1
|
Bahls B, Aljnadi IM, Emídio R, Mendes E, Paulo A. G-Quadruplexes in c-MYC Promoter as Targets for Cancer Therapy. Biomedicines 2023; 11:biomedicines11030969. [PMID: 36979947 PMCID: PMC10046398 DOI: 10.3390/biomedicines11030969] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Cancer is a societal burden demanding innovative approaches. A major problem with the conventional chemotherapeutic agents is their strong toxicity and other side effects due to their poor selectivity. Uncontrolled proliferation of cancer cells is due to mutations, deletions, or amplifications in genes (oncogenes) encoding for proteins that regulate cell growth and division, such as transcription factors, for example, c-MYC. The direct targeting of the c-MYC protein has been attempted but so far unsuccessfully, as it lacks a definite binding site for the modulators. Meanwhile, another approach has been explored since the discovery that G-quadruplex secondary DNA structures formed in the guanine-rich sequences of the c-MYC promoter region can downregulate the transcription of this oncogene. Here, we will overview the major achievements made in the last decades towards the discovery of a new class of anticancer drugs targeting G-quadruplexes in the c-MYC promoter of cancer cells.
Collapse
Affiliation(s)
- Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Israa M Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Rita Emídio
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| |
Collapse
|
2
|
Luo X, Zhang J, Gao Y, Pan W, Yang Y, Li X, Chen L, Wang C, Wang Y. Emerging roles of i-motif in gene expression and disease treatment. Front Pharmacol 2023; 14:1136251. [PMID: 37021044 PMCID: PMC10067743 DOI: 10.3389/fphar.2023.1136251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/27/2023] [Indexed: 03/22/2023] Open
Abstract
As non-canonical nucleic acid secondary structures consisting of cytosine-rich nucleic acids, i-motifs can form under certain conditions. Several i-motif sequences have been identified in the human genome and play important roles in biological regulatory functions. Due to their physicochemical properties, these i-motif structures have attracted attention and are new targets for drug development. Herein, we reviewed the characteristics and mechanisms of i-motifs located in gene promoters (including c-myc, Bcl-2, VEGF, and telomeres), summarized various small molecule ligands that interact with them, and the possible binding modes between ligands and i-motifs, and described their effects on gene expression. Furthermore, we discussed diseases closely associated with i-motifs. Among these, cancer is closely associated with i-motifs since i-motifs can form in some regions of most oncogenes. Finally, we introduced recent advances in the applications of i-motifs in multiple areas.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Chang Wang
- *Correspondence: Chang Wang, ; Yuqing Wang,
| | | |
Collapse
|
3
|
Joshi S, Singh A, Kukreti S. Porphyrin induced structural destabilization of a parallel DNA G-quadruplex in human MRP1 gene promoter. J Mol Recognit 2022; 35:e2950. [PMID: 34990028 DOI: 10.1002/jmr.2950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 01/01/2023]
Abstract
Porphyrins are among the first ligands that have been tested for their quadruplex binding and stabilization potential. We report the differential interaction of the positional cationic porphyrin isomers TMPyP3 and TMPyP4 with a parallel G-quadruplex (GQ) formed by 33-mer (TP) regulatory sequence present in the promoter region of the human multidrug resistance protein 1 (MRP1) transporter gene. This GQ element encompasses the three evolutionary conserved SP1 transcription factor binding sites. Taking into account that SP1 binds to a non-canonical GQ motif with higher affinity than to a canonical duplex DNA consensus motif, it is suggestive that GQ distortion by cationic porphyrin will have important implications in the regulation of MRP1 expression. Herein, we employed biophysical analysis using circular dichroism, visible absorption, UV-thermal melting and steady-state fluorescence spectroscopy, reporting destabilization of MRP1 GQ by cationic porphyrins. Results suggest that TMPyP4 and TMPyP3 interact with GQ with a binding affinity of 106 to 107 M-1 . Thermodynamic analysis indicated a significant decrease in melting temperature of GQ (ΔTm of 15.5°C-23.5°C), in the presence of 2 times excess of porphyrins. This study provides the biophysical evidence indicating the destabilisation of a parallel DNA G-quadruplex by cationic porphyrins.
Collapse
Affiliation(s)
- Savita Joshi
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi, India
| | - Anju Singh
- Department of Chemistry, Ramjas College, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi, India
| |
Collapse
|
4
|
Ashrafizadeh M, Zarabi A, Hushmandi K, Moghadam ER, Hashemi F, Daneshi S, Hashemi F, Tavakol S, Mohammadinejad R, Najafi M, Dudha N, Garg M. C-Myc Signaling Pathway in Treatment and Prevention of Brain Tumors. Curr Cancer Drug Targets 2021; 21:2-20. [PMID: 33069197 DOI: 10.2174/1568009620666201016121005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/26/2020] [Accepted: 09/07/2020] [Indexed: 12/16/2022]
Abstract
Brain tumors are responsible for high morbidity and mortality worldwide. Several factors such as the presence of blood-brain barrier (BBB), sensitive location in the brain, and unique biological features challenge the treatment of brain tumors. The conventional drugs are no longer effective in the treatment of brain tumors, and scientists are trying to find novel therapeutics for brain tumors. In this way, identification of molecular pathways can facilitate finding an effective treatment. c-Myc is an oncogene signaling pathway capable of regulation of biological processes such as apoptotic cell death, proliferation, survival, differentiation, and so on. These pleiotropic effects of c-Myc have resulted in much fascination with its role in different cancers, particularly brain tumors. In the present review, we aim to demonstrate the upstream and down-stream mediators of c-Myc in brain tumors such as glioma, glioblastoma, astrocytoma, and medulloblastoma. The capacity of c-Myc as a prognostic factor in brain tumors will be investigated. Our goal is to define an axis in which the c-Myc signaling pathway plays a crucial role and to provide direction for therapeutic targeting in these signaling networks in brain tumors.
Collapse
Affiliation(s)
- Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Universite Caddesi No. 27, Orhanli, Tuzla, 34956 Istanbul, Turkey
| | - Ali Zarabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956, Istanbul, Turkey
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Ebrahim Rahmani Moghadam
- Department of Anatomical sciences, School of Medicine, Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farid Hashemi
- DVM. Graduated, Young Researcher and Elite Club, Kazerun Branch, Islamic Azad University, Kazeroon, Iran
| | - Salman Daneshi
- Department of Public Health, School of Health, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Fardin Hashemi
- Student Research Committee, Department of physiotherapy, Faculty of rehabilitation, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shima Tavakol
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Reza Mohammadinejad
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman 7619813159, Iran
| | - Masoud Najafi
- Medical Technology Research Center, Institute of Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Namrata Dudha
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Gautam Budh Nagar, Uttar Pradesh, India
| | - Manoj Garg
- Amity of Molecular Medicine and Stem cell Research (AIMMSCR), Amity University Uttar Pradesh, Noida-201313, India
| |
Collapse
|
5
|
Elbadawy M, Usui T, Yamawaki H, Sasaki K. Emerging Roles of C-Myc in Cancer Stem Cell-Related Signaling and Resistance to Cancer Chemotherapy: A Potential Therapeutic Target Against Colorectal Cancer. Int J Mol Sci 2019; 20:E2340. [PMID: 31083525 PMCID: PMC6539579 DOI: 10.3390/ijms20092340] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 04/29/2019] [Accepted: 05/09/2019] [Indexed: 12/24/2022] Open
Abstract
Myc is a nuclear transcription factor that mainly regulates cell growth, cell cycle, metabolism, and survival. Myc family proteins contain c-Myc, n-Myc, and l-Myc. Among them, c-Myc can become a promising therapeutic target molecule in cancer. Cancer stem cells (CSCs) are known to be responsible for the therapeutic resistance. In the previous study, we demonstrated that c-Myc mediates drug resistance of colorectal CSCs using a patient-derived primary three-dimensional (3D) organoid culture. In this review, we mainly focus on the roles of c-Myc-related signaling in the regulation of CSCs, chemotherapy resistance, and colorectal cancer organoids. Finally, we introduce the various types of c-Myc inhibitors and propose the possibility of c-Myc as a therapeutic target against colorectal cancer.
Collapse
Affiliation(s)
- Mohamed Elbadawy
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.
- Department of Pharmacology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya 13736, Egypt.
| | - Tatsuya Usui
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.
| | - Hideyuki Yamawaki
- Laboratory of Veterinary Pharmacology, School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan.
| | - Kazuaki Sasaki
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.
| |
Collapse
|
6
|
Mikek C, West SJ, Gwin JC, Dayal N, Sintim HO, Lewis EA. Berenil Binds Tightly to Parallel and Mixed Parallel/Antiparallel G-Quadruplex Motifs with Varied Thermodynamic Signatures. ACS OMEGA 2018; 3:11582-11591. [PMID: 30320266 PMCID: PMC6173502 DOI: 10.1021/acsomega.8b01621] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/06/2018] [Indexed: 06/08/2023]
Abstract
Diminazene, DMZ, (or berenil) has been reported as a tight binder of G-quadruplexes. G-Quadruplex structures are often located in the promotor regions of oncogenes and may play a regulatory role in gene expression based on the stability of the folding topology. In this study, attempts have been made to characterize the specificity of DMZ binding toward multiple G-quadruplex topologies or foldamers. Mutant sequences of the G-quadruplex forming promotor regions of several oncogenes were designed to exhibit restricted loop lengths and folding topologies. Circular dichroism was used to confirm the quadruplex topology of mutant BCL2, KRAS, and c-MYC sequences, human telomere (Na+ and K+) G-quadruplexes and their complexes with DMZ and analogs thereof. Isothermal titration calorimetry was used to generate a complete thermodynamic profile (ΔG, ΔH, -TΔS) for the formation of DMZ and analog complexes with the target G-quadruplexes. DMZ binds to parallel and/or mixed parallel/antiparallel quadruplex DNA motifs with stoichiometries up to 8:1 and via three binding modes with varying affinities. In the case of the parallel G-quadruplexes, with the exception of the long-looped c-MYC mutant, the highest affinity binding event (mode 1) is driven by enthalpy. DMZ binding to the long-looped c-MYC mutant exhibits a very favorable entropy change in addition to a moderately favorable enthalpy change. Mode 1 binding to the antiparallel and mixed parallel/antiparallel hTel quadruplexes is also driven by favorable enthalpy changes. In all cases, the intermediate DMZ affinity binding (mode 2) is driven almost entirely by entropy, with small or unfavorable enthalpic contributions. The weakest binding event (mode 3) is also entropically driven with small or moderate enthalpic contributions.
Collapse
Affiliation(s)
- Clinton
G. Mikek
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Center
for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 47907, United States
| | - Savannah J. West
- Department
of Chemistry, Mississippi State University, 310 President’s Circle, Mississippi, Mississippi State 39762, United States
| | - J. Cole Gwin
- Department
of Chemistry, Mississippi State University, 310 President’s Circle, Mississippi, Mississippi State 39762, United States
| | - Neetu Dayal
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Center
for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 47907, United States
| | - Herman O. Sintim
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Center
for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 47907, United States
| | - Edwin A. Lewis
- Department
of Chemistry, Mississippi State University, 310 President’s Circle, Mississippi, Mississippi State 39762, United States
| |
Collapse
|
7
|
Li Z, Liu C, Huang C, Meng X, Zhang L, He J, Li J. Quinazoline derivative QPB-15e stabilizes the c-myc promoter G-quadruplex and inhibits tumor growth in vivo. Oncotarget 2018; 7:34266-76. [PMID: 27144522 PMCID: PMC5085154 DOI: 10.18632/oncotarget.9088] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 04/16/2016] [Indexed: 12/30/2022] Open
Abstract
The ribozyme-sensitive element NHE-III1 in the P1 promoter region of the important proto-oncogene c-myc contains many guanine (G)-rich sequences. Induction and stabilization of the G-quadruplex formed by NHE-III1 can downregulate c-myc expression. In the present study, we found that QPB-15e, a quinazoline derivative designed and synthesized by our laboratory, binds to and stabilizes the c-myc G-quadruplex in vitro, thereby inhibiting double-stranded DNA replication, downregulating c-myc gene expression and arresting cancer cell proliferation. PCR termination experiments showed that QPB-15e blocked double-stranded DNA replication by inducing or stabilizing the c-myc G-quadruplex. FRET-melting further confirmed that QPB-15e improved the stability of the G-quadruplex, and CD spectroscopy indicated that the compound interacted directly with the G-rich sequence. In competitive dialysis experiments, QPB-15e bound preferentially to quadruplex DNA in various structures, especially the G-quadruplex within the c-myc promoter region. Moreover, QPB-15e reduced the weights and volumes of tumors transplanted into nude mice. These findings strongly suggest that QPB-15e is a c-myc G-quadruplex ligand with anti-tumor properties, and may be efficacious for treating cancer in humans.
Collapse
Affiliation(s)
- Zeng Li
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Chen Liu
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Cheng Huang
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Xiaoming Meng
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Lei Zhang
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Jinhui He
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou 510006, China
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| |
Collapse
|
8
|
Brown RV, Wang T, Chappeta VR, Wu G, Onel B, Chawla R, Quijada H, Camp SM, Chiang ET, Lassiter QR, Lee C, Phanse S, Turnidge MA, Zhao P, Garcia JGN, Gokhale V, Yang D, Hurley LH. The Consequences of Overlapping G-Quadruplexes and i-Motifs in the Platelet-Derived Growth Factor Receptor β Core Promoter Nuclease Hypersensitive Element Can Explain the Unexpected Effects of Mutations and Provide Opportunities for Selective Targeting of Both Structures by Small Molecules To Downregulate Gene Expression. J Am Chem Soc 2017; 139:7456-7475. [PMID: 28471683 PMCID: PMC5977998 DOI: 10.1021/jacs.6b10028] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The platelet-derived growth factor receptor β (PDGFR-β) signaling pathway is a validated and important target for the treatment of certain malignant and nonmalignant pathologies. We previously identified a G-quadruplex-forming nuclease hypersensitive element (NHE) in the human PDGFR-β promoter that putatively forms four overlapping G-quadruplexes. Therefore, we further investigated the structures and biological roles of the G-quadruplexes and i-motifs in the PDGFR-β NHE with the ultimate goal of demonstrating an alternate and effective strategy for molecularly targeting the PDGFR-β pathway. Significantly, we show that the primary G-quadruplex receptor for repression of PDGFR-β is the 3'-end G-quadruplex, which has a GGA sequence at the 3'-end. Mutation studies using luciferase reporter plasmids highlight a novel set of G-quadruplex point mutations, some of which seem to provide conflicting results on effects on gene expression, prompting further investigation into the effect of these mutations on the i-motif-forming strand. Herein we characterize the formation of an equilibrium between at least two different i-motifs from the cytosine-rich (C-rich) sequence of the PDGFR-β NHE. The apparently conflicting mutation results can be rationalized if we take into account the single base point mutation made in a critical cytosine run in the PDGFR-β NHE that dramatically affects the equilibrium of i-motifs formed from this sequence. We identified a group of ellipticines that targets the G-quadruplexes in the PDGFR-β promoter, and from this series of compounds, we selected the ellipticine analog GSA1129, which selectively targets the 3'-end G-quadruplex, to shift the dynamic equilibrium in the full-length sequence to favor this structure. We also identified a benzothiophene-2-carboxamide (NSC309874) as a PDGFR-β i-motif-interactive compound. In vitro, GSA1129 and NSC309874 downregulate PDGFR-β promoter activity and transcript in the neuroblastoma cell line SK-N-SH at subcytotoxic cell concentrations. GSA1129 also inhibits PDGFR-β-driven cell proliferation and migration. With an established preclinical murine model of acute lung injury, we demonstrate that GSA1129 attenuates endotoxin-mediated acute lung inflammation. Our studies underscore the importance of considering the effects of point mutations on structure formation from the G- and C-rich sequences and provide further evidence for the involvement of both strands and associated structures in the control of gene expression.
Collapse
Affiliation(s)
- Robert V. Brown
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Ting Wang
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | | | - Guanhui Wu
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Buket Onel
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Reena Chawla
- BIO5 Institute, 1657 East Helen Street, Tucson, Arizona 85721, United States
| | - Hector Quijada
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Sara M. Camp
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Eddie T. Chiang
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Quinea R. Lassiter
- College of Agriculture & Life Sciences, University of Arizona, 1117 East Lowell Street, Tucson, Arizona 85721, United States
| | - Carmen Lee
- College of Agriculture & Life Sciences, University of Arizona, 1117 East Lowell Street, Tucson, Arizona 85721, United States
- College of Science, University of Arizona, 1040 East Fourth Street, Tucson, Arizona 85721, United States
| | - Shivani Phanse
- College of Science, University of Arizona, 1040 East Fourth Street, Tucson, Arizona 85721, United States
| | - Megan A. Turnidge
- College of Science, University of Arizona, 1040 East Fourth Street, Tucson, Arizona 85721, United States
| | - Ping Zhao
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, No. 280 Waihuandong Road, Education Mega Centre, Guanzhou 510006, Peoples Republic of China
| | - Joe G. N. Garcia
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Vijay Gokhale
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
- BIO5 Institute, 1657 East Helen Street, Tucson, Arizona 85721, United States
| | - Danzhou Yang
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
- BIO5 Institute, 1657 East Helen Street, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Laurence H. Hurley
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
- BIO5 Institute, 1657 East Helen Street, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, United States
| |
Collapse
|
9
|
Chen BJ, Wu YL, Tanaka Y, Zhang W. Small molecules targeting c-Myc oncogene: promising anti-cancer therapeutics. Int J Biol Sci 2014; 10:1084-96. [PMID: 25332683 PMCID: PMC4202025 DOI: 10.7150/ijbs.10190] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 08/25/2014] [Indexed: 02/07/2023] Open
Abstract
The nuclear transcription factor c-Myc is a member of the Myc gene family with multiple functions and located on band q24.1 of chromosome 8. The c-Myc gene is activated by chromosomal translocation, rearrangement, and amplification. Its encoded protein transduces intracellular signals to the nucleus, resulting in the regulation of cell proliferation, differentiation, and apoptosis, and has the ability to transform cells and bind chromosomal DNA. c-Myc also plays a critical role in malignant transformation. The abnormal over-expression of c-Myc is frequently observed in some tumors, including carcinomas of the breast, colon, and cervix, as well as small-cell lung cancer, osteosarcomas, glioblastomas, and myeloid leukemias, therefore making it a possible target for anticancer therapy. In this minireview, we summarize unique characteristics of c-Myc and therapeutic strategies against cancer using small molecules targeting the oncogene, and discuss the prospects in the development of agents targeting c-Myc, in particular G-quadruplexes formed in c-Myc promoter and c-Myc/Max dimerization. Such information will be of importance for the research and development of c-Myc-targeted drugs.
Collapse
Affiliation(s)
- Bing-Jia Chen
- 1. Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Yan-Ling Wu
- 2. Lab of Molecular Immunology, Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, 630 Xincheng Road, Hangzhou, 310051, China. ; 1. Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Yoshimasa Tanaka
- 3. Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Wen Zhang
- 1. Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| |
Collapse
|
10
|
Monaselidze J, Gorgoshidze M, Khachidze D, Kiladze M, Bregadze V, Kiziria E, Margaryan H, Hakobyan N. Conformations of DNA in the presence of nanomole concentrations of Co+2ions and mezo-tetra(4-N-oxyethylpiridil) porphyrin. J Biomol Struct Dyn 2014; 33:267-73. [DOI: 10.1080/07391102.2013.873001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
11
|
Benabou S, Aviñó A, Eritja R, González C, Gargallo R. Fundamental aspects of the nucleic acid i-motif structures. RSC Adv 2014. [DOI: 10.1039/c4ra02129k] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.
Collapse
Affiliation(s)
- S. Benabou
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
| | - A. Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - R. Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - C. González
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid, Spain
| | - R. Gargallo
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
| |
Collapse
|
12
|
The effect of pyridyl substituents on the thermodynamics of porphyrin binding to G-quadruplex DNA. Bioorg Med Chem 2013; 21:7515-22. [DOI: 10.1016/j.bmc.2013.09.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/07/2013] [Accepted: 09/14/2013] [Indexed: 11/22/2022]
|
13
|
Le VH, Nagesh N, Lewis EA. Bcl-2 promoter sequence G-quadruplex interactions with three planar and non-planar cationic porphyrins: TMPyP4, TMPyP3, and TMPyP2. PLoS One 2013; 8:e72462. [PMID: 23977303 PMCID: PMC3748076 DOI: 10.1371/journal.pone.0072462] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/18/2013] [Indexed: 12/31/2022] Open
Abstract
The interactions of three related cationic porphyrins, TMPyP4, TMPyP3 and TMPyP2, with a WT 39-mer Bcl-2 promoter sequence G-quadruplex were studied using Circular Dichroism, ESI mass spectrometry, Isothermal Titration Calorimetry, and Fluorescence spectroscopy. The planar cationic porphyrin TMPyP4 (5, 10, 15, 20-meso-tetra (N-methyl-4-pyridyl) porphine) is shown to bind to a WT Bcl-2 G-quadruplex via two different binding modes, an end binding mode and a weaker mode attributed to intercalation. The related non-planar ligands, TMPyP3 and TMPyP2, are shown to bind to the Bcl-2 G-quadruplex by a single mode. ESI mass spectrometry experiments confirmed that the saturation stoichiometry is 4:1 for the TMPyP4 complex and 2:1 for the TMPyP2 and TMPyP3 complexes. ITC experiments determined that the equilibrium constant for formation of the (TMPyP4)1/DNA complex (K1 = 3.7 × 10(6)) is approximately two orders of magnitude greater than the equilibrium constant for the formation of the (TMPyP2)1/DNA complex, (K1 = 7.0 × 10(4)). Porphyrin fluorescence is consistent with intercalation in the case of the (TMPyP4)3/DNA and (TMPyP4)4/DNA complexes. The non-planar shape of the TMPyP2 and TMPyP3 molecules results in both a reduced affinity for the end binding interaction and the elimination of the intercalation binding mode.
Collapse
Affiliation(s)
- Vu H. Le
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Narayana Nagesh
- Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India
| | - Edwin A. Lewis
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, United States of America
- * E-mail:
| |
Collapse
|
14
|
Monaselidze J, Gorgoshidze M, Khachidze D, Kiladze M, Bregadze V, Kiziria E, Margaryan H, Hakobyan N. Zn Ions Change Binding Mode of TOEPyP4 with DNA and Cause DNA Transition from B to C and Zn-Like Conformations. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajac.2013.412090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
15
|
Dettler JM, Buscaglia R, Le VH, Lewis EA. DSC deconvolution of the structural complexity of c-MYC P1 promoter G-quadruplexes. Biophys J 2011; 100:1517-25. [PMID: 21402034 DOI: 10.1016/j.bpj.2011.01.068] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 01/21/2011] [Accepted: 01/25/2011] [Indexed: 01/01/2023] Open
Abstract
We completed a biophysical characterization of the c-MYC proto-oncogene P1 promoter quadruplex and its interaction with a cationic porphyrin, 5,10,15,20-tetra(N-methyl-4-pyridyl)porphyrin (TMPyP4), using differential scanning calorimetry, isothermal titration calorimetry, and circular dichroism spectroscopy. We examined three different 24-mer oligonucleotides, including the wild-type (WT) sequence found in the c-MYC P(1) promoter and two mutant G→T sequences that are known to fold into single 1:2:1 and 1:6:1 loop isomer quadruplexes. Biophysical experiments were performed on all three oligonucleotide sequences at two different ionic strengths (30 mM [K(+)] and 130 mM [K(+)]). Differential scanning calorimetry experiments demonstrated that the WT quadruplex consists of a mixture of at least two different folded conformers at both ionic strengths, whereas both mutant sequences exhibit a single two-state melting transition at both ionic strengths. Isothermal titration calorimetry experiments demonstrated that both mutant sequences bind 4 mols of TMPyP4 to 1 mol of DNA, in similarity to the WT sequence. The circular dichroism spectroscopy signatures for all three oligonucleotides at both ionic strengths are consistent with an intramolecular parallel stranded G-quadruplex structure, and no change in quadruplex structure is observed upon addition of saturating amounts of TMPyP4 (i.e., 4:1 TMPyP4/DNA).
Collapse
Affiliation(s)
- Jamie M Dettler
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | | | | | | |
Collapse
|
16
|
Regulation of the equilibrium between G-quadruplex and duplex DNA in promoter of human c-myc oncogene by a pyrene derivative. Int J Biol Macromol 2011; 49:1173-6. [PMID: 21683090 DOI: 10.1016/j.ijbiomac.2011.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2011] [Revised: 05/21/2011] [Accepted: 05/24/2011] [Indexed: 11/22/2022]
Abstract
It has been established that the equilibrium between duplex and G-quadruplex of the nuclease hypersensitivity element III1 (NHE III1) in human c-myc promoter is linked with this gene's transcription. Using NMR and ESI-MS, we have found a pyrene derivative, DMAPP, is able to modulate this equilibrium and, thus, might have the potential to regulate this oncogene's transcription. DMAPP has shown as a G-quadruplex binding agent and could induce c-myc G-quadruplex formation out of duplex. These results provide new clue for rational drug design to target transcription control of c-myc.
Collapse
|
17
|
Dettler JM, Buscaglia R, Cui J, Cashman D, Blynn M, Lewis EA. Biophysical characterization of an ensemble of intramolecular i-motifs formed by the human c-MYC NHE III1 P1 promoter mutant sequence. Biophys J 2010; 99:561-7. [PMID: 20643075 DOI: 10.1016/j.bpj.2010.04.042] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 03/16/2010] [Accepted: 04/05/2010] [Indexed: 10/19/2022] Open
Abstract
i-Motif-forming sequences are present in or near the regulatory regions of >40% of all genes, including known oncogenes. We report here the results of a biophysical characterization and computational study of an ensemble of intramolecular i-motifs that model the polypyrimidine sequence in the human c-MYC P1 promoter. Circular dichroism results demonstrate that the mutant sequence (5'-CTT TCC TAC CCTCCC TAC CCT AA-3') can adopt multiple "i-motif-like," classical i-motif, and single-stranded structures as a function of pH. The classical i-motif structures are predominant in the pH range 4.2-5.2. The "i-motif-like" and single-stranded structures are the most significant species in solution at pH higher and lower, respectively, than that range. Differential scanning calorimetry results demonstrate an equilibrium mixture of at least three i-motif folded conformations with Tm values of 38.1, 46.6, and 49.5 degrees C at pH 5.0. The proposed ensemble of three folded conformations includes the three lowest-energy conformations obtained by computational modeling and two folded conformers that were proposed in a previous NMR study. The NMR study did not report the most stable conformer found in this study.
Collapse
Affiliation(s)
- Jamie M Dettler
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | | | | | | | | | | |
Collapse
|
18
|
Collar CJ, Lee M, Wilson WD. Setting Anchor in the Minor Groove: in Silico Investigation into Formamido N-Methylpyrrole and N-Methylimidazole Polyamides Bound by Cognate DNA Sequences. J Chem Inf Model 2010; 50:1611-22. [DOI: 10.1021/ci100191a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Catharine J. Collar
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and Department of Chemistry, Division of Natural and Applied Sciences, Hope College, Holland, Michigan 49423
| | - Moses Lee
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and Department of Chemistry, Division of Natural and Applied Sciences, Hope College, Holland, Michigan 49423
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and Department of Chemistry, Division of Natural and Applied Sciences, Hope College, Holland, Michigan 49423
| |
Collapse
|
19
|
Monchaud D, Granzhan A, Saettel N, Guédin A, Mergny JL, Teulade-Fichou MP. "One ring to bind them all"-part I: the efficiency of the macrocyclic scaffold for g-quadruplex DNA recognition. J Nucleic Acids 2010; 2010. [PMID: 20725629 PMCID: PMC2915875 DOI: 10.4061/2010/525862] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 02/18/2010] [Indexed: 01/01/2023] Open
Abstract
Macrocyclic scaffolds are particularly attractive for designing selective G-quadruplex ligands essentially because, on one hand, they show a poor affinity for the “standard” B-DNA conformation and, on the other hand, they fit nicely with the external G-quartets of quadruplexes. Stimulated by the pioneering studies on the cationic porphyrin TMPyP4 and the natural product telomestatin, follow-up studies have developed, rapidly leading to a large diversity of macrocyclic structures with remarkable-quadruplex binding properties and biological activities. In this review we summarize the current state of the art in detailing the three main categories of quadruplex-binding macrocycles described so far (telomestatin-like polyheteroarenes, porphyrins and derivatives, polyammonium cyclophanes), and in addressing both synthetic issues and biological aspects.
Collapse
Affiliation(s)
- David Monchaud
- Section Recherche, Institut Curie, CNRS UMR176, Centre Universitaire Paris XI, Batiment 110, 91405 Orsay, France
| | | | | | | | | | | |
Collapse
|
20
|
Li MH, Luo Q, Li ZS. Molecular Dynamics Study on the Interactions of Porphyrin with Two Antiparallel Human Telomeric Quadruplexes. J Phys Chem B 2010; 114:6216-24. [DOI: 10.1021/jp101373p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ming-Hui Li
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Quan Luo
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Ze-Sheng Li
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| |
Collapse
|
21
|
Kendrick S, Akiyama Y, Hecht SM, Hurley LH. The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern. J Am Chem Soc 2010; 131:17667-76. [PMID: 19908860 DOI: 10.1021/ja9076292] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Transcriptional regulation of the bcl-2 proto-oncogene is highly complex, with the majority of transcription driven by the P1 promoter site and the interaction of multiple regulatory proteins. A guanine- and cytosine-rich (GC-rich) region directly upstream of the P1 site has been shown to be integral to bcl-2 promoter activity, as deletion or mutation of this region significantly increases transcription. This GC-rich element consists of six contiguous runs of guanines and cytosines that have the potential to adopt DNA secondary structures, the G-quadruplex and i-motif, respectively. Our laboratory has previously demonstrated that the polypurine-rich strand of the bcl-2 promoter can form a mixture of three different G-quadruplex structures. In this current study, we demonstrate that the complementary polypyrimidine-rich strand is capable of forming one major intramolecular i-motif DNA secondary structure with a transition pH of 6.6. Characterization of the i-motif folding pattern using mutational studies coupled with circular dichroic spectra and thermal stability analyses revealed an 8:5:7 loop conformation as the predominant structure at pH 6.1. The folding pattern was further supported by chemical footprinting with bromine. In addition, a novel assay involving the sequential incorporation of a fluorescent thymine analog at each thymine position provided evidence of a capping structure within the top loop region of the i-motif. The potential of the GC-rich element within the bcl-2 promoter region to form DNA secondary structures suggests that the transition from the B-DNA to non-B-DNA conformation may play an important role in bcl-2 transcriptional regulation. Furthermore, the two adjacent large lateral loops in the i-motif structure provide an unexpected opportunity for protein and small molecule recognition.
Collapse
Affiliation(s)
- Samantha Kendrick
- Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, USA
| | | | | | | |
Collapse
|
22
|
Alzeer J, Vummidi B, Roth P, Luedtke N. Guanidinium-modifizierte Phthalocyanine als Fluoreszenzsonden mit hoher G-Quadruplex-Affinität und als Transkriptionsregulatoren. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903685] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
23
|
Alzeer J, Vummidi B, Roth P, Luedtke N. Guanidinium-Modified Phthalocyanines as High-Affinity G-Quadruplex Fluorescent Probes and Transcriptional Regulators. Angew Chem Int Ed Engl 2009; 48:9362-5. [DOI: 10.1002/anie.200903685] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
24
|
Dexheimer TS, Carey SS, Zuohe S, Gokhale VM, Hu X, Murata LB, Maes EM, Weichsel A, Sun D, Meuillet EJ, Montfort WR, Hurley LH. NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III(1). Mol Cancer Ther 2009; 8:1363-77. [PMID: 19435876 DOI: 10.1158/1535-7163.mct-08-1093] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The formation of G-quadruplex structures within the nuclease hypersensitive element (NHE) III(1) region of the c-myc promoter and the ability of these structures to repress c-myc transcription have been well established. However, just how these extremely stable DNA secondary structures are transformed to activate c-myc transcription is still unknown. NM23-H2/nucleoside diphosphate kinase B has been recognized as an activator of c-myc transcription via interactions with the NHE III(1) region of the c-myc gene promoter. Through the use of RNA interference, we confirmed the transcriptional regulatory role of NM23-H2. In addition, we find that further purification of NM23-H2 results in loss of the previously identified DNA strand cleavage activity, but retention of its DNA binding activity. NM23-H2 binds to both single-stranded guanine- and cytosine-rich strands of the c-myc NHE III(1) and, to a lesser extent, to a random single-stranded DNA template. However, it does not bind to or cleave the NHE III(1) in duplex form. Significantly, potassium ions and compounds that stabilize the G-quadruplex and i-motif structures have an inhibitory effect on NM23-H2 DNA-binding activity. Mutation of Arg(88) to Ala(88) (R88A) reduced both DNA and nucleotide binding but had minimal effect on the NM23-H2 crystal structure. On the basis of these data and molecular modeling studies, we have proposed a stepwise trapping-out of the NHE III(1) region in a single-stranded form, thus allowing single-stranded transcription factors to bind and activate c-myc transcription. Furthermore, this model provides a rationale for how the stabilization of the G-quadruplex or i-motif structures formed within the c-myc gene promoter region can inhibit NM23-H2 from activating c-myc gene expression.
Collapse
|
25
|
Abstract
Using spectroscopic techniques, we demonstrate the effect of LNA (locked nucleic acid) nucleotides in modulating the formation and stability of the i-motif structure formed by the c-MYC sequence.
Collapse
Affiliation(s)
- Niti Kumar
- Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, New Delhi 110 007, India
| | | | | |
Collapse
|
26
|
Lane AN, Chaires JB, Gray RD, Trent JO. Stability and kinetics of G-quadruplex structures. Nucleic Acids Res 2008; 36:5482-515. [PMID: 18718931 PMCID: PMC2553573 DOI: 10.1093/nar/gkn517] [Citation(s) in RCA: 571] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Revised: 07/26/2008] [Accepted: 07/29/2008] [Indexed: 12/30/2022] Open
Abstract
In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.
Collapse
Affiliation(s)
- Andrew N Lane
- Structural Biology Program, JG Brown Cancer Center, University of Louisville, KY 40202, USA.
| | | | | | | |
Collapse
|