1
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Jurkowski M, Kogut M, Sappati S, Czub J. Why Are Left-Handed G-Quadruplexes Scarce? J Phys Chem Lett 2024; 15:3142-3148. [PMID: 38477716 PMCID: PMC10961827 DOI: 10.1021/acs.jpclett.3c03589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
G-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear. To address this, we employ all-atom molecular dynamics simulations and quantum chemical methods. Our results reveal that right-handed G4s exhibit greater thermodynamic and kinetic stability as a result of favorable sugar-phosphate backbone conformations in guanine tracts. Moreover, while hydrogen-bonding patterns influence helicity-specific G4 loop conformations, they minimally affect stability differences. We also elucidate the strong correlation between helicity and the strand progression direction, essential for G4 structures. These findings deepen our understanding of G4s, providing molecular-level insights into their structural and energetic preferences, which could inform the design of novel nanodevices.
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Affiliation(s)
- Michał Jurkowski
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| | - Mateusz Kogut
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| | - Subrahmanyam Sappati
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
- BioTechMed
Center, Gdańsk University of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| | - Jacek Czub
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
- BioTechMed
Center, Gdańsk University of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
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2
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Kankia B. Which came first: the chicken, the egg, or guanine? RNA (NEW YORK, N.Y.) 2023; 29:1317-1324. [PMID: 37286207 PMCID: PMC10573290 DOI: 10.1261/rna.079613.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023]
Abstract
The main goal of the origin of life (OoL) hypothesis is to reconstruct the missing link between the primordial soup and the extant biology. However, the OoL itself is just the initial part of the link representing the bootstrapping operation of Darwinian evolution. The rest of the link is the emergence of the evolution to the present day primary biological system-the ribosome-based translation apparatus. A valid hypothesis must (i) not invoke Darwinian evolution in the bootstrapping and (ii) transform the ab initio life form into the translation apparatus without violating the principle of continuity (i.e., only incremental steps without foresight). Currently, no such hypothesis exists. Here, I discuss the Quadruplex World hypothesis, which fully complies with these requirements and suggests a spontaneous emergence of the ab initio life form. The spontaneity of OoL arises from the physicochemical properties of guanine monomers in a manner of causal determinism: each step of the process (i.e., scaffolding, polymerization, and folding) is caused by the most recent past step such that in the end only the specific 3D architecture forms. The architecture (i) has a length-independent folding pattern; (ii) can play the role of the predecessor of tRNA and single-handedly conduct a primitive form of translation; and (iii) can evolve into the extant translation apparatus without any paradoxes.
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Affiliation(s)
- Besik Kankia
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- Institute of Biophysics, Ilia State University, Tbilisi 0162, Republic of Georgia
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3
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Lomidze L, Yang M, Khutsishvili D, Metreveli N, Musier-Forsyth K, Kankia B. Structure of Tetrahelical DNA Homopolymers Supports Quadruplex World Hypothesis. ACS OMEGA 2022; 7:4311-4316. [PMID: 35155924 PMCID: PMC8829921 DOI: 10.1021/acsomega.1c06026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
We previously reported a tetrahelical monomolecular architecture of DNA, tmDNA, which employs G-quartets and an all-parallel GGGTGGGTGGGTGGG (G3T) quadruplex as the repeating unit. Based on thermodynamic and kinetic studies, we proposed that covalently joined (G3T) n units formed an uninterrupted programmable homopolymer; however, structural evidence for the tmDNA architecture was lacking. Here, we used NMR spectroscopy of wild-type and single-inosine-substituted constructs to characterize both monomolecular (G3T)2 and bimolecular quadruplex-Mg-coupled versions of tmDNA. The NMR results support an architecture consisting of uninterrupted stacked G-tetrads in both the monomolecular constructs and bimolecular assemblies. Taken together, these data support the formation of a stable programmable homopolymeric tmDNA architecture, which may have been a precursor to the modern-day Watson-Crick DNA duplex.
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Affiliation(s)
- Levan Lomidze
- Institute of Biophysics, Ilia State University, Tbilisi 0162, Republic of Georgia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mengkun Yang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - David Khutsishvili
- Institute of Biophysics, Ilia State University, Tbilisi 0162, Republic of Georgia
| | - Nunu Metreveli
- Institute of Biophysics, Ilia State University, Tbilisi 0162, Republic of Georgia
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Besik Kankia
- Institute of Biophysics, Ilia State University, Tbilisi 0162, Republic of Georgia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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4
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Boyle EP, Lomidze L, Musier‐Forsyth K, Kankia B. A Chimeric DNA/RNA Antiparallel Quadruplex with Improved Stability. ChemistryOpen 2022; 11:e202100276. [PMID: 35103415 PMCID: PMC8805387 DOI: 10.1002/open.202100276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/13/2021] [Indexed: 11/22/2022] Open
Abstract
Nucleic acid quadruplexes are proposed to play a role in the regulation of gene expression, are often present in aptamers selected for specific binding functions and have potential applications in medicine and biotechnology. Therefore, understanding their structure and thermodynamic properties and designing highly stable quadruplexes is desirable for a variety of applications. Here, we evaluate DNA→RNA substitutions in the context of a monomolecular, antiparallel quadruplex, the thrombin-binding aptamer (TBA, GGTTGGTGTGGTTGG) in the presence of either K+ or Sr2+ . TBA predominantly folds into a chair-type configuration containing two G-tetrads, with G residues in both syn and anti conformation. All chimeras with DNA→RNA substitutions (G→g) at G residues requiring the syn conformation demonstrated strong destabilization. In contrast, G→g substitutions at Gs with anti conformation increased stability without affecting the monomolecular chair-type topology. None of the DNA→RNA substitutions in loop positions affected the quadruplex topology; however, these substitutions varied widely in their stabilizing or destabilizing effects in an unpredictable manner. This analysis allowed us to design a chimeric DNA/RNA TBA construct that demonstrated substantially improved stability relative to the all-DNA construct. These results have implications for a variety of quadruplex-based applications including for the design of dynamic nanomachines.
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Affiliation(s)
- Elaina P. Boyle
- Department of Chemistry and BiochemistryThe Ohio State UniversityColumbusOH 43210USA
- Center for RNA BiologyThe Ohio State UniversityColumbusOH 43210USA
| | - Levan Lomidze
- Institute of BiophysicsIlia State UniversityTbilisi0162Republic of Georgia
| | - Karin Musier‐Forsyth
- Department of Chemistry and BiochemistryThe Ohio State UniversityColumbusOH 43210USA
- Center for RNA BiologyThe Ohio State UniversityColumbusOH 43210USA
| | - Besik Kankia
- Department of Chemistry and BiochemistryThe Ohio State UniversityColumbusOH 43210USA
- Center for RNA BiologyThe Ohio State UniversityColumbusOH 43210USA
- Institute of BiophysicsIlia State UniversityTbilisi0162Republic of Georgia
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5
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Abstract
The RNA world hypothesis relies on the double-helix complementarity principle for both replication and catalytic activity of RNA. However, the de novo appearance of the complementarity rules, without previous evolution steps, is doubtful. Another major problem of the RNA world is its isolated nature, making it almost impossible to accommodate the genetic code and transform it into modern biochemistry. These and many other unanswered questions of the RNA world led to suggestions that some simpler molecules must have preceded RNA. Most of these alternative hypotheses proposed the double-helical polymers with different backbones but used the same complementarity principle. The current paper describes a fundamentally different idea: the de novo appearance of a nucleic acid polymer without any preexisting rules or requirements. This approach, coined as the quadruplex world hypothesis, is based on (i) the ability of guanines to form stable G-tetrads that facilitate polymerization; and (ii) the unique property of polyguanines to fold into a monomolecular tetrahelix with a strictly defined building pattern and tertiary structure. The tetrahelix is capable of high-affinity intermolecular interactions and catalytic activities. The quadruplex world hypothesis has the potential to address almost all the shortcomings of the RNA world.
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Affiliation(s)
- Besik Kankia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA. .,Institute of Biophysics, Ilia State University, Tbilisi, 0162, Republic of Georgia.
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6
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Carrino S, Hennecker CD, Murrieta AC, Mittermaier A. Frustrated folding of guanine quadruplexes in telomeric DNA. Nucleic Acids Res 2021; 49:3063-3076. [PMID: 33693924 PMCID: PMC8034632 DOI: 10.1093/nar/gkab140] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 01/22/2021] [Accepted: 02/19/2021] [Indexed: 11/23/2022] Open
Abstract
Human chromosomes terminate in long, single-stranded, DNA overhangs of the repetitive sequence (TTAGGG)n. Sets of four adjacent TTAGGG repeats can fold into guanine quadruplexes (GQ), four-stranded structures that are implicated in telomere maintenance and cell immortalization and are targets in cancer therapy. Isolated GQs have been studied in detail, however much less is known about folding in long repeat sequences. Such chains adopt an enormous number of configurations containing various arrangements of GQs and unfolded gaps, leading to a highly frustrated energy landscape. To better understand this phenomenon, we used mutagenesis, thermal melting, and global analysis to determine stability, kinetic, and cooperativity parameters for GQ folding within chains containing 8–12 TTAGGG repeats. We then used these parameters to simulate the folding of 32-repeat chains, more representative of intact telomeres. We found that a combination of folding frustration and negative cooperativity between adjacent GQs increases TTAGGG unfolding by up to 40-fold, providing an abundance of unfolded gaps that are potential binding sites for telomeric proteins. This effect was most pronounced at the chain termini, which could promote telomere extension by telomerase. We conclude that folding frustration is an important and largely overlooked factor controlling the structure of telomeric DNA.
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Affiliation(s)
- Simone Carrino
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Christopher D Hennecker
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Ana C Murrieta
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada.,School of Engineering and Sciences, Instituto Tecnológico y de Estudios Superiores De Monterrey, Av. Eugenio Garza Sada 2501 Sur Col. Tecnológico C.P. 64849, Monterrey, Nuevo León, México
| | - Anthony Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
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7
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Cagirici HB, Budak H, Sen TZ. Genome-wide discovery of G-quadruplexes in barley. Sci Rep 2021; 11:7876. [PMID: 33846409 PMCID: PMC8041835 DOI: 10.1038/s41598-021-86838-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/19/2021] [Indexed: 12/04/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5′ untranslated region (5′ UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs.
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Affiliation(s)
- H Busra Cagirici
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture - Agricultural Research Service, 800 Buchanan St, Albany, CA, 94710, USA
| | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT, USA.,Agrogen, LLC., Omaha, NE, USA
| | - Taner Z Sen
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture - Agricultural Research Service, 800 Buchanan St, Albany, CA, 94710, USA.
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8
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Nwokolo OA, Kidd B, Allen T, Minasyan AS, Vardelly S, Johnson KD, Nesterova IV. Rational Design of Memory‐Based Sensors: the Case of Molecular Calorimeters. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Obianuju A. Nwokolo
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Brant Kidd
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Te'Kara Allen
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Alexander S. Minasyan
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Suchitra Vardelly
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Kristopher D. Johnson
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
| | - Irina V. Nesterova
- Department of Chemistry and Biochemistry Northern Illinois University DeKalb IL 60115 USA
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9
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Kankia B. Quadruplex-Templated and Catalyzed Ligation of Nucleic Acids. Chembiochem 2020; 22:1261-1267. [PMID: 33217115 DOI: 10.1002/cbic.202000754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/19/2020] [Indexed: 11/05/2022]
Abstract
Template-guided chemical reactions between nucleic acid strands are an important process in biomedical research. However, almost all of these reactions employ an oligonucleotide-templated approach that is based on the double-helix alignment. The moderate stability of the double helix makes this approach unsuitable for many chemical reactions, so alternative nucleic acid alignment mechanisms, demonstrating higher thermal and chemical stability, are desirable. Earlier, we described a noncovalent coupling mechanism between DNA strands through a quadruplex-and-Mg2+ connection (QMC). QMC is based on G-quadruplexes and allows unusually stable and specific interactions. Herein, a novel catalytic nucleic acid reaction, based on QMC, is described. This approach uses G-tetrads as a structural and recognition element without employing Watson-Crick complementarity rules at any stage of substrate/catalyst formation or interaction between them. Quadruplex-templated ligation can be achieved through the self-ligation of two nucleic acid strands, or through a quadruplex catalyst, which forms a G-triplex and specifically connects the strands. The process is extraordinarily robust and efficient. For instance, the ligation of carbodiimide-activated substrates can proceed in boiling solutions, and complete ligation is demonstrated within a minute. The quadruplex-templated and catalyzed reactions will create new opportunities for chemical reactions requiring harsh experimental conditions.
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Affiliation(s)
- Besik Kankia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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10
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Nwokolo OA, Kidd B, Allen T, Minasyan AS, Vardelly S, Johnson KD, Nesterova IV. Rational Design of Memory-Based Sensors: the Case of Molecular Calorimeters. Angew Chem Int Ed Engl 2020; 60:1610-1614. [PMID: 32996657 DOI: 10.1002/anie.202011422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/22/2020] [Indexed: 12/11/2022]
Abstract
Thermodynamic characterization is crucial for understanding molecular interactions. However, methodologies for measuring heat changes in small open systems are extremely limited. We document a new approach for designing molecular sensors, that function as calorimeters: sensors based on memory. To design a memory-based sensor, we take advantage of the unique kinetic properties of nucleic acid scaffolds. Particularly, we elaborate on the differences in folding and unfolding rates in nucleic acid quadruplexes. DNA-based i-motifs unfold fast in response to small heats but do not fold back when the system is equilibrated with surroundings. We translated this behavior into a molecular memory function that enables the measurement of heat changes in open environments. The new sensors are biocompatible, operate homogeneously, and measure small heats released over long time periods. As a proof-of-concept, we demonstrate how the molecular calorimeters report heat changes generated in water/propanol mixing and in ligand/protein binding.
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Affiliation(s)
- Obianuju A Nwokolo
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Brant Kidd
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Te'Kara Allen
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Alexander S Minasyan
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Suchitra Vardelly
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Kristopher D Johnson
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Irina V Nesterova
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, USA
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11
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Ogloblina AM, Iaccarino N, Capasso D, Di Gaetano S, Garzarella EU, Dolinnaya NG, Yakubovskaya MG, Pagano B, Amato J, Randazzo A. Toward G-Quadruplex-Based Anticancer Agents: Biophysical and Biological Studies of Novel AS1411 Derivatives. Int J Mol Sci 2020; 21:E7781. [PMID: 33096752 PMCID: PMC7590035 DOI: 10.3390/ijms21207781] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
Certain G-quadruplex forming guanine-rich oligonucleotides (GROs), including AS1411, are endowed with cancer-selective antiproliferative activity. They are known to bind to nucleolin protein, resulting in the inhibition of nucleolin-mediated phenomena. However, multiple nucleolin-independent biological effects of GROs have also been reported, allowing them to be considered promising candidates for multi-targeted cancer therapy. Herein, with the aim of optimizing AS1411 structural features to find GROs with improved anticancer properties, we have studied a small library of AS1411 derivatives differing in the sequence length and base composition. The AS1411 derivatives were characterized by using circular dichroism and nuclear magnetic resonance spectroscopies and then investigated for their enzymatic resistance in serum and nuclear extract, as well as for their ability to bind nucleolin, inhibit topoisomerase I, and affect the viability of MCF-7 human breast adenocarcinoma cells. All derivatives showed higher thermal stability and inhibitory effect against topoisomerase I than AS1411. In addition, most of them showed an improved antiproliferative activity on MCF-7 cells compared to AS1411 despite a weaker binding to nucleolin. Our results support the hypothesis that the antiproliferative properties of GROs are due to multi-targeted effects.
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Affiliation(s)
- Anna M. Ogloblina
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Domenica Capasso
- Center for Life Sciences and Technologies (CESTEV), University of Naples Federico II, Via A. De Amicis 95, 80145 Naples, Italy;
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, 80134 Naples, Italy;
| | - Emanuele U. Garzarella
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Marianna G. Yakubovskaya
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
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12
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Highly cooperative fluorescence switching of self-assembled squaraine dye at tunable threshold temperatures using thermosensitive nanovesicles for optical sensing and imaging. Sci Rep 2019; 9:17991. [PMID: 31784685 PMCID: PMC6884458 DOI: 10.1038/s41598-019-54418-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/15/2019] [Indexed: 12/11/2022] Open
Abstract
Thermosensitive fluorescent dyes can convert thermal signals into optical signals as a molecular nanoprobe. These nanoprobes are playing an increasingly important part in optical temperature sensing and imaging at the nano- and microscale. However, the ability of a fluorescent dye itself has sensitivity and accuracy limitations. Here we present a molecular strategy based on self-assembly to overcome such limitations. We found that thermosensitive nanovesicles composed of lipids and a unique fluorescent dye exhibit fluorescence switching characteristics at a threshold temperature. The switch is rapid and reversible and has a high signal to background ratio (>60), and is also highly sensitive to temperature (10–22%/°C) around the threshold value. Furthermore, the threshold temperature at which fluorescence switching is induced, can be tuned according to the phase transition temperature of the lipid bilayer membrane forming the nanovesicles. Spectroscopic analysis indicated that the fluorescence switching is induced by the aggregation-caused quenching and disaggregation-induced emission of the fluorescent dye in a cooperative response to the thermotropic phase transition of the membrane. This mechanism presents a useful approach for chemical and material design to develop fluorescent nanomaterials with superior fluorescence sensitivity to thermal signals for optical temperature sensing and imaging at the nano- and microscales.
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13
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Why do G-quadruplexes dimerize through the 5'-ends? Driving forces for G4 DNA dimerization examined in atomic detail. PLoS Comput Biol 2019; 15:e1007383. [PMID: 31539370 PMCID: PMC6774569 DOI: 10.1371/journal.pcbi.1007383] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/02/2019] [Accepted: 09/09/2019] [Indexed: 12/25/2022] Open
Abstract
G-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order G4 DNA structures. To understand the molecular driving forces for G4 association, here, we study the binding interaction between two parallel-stranded G-quadruplexes using all-atom molecular dynamics simulations. The predicted dimerization free energies show that direct binding through the 5’-G-tetrads is the most preferred of all possible end-to-end stacking orientations, consistently with all available experimental data. Decomposition of dimerization enthalpies in combination with simulations at varying ionic strength further indicate that the observed orientational preferences arise from a fine balance between the electrostatic repulsion of the sugar-phosphate backbones and favorable counterion binding at the dimeric interface. We also demonstrate how these molecular-scale findings can be used to devise means of controlling G4 dimerization equilibrium, e.g., by altering salt concentration and using G4-targeted ligands. Native DNA usually folds to form the canonical double helix, however, under certain conditions, it can also fold into other secondary structures. Some of the most interesting ones are G-quadruplexes (G4)—compact DNA structures in which guanines assemble into multilayered tetrads, and whose formation has been reported at the ends of linear chromosomes (telomeres) and at different regulatory regions of the genome. Although structural and basic energetic properties, as well as some biological functions of G-quadruplexes are quite well understood, not much is known about their propensity to form agregated structures. A very high density of G-quadruplexes at telomeres along with their large exposed planar surfaces indeed favor G4 aggregation through end-to-end stacking, which might be important for the protection of telomeres and DNA packaging. In this research, using computer simulations, we provide insight into molecular origins of stability of the higher-order G-quadruplexes and explain in structural and energetic terms a strong preference for one particular end-to-end stacking orientation. Based on the recognized aggregation driving forces, we also suggest methods for controling the aggregation preferences openining up new opportunities for designing oligomeric G-quadruplexes.
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14
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Peng D, Li Y, Huang Z, Liang RP, Qiu JD, Liu J. Efficient DNA-Catalyzed Porphyrin Metalation for Fluorescent Ratiometric Pb 2+ Detection. Anal Chem 2019; 91:11403-11408. [PMID: 31414597 DOI: 10.1021/acs.analchem.9b02759] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Developing biosensors for Pb2+ is an important analytical topic. DNA-based Pb2+ sensors have been designed mainly based on RNA-cleaving DNAzymes and Pb2+-induced folding of G-quadruplex (G4) DNA. Porphyrin metalation is a key reaction in biology and catalysis. Many enzyme mimics have been developed to catalyze this reaction, and some metalation DNAzymes were reported with a G4 structure. Inspired by the excellent G4 binding properties of certain divalent metal ions, we herein screened a few metals and G-rich DNA sequences. The metalation activity of a DNA named T30695 (sequence: (G3T)4) was significantly accelerated by Pb2+. The reaction of Cu2+ insertion into the mesoporphyrin IX had a kcat of 0.89 min-1 and a Km of 9.8 μM, representing a catalytic efficiency similar to that of human ferrochelatase. The reason for the acceleration was attributed to Pb2+ binding of the G4 DNA and the catalytic activity of the large Pb2+ ion for this reaction. A ratiometric sensor for Pb2+ was developed by inserting Zn2+ with a detection limit of 23.5 nM Pb2+. This work has established a new DNA-based reaction that can be used for Pb2+ detection, and it also provides a highly efficient new DNAzyme for porphyrin metalation, which might be used for signal production for other biosensors.
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Affiliation(s)
- Dong Peng
- College of Chemistry , Nanchang University , 999 Xuefu Avenue , Nanchang , 330031 Jiangxi , China.,Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Ru-Ping Liang
- College of Chemistry , Nanchang University , 999 Xuefu Avenue , Nanchang , 330031 Jiangxi , China
| | - Jian-Ding Qiu
- College of Chemistry , Nanchang University , 999 Xuefu Avenue , Nanchang , 330031 Jiangxi , China.,Environmental Protection Materials and Equipment Engineering Technology Center of Jiangxi, Department of Materials and Chemical Engineering , Pingxiang University , 211 Pingan North Road , Pingxiang , 337055 Jiangxi , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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15
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Kankia B. Stability Factors of the Parallel Quadruplexes: DNA Versus RNA. J Phys Chem B 2019; 123:1060-1067. [PMID: 30648871 DOI: 10.1021/acs.jpcb.8b11559] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
One of the most stable quadruplexes is formed by the G3T sequence (GGGTGGGTGGGTGGG) that folds into a parallel quadruplex with three G-tetrads and chain-reversal T-loops. For example, in 1 mM K+, it unfolds at 75 °C and at physiological conditions, it unfolds above 100 °C. The RNA analogue, ggguggguggguggg (g3u), which employs exactly same folding topology, demonstrates even higher thermal stability. Here, we performed melting experiments of G3T, g3u, and more than 30 chimeric constructs (G3T with RNA nucleotides at certain positions). Although the g3u quadruplex is 13 °C more stable than G3T, majority of G → g (DNA-for-RNA) substitutions destabilize G3T. Only three G → g and loop T → u substitutions stabilize the structure. However, stabilization effects of these six substitutions overcome destabilization of other nine G → g, resulting in higher stability of all-RNA g3u. The present work clearly indicates that the stacking interactions are more favorable in parallel DNA quadruplexes, whereas the chain-reversal loops play an important role in higher stability of RNA quadruplexes. In addition, we have shown that the 5'-end of RNA quadruplexes represents a more favorable target for stacking interactions than the 3'-end. Based on the current study, rational design of the quadruplexes for particular biotechnological applications and drugs, targeting the quadruplexes, may be envisaged.
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Affiliation(s)
- Besik Kankia
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States.,Institute of Biophysics , Ilia State University , Tbilisi 0162 , Republic of Georgia
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16
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Kankia B. Monomolecular tetrahelix of polyguanine with a strictly defined folding pattern. Sci Rep 2018; 8:10115. [PMID: 29973629 PMCID: PMC6031693 DOI: 10.1038/s41598-018-28572-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 06/25/2018] [Indexed: 11/10/2022] Open
Abstract
The G3TG3TG3TG3 (G3T) sequence folds into a monomolecular quadruplex with all-parallel G3 segments connected to each other by chain-reversal loops. The homopolymer consisting of n number of G3T domains directly conjugated to each other folds into an uninterrupted and unusually stable polymer, tetrahelical monomolecular DNA (tmDNA). It was demonstrated that the tmDNA architecture has strong potential in nanotechnologies as highly programmable building material, high affinity coupler and the driving force for endergonic reactions. Here, we explore capability of analogous DNA sequences (i.e., monomolecular quadruplexes with G2 or G4 segments) to construct tmDNA architecture. The study demonstrates that tmDNA can have only one building pattern based on a quadruplex domain with three G-tetrads and single-nucleotide loops, G3N (N = G, A, C and T); all other domains demonstrate antiparallel topologies unsuitable for tmDNA. The present study also suggests that polyguanine is capable of tmDNA formation with strictly defined building pattern; G3 segments connected to each other by chain-reversal G-loops. These findings can have significant impact on (i) DNA nanotechnologies; (ii) structure prediction of G-rich sequences of genome; and (iii) modeling of abiogenesis.
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Affiliation(s)
- Besik Kankia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA.
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17
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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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Lomidze L, Kelley S, Gogichaishvili S, Metreveli N, Musier-Forsyth K, Kankia B. Sr(2+) induces unusually stable d(GGGTGGGTGGGTGGG) quadruplex dimers. Biopolymers 2017; 105:811-8. [PMID: 27416320 DOI: 10.1002/bip.22916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 02/03/2023]
Abstract
Guanine-rich sequences are able to form quadruplexes consisting of G-quartet structural units. Quadruplexes play an important role in the regulation of gene expression and have therapeutic and biotechnological potential. The HIV-1 integrase inhibitor, (GGGT)4 , and its variants demonstrate unusually high thermal stability. This property has been exploited in the use of quadruplex formation to drive various endergonic reactions of nucleic acids such as isothermal DNA amplification. Quadruplex stability is mainly determined by cations, which specifically bind into the inner core of the structure. In the present work, we report a systematic study of a variant of the HIV-1 integrase inhibitor, GGGTGGGTGGGTGGG (G3T), in the presence of alkali and alkaline-earth cations. We show that Sr(2+) -G3T is characterized by the highest thermal stability and that quadruplex formation requires only one Sr(2+) ion that binds with low micromolar affinity. These concentrations are sufficient to drive robust isothermal quadruplex priming DNA amplification reaction. The Sr(2+) -quadruplexes are also able to form unusually stable dimers through end-to-end stacking. The multimerization can be induced by a combination of quadruplex forming cations (i.e., K(+) or Sr(2+) ) and non-specific Mg(2+) .
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Affiliation(s)
- Levan Lomidze
- Institute of Biophysics, Ilia State University, Tbilisi, 0162, Republic of Georgia
| | - Sean Kelley
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, 43210
| | - Shota Gogichaishvili
- Institute of Biophysics, Ilia State University, Tbilisi, 0162, Republic of Georgia
| | - Nunu Metreveli
- Institute of Biophysics, Ilia State University, Tbilisi, 0162, Republic of Georgia
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, 43210
| | - Besik Kankia
- Institute of Biophysics, Ilia State University, Tbilisi, 0162, Republic of Georgia.,Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, 43210
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