fold into G-quadruplex structures. However, it is not understood why V7t1 has a polymorphic structure while its LNA modified counterpart RNV66 has a unique quadruplex fold with higher nuclease resistance, thermal stability and greater binding affinity for VEGF. In this work, we have performed extensive molecular dynamics simulations of RNV66 and V7t1 to study and compare the structural and dynamic consequences of the insertion of LNAs. It was observed that the increase in dynamic stability was significant in the presence of LNA residues and our protocol for combining different torsional parameters using OL15 for the DNA aptamer and parm99_LNA along with parmbsc0 and βOL15 for the LNAs nicely reproduced the experimentally observed conformational features of RNV66. Our observations would help in further theoretical studies in understanding the lack of frustration in the folding of the LNA modified aptamer and its higher affinity for VEGF.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rupak Pal
- Department of Biophysics, Molecular Biology, and Bioinformatics, University of Calcutta, Kolkata, India
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology, and Bioinformatics, University of Calcutta, Kolkata, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology, and Bioinformatics, University of Calcutta, Kolkata, India
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10
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Yu Y, Li W, Gu X, Yang X, Han Y, Ma Y, Wang Z, Zhang J. Inhibition of CRISPR-Cas12a trans-cleavage by lead (II)-induced G-quadruplex and its analytical application. Food Chem 2021; 378:131802. [PMID: 35032802 DOI: 10.1016/j.foodchem.2021.131802] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/05/2021] [Accepted: 12/03/2021] [Indexed: 12/26/2022]
Abstract
In this work, the inhibition of clustered regularly interspaced short palindromic repeats (CRISPR) - CRISPR associated protein (Cas) trans-cleavage by Pb2+-induced G-quadruplex has been firstly explored to detect Pb2+ in tea beverage and milk. In absence of Pb2+, the Na+-induced G-quadruplex can be cleaved by CRISPR-Cas12a. In contrast, Pb2+ can competitively combine with G-quadruplex, resulting in its conformational changes and resistance to trans-cleavage of CRISPR-Cas12a. Therefore, the fluorescence resonance energy transfer can happen. Pb2+ can be detected in a linear range from 100 nM to 5 µM with a lowest detection limit of 2.6 nM and a relative standard deviation of 4.32%. In summary, this work not only provides a new method for Pb2+ detection based on its induced G-quadruplex inhibition on CRISPR-Cas12a trans-cleavage, but also broadens the application of CRISPR-Cas system for heavy metal analysis in the field of food safety.
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Affiliation(s)
- Ying Yu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China; Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Wenhui Li
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Xinzhe Gu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Xiaojun Yang
- Shanghai Center of Agri-products Quality and Safety, Shanghai 201708, PR China
| | - Yiyi Han
- Shanghai Center of Agri-products Quality and Safety, Shanghai 201708, PR China
| | - Yingqing Ma
- Shanghai Center of Agri-products Quality and Safety, Shanghai 201708, PR China
| | - Zhengwu Wang
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China.
| | - Juan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China.
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11
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Fu W, Jing H, Xu X, Xu S, Wang T, Hu W, Li H, Zhang N. Two coexisting pseudo-mirror heteromolecular telomeric G-quadruplexes in opposite loop progressions differentially recognized by a low equivalent of Thioflavin T. Nucleic Acids Res 2021; 49:10717-10734. [PMID: 34500466 PMCID: PMC8501994 DOI: 10.1093/nar/gkab755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/24/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
The final 3′-terminal residue of the telomeric DNA G-overhang is inherently less precise. Here, we describe how alteration of the last 3′-terminal base affects the mutual recognition between two different G-rich oligomers of human telomeric DNA in the formation of heteromolecular G-quadruplexes (hetero-GQs). Associations between three- and single-repeat fragments of human telomeric DNA, target d(GGGTTAGGGTTAGGG) and probe d(TAGGGT), in Na+ solution yield two coexisting forms of (3 + 1) hybrid hetero-GQs: the kinetically favourable LLP-form (left loop progression) and the thermodynamically controlled RLP-form (right loop progression). However, only the adoption of a single LLP-form has been previously reported between the same probe d(TAGGGT) and a target variant d(GGGTTAGGGTTAGGGT) having one extra 3′-end thymine. Moreover, the flanking base alterations of short G-rich probe variants also significantly affect the loop progressions of hetero-GQs. Although seemingly two pseudo-mirror counter partners, the RLP-form exhibits a preference over the LLP-form to be recognized by a low equivalent of fluorescence dye thioflavin T (ThT). To a greater extent, ThT preferentially binds to RLP hetero-GQ than with the corresponding telomeric DNA duplex context or several other representative unimolecular GQs.
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Affiliation(s)
- Wenqiang Fu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Haitao Jing
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Xiaojuan Xu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Suping Xu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Tao Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Wenxuan Hu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Huihui Li
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Na Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of Anhui Province for High Field Magnetic Resonance Imaging, Hefei 230031, China.,High Magnetic Field Laboratory of Anhui Province, Hefei 230031, China
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12
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Jana J, Weisz K. Thermodynamic Stability of G-Quadruplexes: Impact of Sequence and Environment. Chembiochem 2021; 22:2848-2856. [PMID: 33844423 PMCID: PMC8518667 DOI: 10.1002/cbic.202100127] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/09/2021] [Indexed: 12/19/2022]
Abstract
G-quadruplexes have attracted growing interest in recent years due to their occurrence in vivo and their possible biological functions. In addition to being promising targets for drug design, these four-stranded nucleic acid structures have also been recognized as versatile tools for various technological applications. Whereas a large number of studies have yielded insight into their remarkable structural diversity, our current knowledge on G-quadruplex stabilities as a function of sequence and environmental factors only gradually emerges with an expanding collection of thermodynamic data. This minireview provides an overview of general rules that may be used to better evaluate quadruplex thermodynamic stabilities but also discusses present challenges in predicting most stable folds for a given sequence and environment.
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Affiliation(s)
- Jagannath Jana
- Institute of BiochemistryUniversität GreifswaldFelix-Hausdorff Str. 417489GreifswaldGermany
| | - Klaus Weisz
- Institute of BiochemistryUniversität GreifswaldFelix-Hausdorff Str. 417489GreifswaldGermany
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13
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Laouer K, Schmid M, Wien F, Changenet P, Hache F. Folding Dynamics of DNA G-Quadruplexes Probed by Millisecond Temperature Jump Circular Dichroism. J Phys Chem B 2021; 125:8088-8098. [PMID: 34279936 DOI: 10.1021/acs.jpcb.1c01993] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
G-quadruplexes play important roles in cellular regulatory functions, but despite significant experimental and theoretical efforts, their folding mechanisms remain poorly understood. In this context, we developed a T-jump experiment to access the thermal denaturation and renaturation dynamics of short intramolecular G-quadruplexes in vitro, on the time scale of a few hundred milliseconds. With this new setup, we compared the thermal denaturation and renaturation kinetics of three antiparallel topologies made of the human telomeric sequences d[(5'-GGG(TTAGGG)3-3']/Na+ and d[5'-AGGG(TTAGGG)3-3']/Na+ and the thrombin-binding aptamer sequence d[5'-GGTTGGTGTGGTTGG-3']/K+, with those of the parallel topology made of the human CEB25 minisatellite d[5'-AAGGGTGGGTGTAAGTGTGGGTGGGT-3']/Na+. In all cases, exponential kinetics of the order of several hundred milliseconds were observed. Measurements performed for different initial temperatures revealed distinct denaturation and renaturation dynamics, ruling out a simple two-state mechanism. The parallel topology, in which all guanines adopt an anti conformation, displays much slower dynamics than antiparallel topologies associated with very low activation barriers. This behavior can be explained by the constrained conformational space due to the presence of the single-base propeller loops that likely hinders the movement of the coiled DNA strand and reduces the contribution of the entropy during the renaturation process at high temperatures.
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Affiliation(s)
- K Laouer
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS -INSERM, Institut Polytechnique de Paris, 91128 Cedex Palaiseau, France
| | - M Schmid
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS -INSERM, Institut Polytechnique de Paris, 91128 Cedex Palaiseau, France
| | - F Wien
- L'orme des merisiers, Synchrotron SOLEIL, 91192 Gif sur Yvette, France
| | - P Changenet
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS -INSERM, Institut Polytechnique de Paris, 91128 Cedex Palaiseau, France
| | - F Hache
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS -INSERM, Institut Polytechnique de Paris, 91128 Cedex Palaiseau, France
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14
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Peng SX, Wang YY, Zhang M, Zang YY, Wu D, Pei J, Li Y, Dai J, Guo X, Luo X, Zhang N, Yang JJ, Zhang C, Gao X, Liu N, Shi YS. SNP rs10420324 in the AMPA receptor auxiliary subunit TARP γ-8 regulates the susceptibility to antisocial personality disorder. Sci Rep 2021; 11:11997. [PMID: 34099816 PMCID: PMC8184779 DOI: 10.1038/s41598-021-91415-9] [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: 02/18/2021] [Accepted: 05/25/2021] [Indexed: 11/08/2022] Open
Abstract
In the brain, AMPA receptors mediate fast excitatory neurotransmission, the dysfunction of which leads to neuropsychiatric disorders. Synaptic function of AMPA receptors is tightly controlled by a protein group called transmembrane AMPAR regulatory proteins (TARPs). TARP γ-8 (also known as CACNG8) preferentially expresses in the hippocampus, cortex and subcortical regions that are critical for emotion generation indicating its association with psychiatric disorders. Here, we identified rs10420324 (T/G), a SNP located in the human CACNG8 gene, regulated reporter gene expression in vitro and TARP γ-8 expression in the human brain. A guanine at the locus (rs10420324G) suppressed transcription likely through modulation of a local G-quadruplex DNA structure. Consistent with these observations, the frequency of rs10420324G was higher in patients with anti-social personality disorder (ASPD) than in controls, indicating that rs10420324G in CACNG8 is more voluntary for ASPD. We then characterized the behavior of TARP γ-8 knockout and heterozygous mice and found that consistent with ASPD patients who often exhibit impulsivity, aggression, risk taking, irresponsibility and callousness, a decreased γ-8 expression in mice displayed similar behaviors. Furthermore, we found that a decrease in TARP γ-8 expression impaired synaptic AMPAR functions in layer 2-3 pyramidal neurons of the prefrontal cortex, a brain region that inhibition leads to aggression, thus explaining, at least partially, the neuronal basis for the behavioral abnormality. Taken together, our study indicates that TARP γ-8 expression level is associated with ASPD, and that the TARP γ-8 knockout mouse is a valuable animal model for studying this psychiatric disease.
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Affiliation(s)
- Shi-Xiao Peng
- MOE Key Laboratory of Model Animal for Disease Study, Department of Neurology, Drum Tower Hospital, Medical School, Nanjing University, Nanjing, 210032, China
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, National Resource Center for Mutant Mice, Medical School, Nanjing University, Nanjing, 210032, China
| | - Yue-Ying Wang
- MOE Key Laboratory of Model Animal for Disease Study, Department of Neurology, Drum Tower Hospital, Medical School, Nanjing University, Nanjing, 210032, China
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, National Resource Center for Mutant Mice, Medical School, Nanjing University, Nanjing, 210032, China
| | - Min Zhang
- School of Psychology, Nanjing Normal University, Nanjing, 210029, China
| | - Yan-Yu Zang
- MOE Key Laboratory of Model Animal for Disease Study, Department of Neurology, Drum Tower Hospital, Medical School, Nanjing University, Nanjing, 210032, China
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, National Resource Center for Mutant Mice, Medical School, Nanjing University, Nanjing, 210032, China
| | - Dan Wu
- MOE Key Laboratory of Model Animal for Disease Study, Department of Neurology, Drum Tower Hospital, Medical School, Nanjing University, Nanjing, 210032, China
| | - Jingwen Pei
- MOE Key Laboratory of Model Animal for Disease Study, Department of Neurology, Drum Tower Hospital, Medical School, Nanjing University, Nanjing, 210032, China
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, National Resource Center for Mutant Mice, Medical School, Nanjing University, Nanjing, 210032, China
| | - Yansong Li
- Reward, Competition and Social Neuroscience Lab, Department of Psychology, School of Social and Behavioral Sciences, Nanjing University, Nanjing, 210023, China
| | - Jiapei Dai
- Chinese Brain Bank Center, Wuhan, 430074, China
| | - Xiaoyun Guo
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xingguang Luo
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Ning Zhang
- School of Psychology, Nanjing Normal University, Nanjing, 210029, China
- Department of Medical Psychology, Nanjing Medical University Affiliated Nanjing Brain Hospital, Nanjing, 210029, China
| | - Jian-Jun Yang
- Department of Anesthesiology and Perioperative Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan Province, China
| | - Chen Zhang
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China
| | - Xiang Gao
- MOE Key Laboratory of Model Animal for Disease Study, Department of Neurology, Drum Tower Hospital, Medical School, Nanjing University, Nanjing, 210032, China
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, National Resource Center for Mutant Mice, Medical School, Nanjing University, Nanjing, 210032, China
| | - Na Liu
- Department of Medical Psychology, Nanjing Medical University Affiliated Nanjing Brain Hospital, Nanjing, 210029, China.
| | - Yun Stone Shi
- MOE Key Laboratory of Model Animal for Disease Study, Department of Neurology, Drum Tower Hospital, Medical School, Nanjing University, Nanjing, 210032, China.
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, National Resource Center for Mutant Mice, Medical School, Nanjing University, Nanjing, 210032, China.
- Institute for Brain Sciences, Nanjing University, Nanjing, 210032, China.
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210032, China.
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15
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Haase L, Weisz K. Locked nucleic acid building blocks as versatile tools for advanced G-quadruplex design. Nucleic Acids Res 2020; 48:10555-10566. [PMID: 32890406 PMCID: PMC7544228 DOI: 10.1093/nar/gkaa720] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/24/2020] [Accepted: 08/20/2020] [Indexed: 01/21/2023] Open
Abstract
A hybrid-type G-quadruplex is modified with LNA (locked nucleic acid) and 2′-F-riboguanosine in various combinations at the two syn positions of its third antiparallel G-tract. LNA substitution in the central tetrad causes a complete rearrangement to either a V-loop or antiparallel structure, depending on further modifications at the 5′-neighboring site. In the two distinct structural contexts, LNA-induced stabilization is most effective compared to modifications with other G surrogates, highlighting a potential use of LNA residues for designing not only parallel but various more complex G4 structures. For instance, the conventional V-loop is a structural element strongly favored by an LNA modification at the V-loop 3′-end in contrast with an alternative V-loop, clearly distinguishable by altered conformational properties and base-backbone interactions as shown in a detailed analysis of V-loop structures.
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Affiliation(s)
- Linn Haase
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Klaus Weisz
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
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16
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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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17
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Kundu S. Mathematical model of a short translatable G-quadruplex and an assessment of its relevance to misfolding-induced proteostasis. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2020; 17:2470-2493. [PMID: 32233549 DOI: 10.3934/mbe.2020135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
G-quadruplexes can form in protein coding and non-coding segments such as the untranslated regions and introns of the mRNA transcript of several genes. This implies that amino acid forms of the G-quadruplex may have important consequences for protein homeostasis and the diseases caused by their alterations thereof. However, the absence of a suitable model and multitude of predicted physical forms has precluded a comprehensive enumeration and analysis of potential translatable G-quadruplexes. In this manuscript a mathematical model of a short translatable G-quadruplex (TG4) in the protein coding segment of the mRNA of a hypothetical gene is presented. Several novel indices (α, β) are formulated and utilized to categorize and select codons along with the amino acids that they code for. A generic algorithm is then iteratively deployed which computes the entire complement of peptide members that TG4 corresponds to, i.e., PTG4~TG4. The presence, distribution and relevance of this peptidome to protein sequence is investigated by comparing it with disorder promoting short linear motifs. In frame termination codon, co-occurrence, homology and distribution of overlapping/shared amino acids suggests that TG4 (~PTG4) may facilitate misfolding-induced proteostasis. The findings presented rigorously argue for the existence of a unique and potentially clinically relevant peptidome of a short translatable G-quadruplex that could be used as a diagnostic- or prognostic-screen of certain proteopathies.
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, INDIA
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18
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Haase L, Dickerhoff J, Weisz K. Sugar Puckering Drives G-Quadruplex Refolding: Implications for V-Shaped Loops. Chemistry 2020; 26:524-533. [PMID: 31609483 PMCID: PMC6973071 DOI: 10.1002/chem.201904044] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/10/2019] [Indexed: 01/04/2023]
Abstract
A DNA G-quadruplex adopting a (3+1) hybrid structure was modified in two adjacent syn positions of the antiparallel strand with anti-favoring 2'-deoxy-2'-fluoro-riboguanosine (F rG) analogues. The two substitutions promoted a structural rearrangement to a topology with the 5'-terminal G residue located in the central tetrad and the two modified residues linked by a V-shaped zero-nucleotide loop. Strikingly, whereas a sugar pucker in the preferred north domain is found for both modified nucleotides, the F rG analogue preceding the V-loop is forced to adopt the unfavored syn conformation in the new quadruplex fold. Apparently, a preferred C3'-endo sugar pucker within the V-loop architecture outweighs the propensity of the F rG analogue to adopt an anti glycosidic conformation. Refolding into a V-loop topology is likewise observed for a sequence modified at corresponding positions with two riboguanosine substitutions. In contrast, 2'-F-arabinoguanosine analogues with their favored south-east sugar conformation do not support formation of the V-loop topology. Examination of known G-quadruplexes with a V-shaped loop highlights the critical role of the sugar conformation for this distinct structural motif.
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Affiliation(s)
- Linn Haase
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417487GreifswaldGermany
| | - Jonathan Dickerhoff
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417487GreifswaldGermany
- Present address: Department of Medicinal Chemistry and Molecular PharmacologyCollege of PharmacyPurdue UniversityWest LafayetteIN47907USA
| | - Klaus Weisz
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417487GreifswaldGermany
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19
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Nakano SI, Ayusawa T, Tanino Y, Sugimoto N. Stabilization of DNA Loop Structures by Large Cations. J Phys Chem B 2019; 123:7687-7694. [PMID: 31465227 DOI: 10.1021/acs.jpcb.9b06074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The DNA-binding properties of large cations differ from those of metal ions due to steric exclusion from base-paired regions. In this study, the thermal stability of DNA secondary structures, including duplexes, internal loops, bulge loops, hairpin loops, dangling ends, and G-quadruplexes, was investigated in the presence of cations of different sizes. Large cations, such as tetrabutylammonium and tetrapentylammonium ions, reduced the stability of fully matched duplexes but increased the stability of duplexes with a long loop. The cations also increased the stability of G-quadruplexes with a long loop, and the degree of stabilization was greater for low-stability G-quadruplexes. Analysis of the salt concentration dependence indicates that large cations bind to the loop nucleotides, leading to counteracting the destabilization effect on base pairing. It is likely that binding occurs when loop nucleotides are sufficiently flexible to allow for greater accessibility for large cations. These results provide insight into nucleic acid interactions with large cationic molecules and suggest a potential method for stabilizing noncanonical DNA structures under intracellular conditions.
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Affiliation(s)
- Shu-Ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
| | - Toshiya Ayusawa
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
| | - Yuichi Tanino
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
| | - Naoki Sugimoto
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan.,Frontier Institute for Biomolecular Engineering Research (FIBER) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
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20
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Lightfoot HL, Hagen T, Tatum NJ, Hall J. The diverse structural landscape of quadruplexes. FEBS Lett 2019; 593:2083-2102. [PMID: 31325371 DOI: 10.1002/1873-3468.13547] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022]
Abstract
G-quadruplexes are secondary structures formed in G-rich sequences in DNA and RNA. Considerable research over the past three decades has led to in-depth insight into these unusual structures in DNA. Since the more recent exploration into RNA G-quadruplexes, such structures have demonstrated their in cellulo existence, function and roles in pathology. In comparison to Watson-Crick-based secondary structures, most G-quadruplexes display highly redundant structural characteristics. However, numerous reports of G-quadruplex motifs/structures with unique features (e.g. bulges, long loops, vacancy) have recently surfaced, expanding the repertoire of G-quadruplex scaffolds. This review addresses G-quadruplex formation and structure, including recent reports of non-canonical G-quadruplex structures. Improved methods of detection will likely further expand this collection of novel structures and ultimately change the face of quadruplex-RNA targeting as a therapeutic strategy.
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Affiliation(s)
- Helen L Lightfoot
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
| | - Timo Hagen
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
| | - Natalie J Tatum
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
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21
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Masaki Y, Inde T, Maruyama A, Seio K. Tolerance of N 2-heteroaryl modifications on guanine bases in a DNA G-quadruplex. Org Biomol Chem 2019; 17:859-866. [DOI: 10.1039/c8ob03100b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To systematically determine the effect of N2-heteroaryl modification on the stability of G-quadruplex structures, six types of N2-heteroarylated deoxyguanosines were incorporated into oligonucleotides with intramolecular quadruplex-forming sequences obtained from the human telomere sequence.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Takeshi Inde
- Department of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Atsuya Maruyama
- Department of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Kohji Seio
- Department of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
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22
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Alford A, Tucker B, Kozlovskaya V, Chen J, Gupta N, Caviedes R, Gearhart J, Graves D, Kharlampieva E. Encapsulation and Ultrasound-Triggered Release of G-Quadruplex DNA in Multilayer Hydrogel Microcapsules. Polymers (Basel) 2018; 10:E1342. [PMID: 30961267 PMCID: PMC6401949 DOI: 10.3390/polym10121342] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 01/01/2023] Open
Abstract
Nucleic acid therapeutics have the potential to be the most effective disease treatment strategy due to their intrinsic precision and selectivity for coding highly specific biological processes. However, freely administered nucleic acids of any type are quickly destroyed or rendered inert by a host of defense mechanisms in the body. In this work, we address the challenge of using nucleic acids as drugs by preparing stimuli responsive poly(methacrylic acid)/poly(N-vinylpyrrolidone) (PMAA/PVPON)n multilayer hydrogel capsules loaded with ~7 kDa G-quadruplex DNA. The capsules are shown to release their DNA cargo on demand in response to both enzymatic and ultrasound (US)-triggered degradation. The unique structure adopted by the G-quadruplex is essential to its biological function and we show that the controlled release from the microcapsules preserves the basket conformation of the oligonucleotide used in our studies. We also show that the (PMAA/PVPON) multilayer hydrogel capsules can encapsulate and release ~450 kDa double stranded DNA. The encapsulation and release approaches for both oligonucleotides in multilayer hydrogel microcapsules developed here can be applied to create methodologies for new therapeutic strategies involving the controlled delivery of sensitive biomolecules. Our study provides a promising methodology for the design of effective carriers for DNA vaccines and medicines for a wide range of immunotherapies, cancer therapy and/or tissue regeneration therapies in the future.
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Affiliation(s)
- Aaron Alford
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Brenna Tucker
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Veronika Kozlovskaya
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Jun Chen
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Nirzari Gupta
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Racquel Caviedes
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Jenna Gearhart
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - David Graves
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
- Center of Nanoscale Materials and Biointegration, Birmingham, AL 35294, USA.
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23
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Pal S, Paul S. Conformational deviation of Thrombin binding G-quadruplex aptamer (TBA) in presence of divalent cation Sr 2+: A classical molecular dynamics simulation study. Int J Biol Macromol 2018; 121:350-363. [PMID: 30308284 DOI: 10.1016/j.ijbiomac.2018.09.102] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/27/2018] [Accepted: 09/17/2018] [Indexed: 11/28/2022]
Abstract
Thrombin binding TBA-G-quadruplex aptamer (TBA) plays a major role in blood coagulation cascade. The 15-mer TBA sequence tends to form four-stranded TBA-G-quadruplex structure. In this research work, a series of explicit solvent classical MD simulations of the TBA is carried out using different salt (SrCl2) concentrations (0, 50, 100 and 200 mM). Here we have also testified the effect of salt concentration of divalent cation Sr2+ on the conformational change of quadruplex DNA. The structural deviations, fluctuations, torsional angles and the affinity of the ion are explored at different salt concentrations. It is found that the conformation of TBA-G-quadruplex at 0 mM and 50 mM salt concentrations, is very much different than the other salt concentrations (100 mM and 200 mM). Also observed are as follows: (i) no exchange of Sr2+ ion between inside and outside of the channel, (ii) an enhancement in the Sr2+ ion density around the phosphate region of the loop residues as salt concentration increases and (iii) the stacking of T3 and T4 residues of loop-1 that appears up to 50 mM concentration, vanishes as the salt concentration is increased further.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India.
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