1
|
El-Khoury R, Damha MJ. End-ligation can dramatically stabilize i-motifs at neutral pH. Chem Commun (Camb) 2023; 59:3715-3718. [PMID: 36883338 DOI: 10.1039/d2cc07063d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Stabilizing i-motif structures at neutral pH and physiological temperature remains a major challenge. Here, we demonstrate the use of chemical end-ligation to stabilize intramolecular i-motifs at both acidic and neutral pH. We also demonstrate that combining 2'-deoxy-2'-fluoroarabinocytidine substitutions and end-ligation results in an i-motif with an unparalleled thermal stability of 54 °C at neutral pH. Overall, the ligated i-motifs presented herein may be used in screens for selective i-motif ligands and proteins and could find important applications in nanotechnology.
Collapse
Affiliation(s)
- Roberto El-Khoury
- Department of Chemistry, McGill University, Montréal, H3A0B8, Canada.
| | - Masad J Damha
- Department of Chemistry, McGill University, Montréal, H3A0B8, Canada.
| |
Collapse
|
2
|
Nguyen LTA, Dang DT. RHAU Peptides Specific for Parallel G-Quadruplexes: Potential Applications in Chemical Biology. Mol Biotechnol 2023; 65:291-299. [PMID: 35984625 DOI: 10.1007/s12033-022-00552-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/09/2022] [Indexed: 11/28/2022]
Abstract
G-quadruplexes (G4s) are non-canonical nucleic acid structures formed by guanine (G)-rich sequences, which are ubiquitously found in the human genome and transcriptome. Targeting G4s by specific ligands provides a powerful tool to monitor and regulate G4s-associated biological processes. RHAU peptides, derived from the G4-binding motif of "RNA Helicase associated with AU-rich element" (RHAU), have emerged as extraordinary ligands for specific recognition of parallel G4s. This review highlights the significances of recent studies investigating potential applications of the engineered RHAU peptides incorporated to different functional moieties.
Collapse
Affiliation(s)
- Le Tuan Anh Nguyen
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City, Vietnam
| | - Dung Thanh Dang
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City, Vietnam.
| |
Collapse
|
3
|
Mohammadinejad A, Heydari M, Kazemi Oskuee R, Rezayi M. A Critical Systematic Review of Developing Aptasensors for Diagnosis and Detection of Diabetes Biomarkers. Crit Rev Anal Chem 2022; 52:1795-1817. [DOI: 10.1080/10408347.2021.1919986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Arash Mohammadinejad
- Targeted Drug Delivery Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Biotechnology and Nanotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Heydari
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Kazemi Oskuee
- Targeted Drug Delivery Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Biotechnology and Nanotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Rezayi
- Department of Medical Biotechnology and Nanotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
4
|
Wickhorst PJ, Ihmels H, Paululat T. Studies on the Interactions of 3,11-Difluoro-6,8,13-trimethyl-8 H-quino[4,3,2- kl]acridinium and Insulin with the Quadruplex-Forming Oligonucleotide Sequence a2 from the Insulin-Linked Polymorphic Region. Molecules 2021; 26:molecules26216595. [PMID: 34771003 PMCID: PMC8587938 DOI: 10.3390/molecules26216595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Recently, several quadruplex-DNA-forming sequences have been identified in the insulin-linked polymorphic region (ILPR), which is a guanine-rich oligonucleotide sequence in the promoter region of insulin. The formation of this non-canonical quadruplex DNA (G4-DNA) has been shown to be involved in the biological activity of the ILPR, specifically with regard to its interplay with insulin. In this context, this contribution reports on the investigation of the association of the quadruplex-forming ILPR sequence a2 with insulin as well as with the well-known G4-DNA ligand 3,11-difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl]acridinium (1), also named RHPS4, by optical and NMR spectroscopy. CD- and NMR-spectroscopic measurements confirmed the preferential formation of an antiparallel quadruplex structure of a2 with four stacked guanine quartets. Furthermore, ligand 1 has high affinity toward a2 and binds by terminal π stacking to the G1-G11-G15-G25 quartet. In addition, the spectroscopic studies pointed to an association of insulin to the deoxyribose backbone of the loops of a2.
Collapse
|
5
|
Sabu C, Henna T, Raphey V, Nivitha K, Pramod K. Advanced biosensors for glucose and insulin. Biosens Bioelectron 2019; 141:111201. [DOI: 10.1016/j.bios.2019.03.034] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/06/2019] [Accepted: 03/18/2019] [Indexed: 12/20/2022]
|
6
|
Šolínová V, Žáková L, Jiráček J, Kašička V. Pressure assisted partial filling affinity capillary electrophoresis employed for determination of binding constants of human insulin hexamer complexes with serotonin, dopamine, arginine, and phenol. Anal Chim Acta 2019; 1052:170-178. [DOI: 10.1016/j.aca.2018.11.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/10/2018] [Accepted: 11/12/2018] [Indexed: 11/30/2022]
|
7
|
Qu X, Bian F, Guo Q, Ge Q, Sun Q, Huang X. Ligation-Rolling Circle Amplification on Quantum Dot-Encoded Microbeads for Detection of Multiplex G-Quadruplex-Forming Sequences. Anal Chem 2018; 90:12051-12058. [DOI: 10.1021/acs.analchem.8b02820] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xiaojun Qu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Feika Bian
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingsheng Guo
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xuebin Huang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| |
Collapse
|
8
|
Albanese CM, Suttapitugsakul S, Perati S, McGown LB. A genome-inspired, reverse selection approach to aptamer discovery. Talanta 2017; 177:150-156. [PMID: 29108569 DOI: 10.1016/j.talanta.2017.08.093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/08/2017] [Accepted: 08/29/2017] [Indexed: 11/29/2022]
Abstract
Limitations of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and related methods that depend upon combinatorial oligonucleotide libraries have hindered progress in this area. Our laboratory has introduced a new approach to aptamer discovery that uses oligonucleotides with sequences drawn from the human genome to capture proteins from biological samples. Specifically, we have focused on capture of proteins in nuclear extracts from human cell lines using G-quadruplex (G4) forming genomic sequences. Previous studies identified capture of several proteins both in vitro and in live cells by the Pu28-mer sequence from the ERBB2 promoter region. Here we provide a more comprehensive study of protein capture from BT474 and MCF7 human breast cancer cells using G4-forming sequences from the CMYC, RB, VEGF and ERBB2 human oncogene promoter regions. Mass spectrometric analysis and Western blot analysis of protein capture at oligonucleotide-modified surfaces revealed capture of nucleolin by all three of the oligonucleotides in BT474 and MCF7 cells, and also of ribosomal protein L19 (RPL19) in BT474 cells. Chromatin immunoprecipitation (ChIP) analysis confirmed the interaction of nucleolin with all three promoter sequences in MCF7 cells and with RB in BT474 cells. ChIP also revealed interactions of RPL19 with CMYC in BT474 cells and of both RPL19 and ribosomal protein L14 (RPL14) with ERBB2 in BT474 cells. These results offer the basis for development of new aptamers based on the G4 sequences from the CMYC, RB, VEGF, and ERBB2 promoters toward proteins including nucleolin, RPL19 and RPL14. These interactions also may have biological and therapeutic significance.
Collapse
Affiliation(s)
- Christina M Albanese
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Suttipong Suttapitugsakul
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Shruthi Perati
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Linda B McGown
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA.
| |
Collapse
|
9
|
Platella C, Riccardi C, Montesarchio D, Roviello GN, Musumeci D. G-quadruplex-based aptamers against protein targets in therapy and diagnostics. Biochim Biophys Acta Gen Subj 2017; 1861:1429-1447. [PMID: 27865995 PMCID: PMC7117017 DOI: 10.1016/j.bbagen.2016.11.027] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 12/17/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA molecules identified to recognize with high affinity specific targets including proteins, small molecules, ions, whole cells and even entire organisms, such as viruses or bacteria. They can be identified from combinatorial libraries of DNA or RNA oligonucleotides by SELEX technology, an in vitro iterative selection procedure consisting of binding (capture), partitioning and amplification steps. Remarkably, many of the aptamers selected against biologically relevant protein targets are G-rich sequences that can fold into stable G-quadruplex (G4) structures. Aiming at disseminating novel inspiring ideas within the scientific community in the field of G4-structures, the emphasis of this review is placed on: 1) recent advancements in SELEX technology for the efficient and rapid identification of new candidate aptamers (introduction of microfluidic systems and next generation sequencing); 2) recurrence of G4 structures in aptamers selected by SELEX against biologically relevant protein targets; 3) discovery of several G4-forming motifs in important regulatory regions of the human or viral genome bound by endogenous proteins, which per se can result into potential aptamers; 4) an updated overview of G4-based aptamers with therapeutic potential and 5) a discussion on the most attractive G4-based aptamers for diagnostic applications. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
Collapse
Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | | | - Domenica Musumeci
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy; Institute of Biostructures and Bioimages, CNR, Napoli, Italy.
| |
Collapse
|
10
|
Prokofjeva M, Tsvetkov V, Basmanov D, Varizhuk A, Lagarkova M, Smirnov I, Prusakov K, Klinov D, Prassolov V, Pozmogova G, Mikhailov SN. Anti-HIV Activities of Intramolecular G4 and Non-G4 Oligonucleotides. Nucleic Acid Ther 2016; 27:56-66. [PMID: 27763826 DOI: 10.1089/nat.2016.0624] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
New natural and chemically modified DNA aptamers that inhibit HIV-1 activity at submicromolar concentrations (presumably via preventing viral entry into target cells) are reported. The new DNA aptamers were developed based on known intramolecular G-quadruplexes (G4s) that were functionally unrelated to HIV inhibition [the thrombin-binding aptamer and the fragment of the human oncogene promoter (Bcl2)]. The majority of previously described DNA inhibitors of HIV infection adopt intermolecular structures, and thus their folding variability represents an obvious disadvantage. Intramolecular architectures refold correctly after denaturation and are generally easier to handle. However, whether the G4 topology or other factors account for the anti-HIV activity of our aptamers is unknown. The impact of chemical modification (thiophosphoryl internucleotide linkages) on aptamer activity is discussed. The exact secondary structures of the active compounds and further elucidation of their mechanisms of action hopefully will be the subjects of future studies.
Collapse
Affiliation(s)
- Maria Prokofjeva
- 1 Engelhardt Institute of Molecular Biology RAS , Moscow, Russia
| | - Vladimir Tsvetkov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia .,3 Topchiev Institute of Petrochemical Synthesis Russian Academy of Sciences , Moscow, Russia
| | - Dmitry Basmanov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Anna Varizhuk
- 1 Engelhardt Institute of Molecular Biology RAS , Moscow, Russia .,2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Maria Lagarkova
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Igor Smirnov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Kirill Prusakov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | - Dmitry Klinov
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia .,4 Moscow Institute of Physics and Technology (State University) , Moscow Region, Russia
| | | | - Galina Pozmogova
- 2 Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency , Moscow, Russia
| | | |
Collapse
|
11
|
Lei C, Xu C, Noonan O, Meka AK, Zhang L, Nouwens A, Yu C. Mesoporous materials modified by aptamers and hydrophobic groups assist ultra-sensitive insulin detection in serum. Chem Commun (Camb) 2016; 51:13642-5. [PMID: 26226380 DOI: 10.1039/c5cc04458h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel mesoporous material modified with both insulin-binding-aptamers and hydrophobic methyl groups is synthesized. With rationally designed pore structures and surface chemistry, this material is applied in sample pre-treatment for ELISA, and enables the quantification (0.25-5 pg ml(-1)) of insulin in serum, 30-fold enhancement of the limit-of-detection compared to the commercial ELISA kit.
Collapse
Affiliation(s)
- Chang Lei
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
| | | | | | | | | | | | | |
Collapse
|
12
|
Dzubiel D, Ihmels H, Mahmoud MMA, Thomas L. A comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR). Beilstein J Org Chem 2014; 10:2963-74. [PMID: 25550763 PMCID: PMC4273293 DOI: 10.3762/bjoc.10.314] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 11/26/2014] [Indexed: 11/23/2022] Open
Abstract
The interactions of the ILPR sequence (ILPR = "insulin-linked polymorphic region") a2 [d(ACAG4TGTG4ACAG4TGTG4)] with [2.2.2]heptamethinecyanine derivatives 1a–e and with the already established quadruplex ligands coralyne (2), 3,3′-[2,6-pyridinediylbis(carbonylimino)]bis[1-methylquinolinium] (3), 4,4′,4′′,4′′′-(21H,23H-porphine-5,10,15,20-tetrayl)tetrakis[1-methylpyridinium] (4), naphtho[2,1-b:3,4-b′:6,5-b′′:7,8-b′′′]tetraquinolizinium (5) and thiazole orange (6) were studied. It is demonstrated with absorption, fluorescence and CD spectroscopy that all investigated ligands bind with relatively high affinity to the ILPR-quadruplex DNA a2 (0.2–5.5 × 106 M−1) and that in most cases the binding parameters of ligand-ILPR complexes are different from the ones observed with other native quadruplex-forming DNA sequences.
Collapse
Affiliation(s)
- Darinka Dzubiel
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Mohamed M A Mahmoud
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Laura Thomas
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| |
Collapse
|
13
|
Cassidy LM, Burcar BT, Stevens W, Moriarty EM, McGown LB. Guanine-centric self-assembly of nucleotides in water: an important consideration in prebiotic chemistry. ASTROBIOLOGY 2014; 14:876-886. [PMID: 25285982 PMCID: PMC4201266 DOI: 10.1089/ast.2014.1155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 09/03/2014] [Indexed: 06/03/2023]
Abstract
Investigations of plausible prebiotic chemistry on early Earth must consider not only chemical reactions to form more complex products such as proto-biopolymers but also reversible, molecular self-assembly that would influence the availability, organization, and sequestration of reactant molecules. The self-assembly of guanosine compounds into higher-order structures and lyotropic liquid crystalline "gel" phases through formation of hydrogen-bonded guanine tetrads (G-tetrads) is one such consideration that is particularly relevant to an RNA-world scenario. G-tetrad-based gelation has been well studied for individual guanosine compounds and was recently observed in mixtures of guanosine with 5'-guanosine monophosphate (GMP) as well. The present work investigates the self-assembly of GMP in the presence of the other RNA nucleotides. Effects of the total concentration and relative proportion of the nucleotides in the mixtures, the form (disodium salt vs. free acid) of the nucleotides, temperature, pH, and salt concentration were determined by visual observations and circular dichroism (CD) spectroscopy. The results show that formation of cholesteric G-tetrad phases is influenced by interactions with other nucleotides, likely through association (e.g., intercalation) of the nucleotides with the G-tetrad structures. These interactions affect the structure and stability of the G-tetrad gel phase, as well as the formation of alternate self-assembled GMP structures such as a continuous, hydrogen-bonded GMP helix or dimers and aggregates of GMP. These interactions and multiple equilibria are influenced by the presence of cations, especially in the presence of K(+). This work could have important implications for the emergence of an RNA or proto-RNA world, which would require mixtures of nucleotides at sufficiently high, local concentrations for abiotic polymerization to occur.
Collapse
Affiliation(s)
- Lauren M Cassidy
- New York Center for Astrobiology and Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute , Troy, New York
| | | | | | | | | |
Collapse
|
14
|
Timmer CM, Michmerhuizen NL, Witte AB, Van Winkle M, Zhou D, Sinniah K. An Isothermal Titration and Differential Scanning Calorimetry Study of the G-Quadruplex DNA–Insulin Interaction. J Phys Chem B 2014; 118:1784-90. [DOI: 10.1021/jp411293r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Christine M. Timmer
- Department
of Chemistry and Biochemistry, Calvin College, 3201 Burton Street Southeast, Grand Rapids, Michigan 49546, United States
| | - Nicole L. Michmerhuizen
- Department
of Chemistry and Biochemistry, Calvin College, 3201 Burton Street Southeast, Grand Rapids, Michigan 49546, United States
| | - Amanda B. Witte
- Department
of Chemistry and Biochemistry, Calvin College, 3201 Burton Street Southeast, Grand Rapids, Michigan 49546, United States
| | - Margaret Van Winkle
- Department
of Chemistry and Biochemistry, Calvin College, 3201 Burton Street Southeast, Grand Rapids, Michigan 49546, United States
| | - Dejian Zhou
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Kumar Sinniah
- Department
of Chemistry and Biochemistry, Calvin College, 3201 Burton Street Southeast, Grand Rapids, Michigan 49546, United States
| |
Collapse
|
15
|
Yoshida W, Saito T, Yokoyama T, Ferri S, Ikebukuro K. Aptamer selection based on G4-forming promoter region. PLoS One 2013; 8:e65497. [PMID: 23750264 PMCID: PMC3672139 DOI: 10.1371/journal.pone.0065497] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 04/25/2013] [Indexed: 11/19/2022] Open
Abstract
We developed a method for aptamer identification without in vitro selection. We have previously obtained several aptamers, which may fold into the G-quadruplex (G4) structure, against target proteins; therefore, we hypothesized that the G4 structure would be an excellent scaffold for aptamers to recognize the target protein. Moreover, the G4-forming sequence contained in the promoter region of insulin can reportedly bind to insulin. We thus expected that G4 DNAs, which are contained in promoter regions, could act as DNA aptamers against their gene products. We designated this aptamer identification method as “G4 promoter-derived aptamer selection (G4PAS).” Using G4PAS, we identified vascular endothelial growth factor (VEGF)165, platelet-derived growth factor-AA (PDGF)-AA, and RB1 DNA aptamers. Surface plasmon resonance (SPR) analysis revealed that the dissociation constant (Kd) values of VEGF165, PDGF-AA, and RB1 DNA aptamers were 1.7 × 10−7 M, 6.3 × 10−9 M, and 4.4 × 10−7 M, respectively. G4PAS is a simple and rapid method of aptamer identification because it involves only binding analysis of G4 DNAs to the target protein. In the human genome, over 40% of promoters contain one or more potential G4 DNAs. G4PAS could therefore be applied to identify aptamers against target proteins that contain G4 DNAs on their promoters.
Collapse
Affiliation(s)
- Wataru Yoshida
- Department of Biotechnology and Life Science, Tokyo University of Agriculture & Technology, Koganei, Tokyo, Japan
| | - Taiki Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture & Technology, Koganei, Tokyo, Japan
| | - Tomomi Yokoyama
- Department of Biotechnology and Life Science, Tokyo University of Agriculture & Technology, Koganei, Tokyo, Japan
| | - Stefano Ferri
- Department of Biotechnology and Life Science, Tokyo University of Agriculture & Technology, Koganei, Tokyo, Japan
- Japan Science and Technology Agency, CREST, Koganei, Tokyo, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture & Technology, Koganei, Tokyo, Japan
- Japan Science and Technology Agency, CREST, Koganei, Tokyo, Japan
- * E-mail:
| |
Collapse
|
16
|
Gerasimov JY, Schaefer CS, Yang W, Grout RL, Lai RY. Development of an electrochemical insulin sensor based on the insulin-linked polymorphic region. Biosens Bioelectron 2012. [PMID: 23202332 DOI: 10.1016/j.bios.2012.10.046] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Here we report the design and fabrication of an electrochemical aptamer-based (E-AB) sensor for detection of insulin. The aptamer used in this study is the insulin-linked polymorphic region (ILPR) sequence, a G-rich sequence that presumably undergoes ligand-induced folding to form a G-quadruplex in presence of insulin. Our circular dichroism data, however, suggests that the ILPR sequence, even in absence of the target, is predominantly in a G-quadruplex-like form. Insulin binding, however, has shown to further induce the formation of the G-quadruplex. To evaluate the potential of the ILPR sequence as a biosensing element, we constructed two E-AB insulin sensors that are identical in all aspects but the location of the methylene blue (MB) redox label. We find that the sensor fabricated with internal MB-modified probes (In-IT) shows enhanced sensing behavior when compared to one fabricated using terminal-MB modified probes (In1). The improvements observed with the In-IT sensor could be attributed to the more effective obstruction of electron transfer upon insulin binding. Overall, both sensors perform well, affording a detection limit of 10 nM and 50 nM for the In-IT and In1 sensors, respectively.
Collapse
Affiliation(s)
- Jennifer Y Gerasimov
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | | | | | | | | |
Collapse
|
17
|
Zhang T, Zhang H, Wang Y, McGown LB. Capture and identification of proteins that bind to a GGA-rich sequence from the ERBB2 gene promoter region. Anal Bioanal Chem 2012; 404:1867-76. [PMID: 22899247 DOI: 10.1007/s00216-012-6322-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/15/2012] [Accepted: 07/31/2012] [Indexed: 02/07/2023]
Abstract
The ERBB2 gene (HER2/neu) is overexpressed in many human breast cancers. It is an important therapeutic target and its product protein is a key biomarker for breast cancer. A 28-bp GGA repeat sequence (Pu28-mer) in the nuclease hypersensitive site of the ERBB2 promoter region may play an important role in the regulation of ERBB2 transcription, possibly involving the formation of a G-quadruplex. In order to investigate this possibility, an affinity MALDI-MS approach was used for in vitro protein capture from nuclear extracts from cultured MCF-7 and BT-474 cancer cells at Pu28-mer and control oligonucleotide-modified surfaces. Captured proteins from MCF-7 cells were analyzed by LC-MS/MS. Based on these results, Western blot was then used to interrogate captured proteins from both MCF-7 and the Her-2/neu-positive BT-474 cells. Results support the formation of a G-quadruplex by Pu28-mer, indicated by circular dichroism spectroscopy, that selectively captures transcription factors including Ku70, Ku80, PURA, nucleolin, and hnRNP K. Chromatin immunoprecipitation confirmed binding of Ku70, Ku80, PURA, and nucleolin to ERBB2 promoter in the live BT-474 cells. These findings may lead to a better understanding of the role of non-duplex DNA structures in gene regulation and provide a more complete picture of the regulation of ErbB2 expression in breast cancer. The results also provide a blueprint for development of "genome-inspired" aptamers based on the Pu28-mer sequence for in vitro and in vivo detection of proteins related to regulation of ERBB2 gene expression and breast cancer.
Collapse
Affiliation(s)
- Tian Zhang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | | | | | | |
Collapse
|
18
|
Collie GW, Parkinson GN. The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem Soc Rev 2011; 40:5867-92. [PMID: 21789296 DOI: 10.1039/c1cs15067g] [Citation(s) in RCA: 461] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The intriguing structural diversity in folded topologies available to guanine-rich nucleic acid repeat sequences have made four-stranded G-quadruplex structures the focus of both basic and applied research, from cancer biology and novel therapeutics through to nanoelectronics. Distributed widely in the human genome as targets for regulating gene expression and chromosomal maintenance, they offer unique avenues for future cancer drug development. In particular, the recent advances in chemical and structural biology have enabled the construction of bespoke selective DNA based aptamers to be used as novel therapeutic agents and access to detailed structural models for structure based drug discovery. In this critical review, we will explore the important underlying characteristics of G-quadruplexes that make them functional, stable, and predictable nanoscaffolds. We will review the current structural database of folding topologies, molecular interfaces and novel interaction surfaces, with a consideration to their future exploitation in drug discovery, molecular biology, supermolecular assembly and aptamer design. In recent years the number of potential applications for G-quadruplex motifs has rapidly grown, so in this review we aim to explore the many future challenges and highlight where possible successes may lie. We will highlight the similarities and differences between DNA and RNA folded G-quadruplexes in terms of stability, distribution, and exploitability as small molecule targets. Finally, we will provide a detailed review of basic G-quadruplex geometry, experimental tools used, and a critical evaluation of the application of high-resolution structural biology and its ability to provide meaningful and valid models for future applications (255 references).
Collapse
Affiliation(s)
- Gavin W Collie
- CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, UK WC1N 1AX
| | | |
Collapse
|
19
|
Sissi C, Gatto B, Palumbo M. The evolving world of protein-G-quadruplex recognition: a medicinal chemist's perspective. Biochimie 2011; 93:1219-30. [PMID: 21549174 PMCID: PMC7126356 DOI: 10.1016/j.biochi.2011.04.018] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 04/20/2011] [Indexed: 01/02/2023]
Abstract
The physiological and pharmacological role of nucleic acids structures folded into the non canonical G-quadruplex conformation have recently emerged. Their activities are targeted at vital cellular processes including telomere maintenance, regulation of transcription and processing of the pre-messenger or telomeric RNA. In addition, severe conditions like cancer, fragile X syndrome, Bloom syndrome, Werner syndrome and Fanconi anemia J are related to genomic defects that involve G-quadruplex forming sequences. In this connection G-quadruplex recognition and processing by nucleic acid directed proteins and enzymes represents a key event to activate or deactivate physiological or pathological pathways. In this review we examine protein-G-quadruplex recognition in physiologically significant conditions and discuss how to possibly exploit the interactions' selectivity for targeted therapeutic intervention.
Collapse
Affiliation(s)
- Claudia Sissi
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, Padua, Italy
| | | | | |
Collapse
|
20
|
Jonker N, Kool J, Irth H, Niessen WMA. Recent developments in protein-ligand affinity mass spectrometry. Anal Bioanal Chem 2010; 399:2669-81. [PMID: 21058031 PMCID: PMC3043251 DOI: 10.1007/s00216-010-4350-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 10/16/2010] [Accepted: 10/17/2010] [Indexed: 11/27/2022]
Abstract
This review provides an overview of direct and indirect technologies to screen protein–ligand interactions with mass spectrometry. These technologies have as a key feature the selection or affinity purification of ligands in mixtures prior to detection. Specific fields of interest for these technologies are metabolic profiling of bioactive metabolites, natural extract screening, and the screening of libraries for bioactives, such as parallel synthesis libraries and small combichem libraries. The review addresses the principles of each of the methods discussed, with a focus on developments in recent years, and the applicability of the methods to lead generation and development in drug discovery. Schematic view of the principle of filtration based 96-well affinity selection MS binding assays ![]()
Collapse
Affiliation(s)
- Niels Jonker
- BioMolecular Analysis, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, The Netherlands
| | | | | | | |
Collapse
|
21
|
Paritala H, Firestine SM. Characterization of insulin ILPR sequences for their ability to adopt a G-quadruplex structure. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 29:81-90. [PMID: 20391195 DOI: 10.1080/15257771003597691] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
A major genetic factor linked to the progression of type 1 diabetes occurs in the insulin-linked polymorphic repeat region (ILPR) located 363 bp upstream of the human insulin gene. Genetic studies have shown that individuals with class I repeats (30-60) are predisposed to the development of type 1 diabetes while individuals with longer repeats are protected. Previous research has suggested that some sequences found within the ILPR can adopt a G-quadruplex structure, and this finding has lead to speculation that G-quadruplexes may control insulin expression in certain circumstances. Unfortunately, relatively little study has been done on whether sequences found in the ILPR can adopt a quadruplex fold. In this study, we have utilized circular dichroism, thermal difference spectroscopy and ultraviolet (UV) melting studies to examine the first seven common repeat sequences (A-G) found in the ILPR. We find that sequences A-E adopt a quadruplex fold while sequences F and G likely do not. Examination of sequence B and a single nucleotide variant, B2, revealed that both folded into a G-quadruplex. This result casts doubt on previous studies suggesting that the formation of a quadruplex was related to the ability of ILPR sequences to regulate transcription.
Collapse
Affiliation(s)
- Hanumantharao Paritala
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | | |
Collapse
|
22
|
Schonhoft JD, Das A, Achamyeleh F, Samdani S, Sewell A, Mao H, Basu S. ILPR repeats adopt diverse G-quadruplex conformations that determine insulin binding. Biopolymers 2010; 93:21-31. [PMID: 19688813 DOI: 10.1002/bip.21289] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The insulin-linked polymorphic region (ILPR) is a VNTR region located upstream of the insulin (INS) gene consisting of the repeat 5'-ACAGGGGTGTGGGG (repeat a) and several less abundant sequence repeats (b-n). Here, we have investigated the structural polymorphism of G-quadruplexes formed from the most common repeat sequences (a-c) and their effect on insulin protein binding. We first established that the ILPR repeats "b" and "c" can form quadruplex structures. Insulin has previously been shown to bind a G-quadruplex formed by a dimer of the repeat "a". Our findings show that insulin binds preferentially to the repeat "a" G-quadruplex (K(d) = 0.17 + or - 0.03 microM) over G-quadruplexes formed from other ILPR repeats that were tested (K(d)s from 0.71 + or - 0.15 to 1.07 + or - 0.09 microM). Additionally, the Watson-Crick complementary relationship between the loop regions of repeat "a" (ACA and TGT) seemingly play an important role in favoring a specific G-quadruplex conformation, which based on our data is critical for insulin binding. Affinity for insulin is reduced in sequences lacking the putative WC complementarity, however upon engineered restoration of complementarity, insulin binding is recovered. A DMS footprinting assay on the repeat "a" G-quadruplex in the presence of insulin, combined with binding affinities for ILPR mutants led to identification of a loop nucleotide critical for binding. Uniquely, insulin shows clear preference for binding to the G-quadruplexes with the more antiparallel feature. Collectively, our results illustrate the specific nature of insulin binding to the ILPR G-quadruplexes and begin to provide molecular details on such interactions.
Collapse
Affiliation(s)
- Joseph D Schonhoft
- Department of Chemistry, School of Biomedical Sciences, Kent State University, Kent, OH 44242, USA
| | | | | | | | | | | | | |
Collapse
|
23
|
Xiao J, McGown LB. Mass spectrometric determination of ILPR G-quadruplex binding sites in insulin and IGF-2. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1974-1982. [PMID: 19747845 PMCID: PMC2763926 DOI: 10.1016/j.jasms.2009.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 08/04/2009] [Accepted: 08/04/2009] [Indexed: 05/28/2023]
Abstract
The insulin-linked polymorphic region (ILPR) of the human insulin gene promoter region forms G-quadruplex structures in vitro. Previous studies show that insulin and insulin-like growth factor-2 (IGF-2) exhibit high affinity binding in vitro to 2-repeat sequences of ILPR variants a and h, but negligible binding to variant i. Two-repeat sequences of variants a and h form intramolecular G-quadruplex structures that are not evidenced for variant i. Here we report on the use of protein digestion combined with affinity capture and MALDI-MS detection to pinpoint ILPR binding sites in insulin and IGF-2. Peptides captured by ILPR variants a and h were sequenced by MALDI-MS/MS, LC-MS and in silico digestion. On-bead digestion of insulin-ILPR variant a complexes supported the conclusions. The results indicate that the sequence VCG(N)RGF is generally present in the captured peptides and is likely involved in the affinity binding interactions of the proteins with the ILPR G-quadruplexes. The significance of arginine in the interactions was studied by comparing the affinities of synthesized peptides VCGERGF and VCGEAGF with ILPR variant a. Peptides from other regions of the proteins that are connected through disulfide linkages were also detected in some capture experiments. Identification of binding sites could facilitate design of DNA binding ligands for capture and detection of insulin and IGF-2. The interactions may have biological significance as well.
Collapse
Affiliation(s)
- JunFeng Xiao
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | | |
Collapse
|
24
|
Wang Y, Zhang H, Ligon LA, McGown LB. Association of insulin-like growth factor 2 with the insulin-linked polymorphic region in cultured fetal thymus cells. Biochemistry 2009; 48:8189-94. [PMID: 19588890 DOI: 10.1021/bi900958x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The insulin-linked polymorphic region (ILPR) is a regulatory sequence in the promoter region upstream of the human insulin gene and is widely recognized as a locus of type 1 diabetes susceptibility. Polymorphism of the ILPR sequence can affect expression of both insulin and the adjacent insulin-like growth factor 2 (IGF-2) gene. Several ILPR variants form G-quadruplex DNA structures in vitro that exhibit affinity binding to insulin and IGF-2. It has been suggested that the ILPR may form G-quadruplexes in vivo as well, raising the possibility that insulin and IGF-2 may bind to these structures in the ILPR in chromatin of live cells. This work establishes the presence of IGF-2 in the nucleus of cells cultured from human fetal thymus and its association with the ILPR in the chromatin of these cells. In vitro experiments support the involvement of G-quadruplex DNA in the binding interaction.
Collapse
Affiliation(s)
- Yuexi Wang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | | | | | | |
Collapse
|