1
|
Lee Y, Nam K, Kim YM, Yang K, Kim Y, Oh JW, Roh YH. Functional polymeric DNA nanostructure-decorated cellulose nanocrystals for targeted and stimuli-responsive drug delivery. Carbohydr Polym 2024; 340:122270. [PMID: 38858000 DOI: 10.1016/j.carbpol.2024.122270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/20/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024]
Abstract
Targeted and stimuli-responsive drug delivery enhances therapeutic efficacy and minimizes undesirable side effects of cancer treatment. Although cellulose nanocrystals (CNCs) are used as drug carriers because of their robustness, spindle shape, biocompatibility, renewability, and nontoxicity, the lack of programmability and functionality of CNCs-based platforms hampers their application. Thus, high adaptability and the capacity to form dynamic 3D nanostructures of DNA may be advantageous, as they can provide functionalities such as target-specific and stimuli-responsive drug release. Using DNA nanotechnology, the functional polymeric form of DNA nanostructures can be replicated using rolling circle amplification (RCA), and the biologically and physiologically stable DNA nanostructures may overcome the challenges of CNCs. In this study, multifunctional polymeric DNAs produced with RCA were strongly complexed with surface-modified CNCs via electrostatic interactions to form polymeric DNA-decorated CNCs (pDCs). Particle size, polydispersity, zeta potential, and biostability of the nanocomplexes were analyzed. As a proof of concept, the dynamic structural functionalities of DNA nanostructures were verified by observing cancer-targeted intracellular delivery and pH-responsive drug release. pDCs showed anticancer properties without side effects in vitro, owing to their aptamer and i-motif functionalities. In conclusion, pDCs exhibited multifunctional anticancer activities, demonstrating their potential as a promising hybrid nanocomplex platform for targeted cancer therapy.
Collapse
Affiliation(s)
- Yuyeon Lee
- Graduate Program in Bioindustrial Engineering, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Keonwook Nam
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Young Min Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Kyungjik Yang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Yeongmok Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Jong-Won Oh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Young Hoon Roh
- Graduate Program in Bioindustrial Engineering, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea; Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea.
| |
Collapse
|
2
|
Guneri D, Alexandrou E, El Omari K, Dvořáková Z, Chikhale RV, Pike DTS, Waudby CA, Morris CJ, Haider S, Parkinson GN, Waller ZAE. Structural insights into i-motif DNA structures in sequences from the insulin-linked polymorphic region. Nat Commun 2024; 15:7119. [PMID: 39164244 PMCID: PMC11336075 DOI: 10.1038/s41467-024-50553-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/12/2024] [Indexed: 08/22/2024] Open
Abstract
The insulin-linked polymorphic region is a variable number of tandem repeats region of DNA in the promoter of the insulin gene that regulates transcription of insulin. This region is known to form the alternative DNA structures, i-motifs and G-quadruplexes. Individuals have different sequence variants of tandem repeats and although previous work investigated the effects of some variants on G-quadruplex formation, there is not a clear picture of the relationship between the sequence diversity, the DNA structures formed, and the functional effects on insulin gene expression. Here we show that different sequence variants of the insulin linked polymorphic region form different DNA structures in vitro. Additionally, reporter genes in cellulo indicate that insulin expression may change depending on which DNA structures form. We report the crystal structure and dynamics of an intramolecular i-motif, which reveal sequences within the loop regions forming additional stabilising interactions that are critical to formation of stable i-motif structures. The outcomes of this work reveal the detail in formation of stable i-motif DNA structures, with potential for rational based drug design for compounds to target i-motif DNA.
Collapse
Affiliation(s)
- Dilek Guneri
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Effrosyni Alexandrou
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, OX11 0DE, UK
| | - Zuzana Dvořáková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00, Brno, Czech Republic
| | - Rupesh V Chikhale
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Daniel T S Pike
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Christopher A Waudby
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Christopher J Morris
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
| | - Shozeb Haider
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
- UCL Centre for Advanced Research Computing, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Gary N Parkinson
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
| | - Zoë A E Waller
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
| |
Collapse
|
3
|
Mir B, Serrano-Chacón I, Medina P, Macaluso V, Terrazas M, Gandioso A, Garavís M, Orozco M, Escaja N, González C. Site-specific incorporation of a fluorescent nucleobase analog enhances i-motif stability and allows monitoring of i-motif folding inside cells. Nucleic Acids Res 2024; 52:3375-3389. [PMID: 38366792 PMCID: PMC11014255 DOI: 10.1093/nar/gkae106] [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: 04/28/2023] [Revised: 01/17/2024] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Abstract
The i-motif is an intriguing non-canonical DNA structure, whose role in the cell is still controversial. Development of methods to study i-motif formation under physiological conditions in living cells is necessary to study its potential biological functions. The cytosine analog 1,3-diaza-2-oxophenoxazine (tCO) is a fluorescent nucleobase able to form either hemiprotonated base pairs with cytosine residues, or neutral base pairs with guanines. We show here that when tCO is incorporated in the proximity of a G:C:G:C minor groove tetrad, it induces a strong thermal and pH stabilization, resulting in i-motifs with Tm of 39ºC at neutral pH. The structural determination by NMR methods reveals that the enhanced stability is due to a large stacking interaction between the guanines of the tetrad with the tCO nucleobase, which forms a tCO:C+ in the folded structure at unusually-high pHs, leading to an increased quenching in its fluorescence at neutral conditions. This quenching is much lower when tCO is base-paired to guanines and totally disappears when the oligonucleotide is unfolded. By taking profit of this property, we have been able to monitor i-motif folding in cells.
Collapse
Affiliation(s)
- Bartomeu Mir
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
- Inorganic and Organic Chemistry Department. Organic Chemistry Section and IBUB. University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona. Spain
| | - Israel Serrano-Chacón
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
| | - Pedro Medina
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
- Departament de Bioquímica i Biomedicina. Facultat de Biologia. Universitat de Barcelona. 08028 Barcelona. Spain
| | - Veronica Macaluso
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
| | - Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
- Inorganic and Organic Chemistry Department. Organic Chemistry Section and IBUB. University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona. Spain
| | - Albert Gandioso
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
| | - Miguel Garavís
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
- Departament de Bioquímica i Biomedicina. Facultat de Biologia. Universitat de Barcelona. 08028 Barcelona. Spain
| | - Núria Escaja
- Inorganic and Organic Chemistry Department. Organic Chemistry Section and IBUB. University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona. Spain
| | - Carlos González
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
| |
Collapse
|
4
|
Trajkovski M, Pastore A, Plavec J. Dimeric structures of DNA ATTTC repeats promoted by divalent cations. Nucleic Acids Res 2024; 52:1591-1601. [PMID: 38296828 PMCID: PMC10899783 DOI: 10.1093/nar/gkae052] [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: 10/26/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 02/02/2024] Open
Abstract
Structural studies of repetitive DNA sequences may provide insights why and how certain repeat instabilities in their number and nucleotide sequence are managed or even required for normal cell physiology, while genomic variability associated with repeat expansions may also be disease-causing. The pentanucleotide ATTTC repeats occur in hundreds of genes important for various cellular processes, while their insertion and expansion in noncoding regions are associated with neurodegeneration, particularly with subtypes of spinocerebellar ataxia and familial adult myoclonic epilepsy. We describe a new striking domain-swapped DNA-DNA interaction triggered by the addition of divalent cations, including Mg2+ and Ca2+. The results of NMR characterization of d(ATTTC)3 in solution show that the oligonucleotide folds into a novel 3D architecture with two central C:C+ base pairs sandwiched between a couple of T:T base pairs. This structural element, referred to here as the TCCTzip, is characterized by intercalative hydrogen-bonding, while the nucleobase moieties are poorly stacked. The 5'- and 3'-ends of TCCTzip motif are connected by stem-loop segments characterized by A:T base pairs and stacking interactions. Insights embodied in the non-canonical DNA structure are expected to advance our understanding of why only certain pyrimidine-rich DNA repeats appear to be pathogenic, while others can occur in the human genome without any harmful consequences.
Collapse
Affiliation(s)
- Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Annalisa Pastore
- King's College London, the Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
- EN-FIST, Center of Excellence, 1000 Ljubljana, Slovenia
| |
Collapse
|
5
|
Wang X, Yu B, Sakurabayashi S, Paz-Villatoro JM, Iwahara J. Robust Enzymatic Production of DNA G-Quadruplex, Aptamer, DNAzyme, and Other Oligonucleotides: Applications for NMR. J Am Chem Soc 2024; 146:1748-1752. [PMID: 38191993 PMCID: PMC10926321 DOI: 10.1021/jacs.3c11219] [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] [Indexed: 01/10/2024]
Abstract
Single-stranded DNA (ssDNA) oligonucleotides are widely used in biological research, therapeutics, biotechnology, and nanomachines. Large-scale enzymatic production of ssDNA oligonucleotides forming noncanonical structures has been difficult. Here, we present a simple and robust method named "palindrome-nicking-dependent amplification" (PaNDA) for enzymatic production of a large amount of ssDNA oligonucleotides. It utilizes a strand-displacing DNA polymerase and a nicking enzyme together with input DNA and deoxynucleotide triphosphates at 55 °C. Scaling up of PaNDA is straightforward due to its isothermal nature. The ssDNA products can easily be isolated through anion-exchange chromatography under nondenaturing conditions. We demonstrate applications of PaNDA to 13C/15N-labeling of various DNA strands, including a 22-nt telomere repeat G-quadruplex, a 26-nt therapeutic aptamer, and a 33-nt DNAzyme. The 13C/15N-labeling by PaNDA greatly facilitates the characterization of noncanonical DNA by nuclear magnetic resonance (NMR) spectroscopy. For example, the behavior of therapeutic DNA aptamers in human serum can be investigated.
Collapse
Affiliation(s)
- Xi Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Shuhei Sakurabayashi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Jonathan M Paz-Villatoro
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| |
Collapse
|
6
|
Sengupta P, Jamroskovic J, Sabouri N. A beginner's handbook to identify and characterize i-motif DNA. Methods Enzymol 2023; 695:45-70. [PMID: 38521590 DOI: 10.1016/bs.mie.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
Genomic DNA exhibits an innate ability to manifest diverse sequence-dependent secondary structures, serving crucial functions in gene regulation and cellular equilibrium. While extensive research has confirmed the formation of G-quadruplex structures by guanine-rich sequences in vitro and in cells, recent investigations have turned the quadruplex community's attention to the cytosine (C)-rich complementary strands that can adopt unique tetra-stranded conformation, termed as intercalated motif or i-motif. I-motifs are stabilized by hemi-protonated C:CH+ base pairs under acidic conditions. Initially, the in vivo occurrence of i-motifs was underestimated because their formation is favored at non-physiological pH. However, groundbreaking research utilizing the structure-specific iMab antibody and high-throughput sequencing have recently detected their conserved dispersion throughout the genome, challenging previous assumptions. Given the evolving nature of this research field, it becomes imperative to conduct independent in vitro experiments aimed at identifying potential i-motif formation in C-rich sequences and consolidating the findings to address the properties of i-motifs. This chapter serves as an introductory guide for the swift identification of novel i-motifs, where we present an experimental framework for investigating and characterizing i-motif sequences in vitro. In this chapter, we selected a synthetic oligonucleotide (C7T3) sequence and outlined appropriate methodologies for annealing the i-motif structure into suitable buffers. Then, we validated its formation by CD (Circular Dichroism) and NMR (Nuclear Magnetic Resonance) spectroscopy. Finally, we provided a thorough account of the step-by-step procedures to investigate the effect of i-motif formation on the stalling or retardation of DNA replication using high resolution primer extension assays.
Collapse
Affiliation(s)
- Pallabi Sengupta
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
| |
Collapse
|
7
|
Ghezzo M, Trajkovski M, Plavec J, Sissi C. A Screening Protocol for Exploring Loop Length Requirements for the Formation of a Three Cytosine-Cytosine + Base-Paired i-Motif. Angew Chem Int Ed Engl 2023; 62:e202309327. [PMID: 37611164 DOI: 10.1002/anie.202309327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 08/25/2023]
Abstract
DNA sequences containing at least four runs of repetitive cytosines can fold into tetra-helical structures called i-Motifs (iMs). The interest in these DNA secondary structures is increasing due to their therapeutical and technological applications. Still, limited knowledge of their folding requirements is currently available. We developed a novel step-by-step pipeline for the systematic screening of putative iM-forming model sequences. Focusing on structures comprising only three cytosine-cytosine+ base pairs, we investigated what the minimal lengths of the loops required for formation of an intra-molecular iM are. Our data indicate that two and three nucleotides are required to connect the strands through the minor and majorgrooves of the iM, respectively. Additionally, they highlight an asymmetric behavior according to the distribution of the cytosines. Specifically, no sequence containing a single cytosine in the first and third run was able to fold into intra-molecular iMs with the same stability of those formed when the first and the third run comprise two cytosines. This knowledge represents a step forward toward the development of prediction tools for the proper identification of biologically functional iMs, as well as for the rational design of these secondary structures as technological devices.
Collapse
Affiliation(s)
- Michele Ghezzo
- Department of Pharmaceutical and Pharmacological Science, University of Padua, Via Marzolo 5, 35131, Padua, Italy
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Science, University of Padua, Via Marzolo 5, 35131, Padua, Italy
| |
Collapse
|
8
|
Li KS, Jordan D, Lin LY, McCarthy SE, Schneekloth JS, Yatsunyk LA. Crystal Structure of an i-Motif from the HRAS Oncogene Promoter. Angew Chem Int Ed Engl 2023; 62:e202301666. [PMID: 36995904 PMCID: PMC10330059 DOI: 10.1002/anie.202301666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/22/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023]
Abstract
An i-motif is a non-canonical DNA structure implicated in gene regulation and linked to cancers. The C-rich strand of the HRAS oncogene, 5'-CGCCCGTGCCCTGCGCCCGCAACCCGA-3' (herein referred to as iHRAS), forms an i-motif in vitro but its exact structure was unknown. HRAS is a member of the RAS proto-oncogene family. About 19 % of US cancer patients carry mutations in RAS genes. We solved the structure of iHRAS at 1.77 Å resolution. The structure reveals that iHRAS folds into a double hairpin. The two double hairpins associate in an antiparallel fashion, forming an i-motif dimer capped by two loops on each end and linked by a connecting region. Six C-C+ base pairs form each i-motif core, and the core regions are extended by a G-G base pair and a cytosine stacking. Extensive canonical and non-canonical base pairing and stacking stabilizes the connecting region and loops. The iHRAS structure is the first atomic resolution structure of an i-motif from a human oncogene. This structure sheds light on i-motifs folding and function in the cell.
Collapse
Affiliation(s)
- Kevin S Li
- Department Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Deondre Jordan
- Department Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Linda Y Lin
- Department Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Sawyer E McCarthy
- Department Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, National Institute of Health, Frederick, MD 21702, USA
| | - Liliya A Yatsunyk
- Department Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| |
Collapse
|
9
|
Rodriguez J, Domínguez A, Aviñó A, Borgonovo G, Eritja R, Mazzini S, Gargallo R. Exploring the stabilizing effect on the i-motif of neighboring structural motifs and drugs. Int J Biol Macromol 2023; 242:124794. [PMID: 37182626 DOI: 10.1016/j.ijbiomac.2023.124794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/16/2023]
Abstract
Cytosine-rich DNA sequences may fold into a structure known as i-motif, with potential in vivo modulation of gene expression. The stability of the i-motif is residual at neutral pH values. To increase it, the addition of neighboring moieties, such as Watson-Crick stabilized loops, tetrads, or non-canonical base pairs have been proposed. Taking a recently described i-motif structure as a model, the relative effect of these structural moieties, as well as several DNA ligands, on the stabilization of the i-motif has been studied. To this end, not only the original sequence but different mutants were considered. Spectroscopic techniques, PAGE, and multivariate data analysis methods have been used to model the folding/unfolding equilibria induced by changes of pH, temperature, and the presence of ligands. The results have shown that the duplex is the moiety that is responsible of the stabilization of the i-motif structure at neutral pH. The T:T base pair, on the contrary, shows little stabilization of the i-motif. From several selected DNA-binding ligands, the G-quadruplex ligand BA41 is shown to interact with the duplex moiety, whereas non-specific interaction and little stabilization has been observed within the i-motif.
Collapse
Affiliation(s)
- Judit Rodriguez
- Department of Chemical Engineering and Analytical Chemistry, Faculty of Chemistry, University of Barcelona, Marti i Franqués 1-11, E-08028 Barcelona, Spain
| | - Arnau Domínguez
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Gigliola Borgonovo
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan (Università degli Studi di Milano), Milan, Italy
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan (Università degli Studi di Milano), Milan, Italy
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, Faculty of Chemistry, University of Barcelona, Marti i Franqués 1-11, E-08028 Barcelona, Spain.
| |
Collapse
|
10
|
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
|
11
|
Serrano-Chacón I, Mir B, Cupellini L, Colizzi F, Orozco M, Escaja N, González C. pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs. J Am Chem Soc 2023; 145:3696-3705. [PMID: 36745195 PMCID: PMC9936585 DOI: 10.1021/jacs.2c13043] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Indexed: 02/07/2023]
Abstract
We study here a DNA oligonucleotide having the ability to form two different i-motif structures whose relative stability depends on pH and temperature. The major species at neutral pH is stabilized by two C:C+ base pairs capped by two minor groove G:C:G:C tetrads. The high pH and thermal stability of this structure are mainly due to the favorable effect of the minor groove tetrads on their adjacent positively charged C:C+ base pairs. At pH 5, we observe a more elongated i-motif structure consisting of four C:C+ base pairs capped by two G:T:G:T tetrads. Molecular dynamics calculations show that the conformational transition between the two structures is driven by the protonation state of key cytosines. In spite of large conformational differences, the transition between the acidic and neutral structures can occur without unfolding of the i-motif. These results represent the first case of a conformational switch between two different i-motif structures and illustrate the dramatic pH-dependent plasticity of this fascinating DNA motif.
Collapse
Affiliation(s)
- Israel Serrano-Chacón
- Instituto
de Química Física ”Rocasolano”, CSIC, Serrano 119, 28006Madrid, Spain
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028Barcelona, Spain
| | - Bartomeu Mir
- Instituto
de Química Física ”Rocasolano”, CSIC, Serrano 119, 28006Madrid, Spain
- Inorganic
and Organic Chemistry Department, Organic Chemistry Section, and IBUB, University of Barcelona, Martí i Franquès 1-11, 08028Barcelona, Spain
| | - Lorenzo Cupellini
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028Barcelona, Spain
| | - Francesco Colizzi
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028Barcelona, Spain
| | - Modesto Orozco
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028Barcelona, Spain
- Departament
de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona, 08028Barcelona, Spain
| | - Núria Escaja
- Inorganic
and Organic Chemistry Department, Organic Chemistry Section, and IBUB, University of Barcelona, Martí i Franquès 1-11, 08028Barcelona, Spain
- BIOESTRAN
Associated Unit UB-CSIC, 08028Barcelona, Spain
| | - Carlos González
- Instituto
de Química Física ”Rocasolano”, CSIC, Serrano 119, 28006Madrid, Spain
- BIOESTRAN
Associated Unit UB-CSIC, 08028Barcelona, Spain
| |
Collapse
|
12
|
Yang M, Bakker D, Raghu D, Li ITS. A single strand: A simplified approach to DNA origami. Front Chem 2023; 11:1126177. [PMID: 36891219 PMCID: PMC9986268 DOI: 10.3389/fchem.2023.1126177] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
Just as a single polypeptide strand can self-fold into a complex 3D structure, a single strand of DNA can self-fold into DNA origami. Most DNA origami structures (i.e., the scaffold-staple and DNA tiling systems) utilize hundreds of short single-stranded DNA. As such, these structures come with challenges inherent to intermolecular construction. Many assembly challenges involving intermolecular interactions can be resolved if the origami structure is constructed from one DNA strand, where folding is not concentration dependent, the folded structure is more resistant to nuclease degradation, and the synthesis can be achieved at an industrial scale at a thousandth of the cost. This review discusses the design principles and considerations employed in single-stranded DNA origami and its potential benefits and drawbacks.
Collapse
Affiliation(s)
- Micah Yang
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
| | - David Bakker
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
| | - Dyuti Raghu
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
| | - Isaac T S Li
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
| |
Collapse
|
13
|
Bansal A, Kaushik S, Kukreti S. Non-canonical DNA structures: Diversity and disease association. Front Genet 2022; 13:959258. [PMID: 36134025 PMCID: PMC9483843 DOI: 10.3389/fgene.2022.959258] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
A complete understanding of DNA double-helical structure discovered by James Watson and Francis Crick in 1953, unveil the importance and significance of DNA. For the last seven decades, this has been a leading light in the course of the development of modern biology and biomedical science. Apart from the predominant B-form, experimental shreds of evidence have revealed the existence of a sequence-dependent structural diversity, unusual non-canonical structures like hairpin, cruciform, Z-DNA, multistranded structures such as DNA triplex, G-quadruplex, i-motif forms, etc. The diversity in the DNA structure depends on various factors such as base sequence, ions, superhelical stress, and ligands. In response to these various factors, the polymorphism of DNA regulates various genes via different processes like replication, transcription, translation, and recombination. However, altered levels of gene expression are associated with many human genetic diseases including neurological disorders and cancer. These non-B-DNA structures are expected to play a key role in determining genetic stability, DNA damage and repair etc. The present review is a modest attempt to summarize the available literature, illustrating the occurrence of non-canonical structures at the molecular level in response to the environment and interaction with ligands and proteins. This would provide an insight to understand the biological functions of these unusual DNA structures and their recognition as potential therapeutic targets for diverse genetic diseases.
Collapse
Affiliation(s)
- Aparna Bansal
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Shikha Kaushik
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Rajdhani College, University of Delhi, New Delhi, India
| | - Shrikant Kukreti
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- *Correspondence: Shrikant Kukreti,
| |
Collapse
|
14
|
Escaja N, Mir B, Garavís M, González C. Non-G Base Tetrads. Molecules 2022; 27:5287. [PMID: 36014524 PMCID: PMC9414646 DOI: 10.3390/molecules27165287] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/03/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
Tetrads (or quartets) are arrangements of four nucleobases commonly involved in the stability of four-stranded nucleic acids structures. Four-stranded or quadruplex structures have attracted enormous attention in the last few years, being the most extensively studied guanine quadruplex (G-quadruplex). Consequently, the G-tetrad is the most common and well-known tetrad. However, this is not the only possible arrangement of four nucleobases. A number of tetrads formed by the different nucleobases have been observed in experimental structures. In most cases, these tetrads occur in the context of G-quadruplex structures, either inserted between G-quartets, or as capping elements at the sides of the G-quadruplex core. In other cases, however, non-G tetrads are found in more unusual four stranded structures, such as i-motifs, or different types of peculiar fold-back structures. In this report, we review the diversity of these non-canonical tetrads, and the structural context in which they have been found.
Collapse
Affiliation(s)
- Núria Escaja
- Organic Chemistry Section, Inorganic and Organic Chemistry Department, University of Barcelona, Martí i Franquès 1–11, 08028 Barcelona, Spain
- Institute of Biomedicine, University of Barcelona, Av. Diagonal 645, 08028 Barcelona, Spain
| | - Bartomeu Mir
- Organic Chemistry Section, Inorganic and Organic Chemistry Department, University of Barcelona, Martí i Franquès 1–11, 08028 Barcelona, Spain
- Institute of Biomedicine, University of Barcelona, Av. Diagonal 645, 08028 Barcelona, Spain
| | - Miguel Garavís
- Instituto de Química Física ‘Rocasolano’, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Carlos González
- Instituto de Química Física ‘Rocasolano’, CSIC, Serrano 119, 28006 Madrid, Spain
| |
Collapse
|
15
|
Greco F, Marzano M, Falanga AP, Terracciano M, Piccialli G, Roviello GN, D'Errico S, Borbone N, Oliviero G. Cytosine-rich oligonucleotides incorporating a non-nucleotide loop: A further step towards the obtainment of physiologically stable i-motif DNA. Int J Biol Macromol 2022; 219:626-636. [PMID: 35952813 DOI: 10.1016/j.ijbiomac.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 08/02/2022] [Indexed: 11/05/2022]
Abstract
i-Motifs, also known as i-tetraplexes, are secondary structures of DNA occurring in cytosine-rich oligonucleotides (CROs) that recall increasing interest in the scientific community for their relevance in various biological processes and DNA nanotechnology. This study reports the design of new structurally modified CROs, named Double-Ended-Linker-CROs (DEL-CROs), capable of forming stable i-motif structures. Here, two C-rich strands having sequences d(AC4A) and d(C6) have been attached, in a parallel fashion, to the two linker's edges by their 3' or 5' ends. The resulting DEL-CROs have been investigated for their capability to form i-motif structures by circular dichroism, poly-acrylamide gel electrophoresis, HPLC-size-exclusion chromatography, and NMR studies. This investigation established that DEL-CROs could form more stable i-motif structures than the corresponding unmodified CROs. In particular, the i-motif formed by DEL-5'-d(C6)2 resulted stable enough to be detected even at near physiological conditions (37 °C, pH 7.0). The results open the way to developing pH-switchable nanocarriers and aptamers based on suitably functionalized DEL-CROs.
Collapse
Affiliation(s)
- Francesca Greco
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Maria Marzano
- Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Andrea Patrizia Falanga
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Monica Terracciano
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy
| | - Giovanni Nicola Roviello
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy; ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy.
| | - Giorgia Oliviero
- ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via Sergio Pansini 5, 80131 Napoli, Italy
| |
Collapse
|
16
|
Hu D, Wu D, Lu Y, Liu J, Guo Z, Wang S, Zhai C, Qing Z, Hu Y. Protonation-induced DNA conformational-change dominated electrochemical platform for glucose oxidase and urease analysis. Anal Chim Acta 2022; 1226:340164. [DOI: 10.1016/j.aca.2022.340164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 06/16/2022] [Accepted: 07/09/2022] [Indexed: 11/26/2022]
|
17
|
Novotný A, Novotný J, Kejnovská I, Vorlíčková M, Fiala R, Marek R. Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip. Nucleic Acids Res 2021; 49:11425-11437. [PMID: 34718718 PMCID: PMC8599794 DOI: 10.1093/nar/gkab915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 09/17/2021] [Accepted: 09/27/2021] [Indexed: 11/12/2022] Open
Abstract
Non-canonical forms of nucleic acids represent challenging objects for both structure-determination and investigation of their potential role in living systems. In this work, we uncover a structure adopted by GA repetition locked in a parallel homoduplex by an i-motif. A series of DNA oligonucleotides comprising GAGA segment and C3 clip is analyzed by NMR and CD spectroscopies to understand the sequence-structure-stability relationships. We demonstrate how the relative position of the homopurine GAGA segment and the C3 clip as well as single-base mutations (guanine deamination and cytosine methylation) affect base pairing arrangement of purines, i-motif topology and overall stability. We focus on oligonucleotides C3GAGA and methylated GAGAC3 exhibiting the highest stability and structural uniformity which allowed determination of high-resolution structures further analyzed by unbiased molecular dynamics simulation. We describe sequence-specific supramolecular interactions on the junction between homoduplex and i-motif blocks that contribute to the overall stability of the structures. The results show that the distinct structural motifs can not only coexist in the tight neighborhood within the same molecule but even mutually support their formation. Our findings are expected to have general validity and could serve as guides in future structure and stability investigations of nucleic acids.
Collapse
Affiliation(s)
- Aleš Novotný
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia
| | - Jan Novotný
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia
| | - Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65 Brno, Czechia
| | - Michaela Vorlíčková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-612 65 Brno, Czechia
| | - Radovan Fiala
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia
| | - Radek Marek
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia
| |
Collapse
|
18
|
Ruiz N, Jarosova P, Taborsky P, Gargallo R. Study of the interaction of the palmatine alkaloid with hybrid G-quadruplex/duplex and i-motif/duplex DNA structures. Biophys Chem 2021; 281:106715. [PMID: 34784553 DOI: 10.1016/j.bpc.2021.106715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/22/2021] [Accepted: 11/04/2021] [Indexed: 11/19/2022]
Abstract
There is an increasing interest in the study of guanine or cytosine-rich sequences that may fold into G-quadruplex (G4) or i-motif (iM) structures showing a short hairpin (or stem-loop) stabilized by Watson-Crick base pairs. These hybrid spatial arrangements may be target of ligands that have been shown to interact strongly with B-DNA. In this work, the interaction of the palmatine alkaloid with several sequences forming different G4s, iMs, and hybrid structures has been studied by means of spectroscopic and separation techniques, as well as multivariate data analysis methods. At the experimental conditions used in this work, the results have shown that this ligand strongly stabilizes parallel G4 structures, whereas a weaker interaction was observed with the antiparallel G4 adopted by the thrombin-binding aptamer or iMs. The presence of hairpins within the loops scarcely affects the affinity of this ligand for the hybrid G4/duplex or iM/duplex structures. Fluorescence measurements have provided evidence of a certain interaction with iMs at pH 5.1, despite the absence of thermal stabilization effects.
Collapse
Affiliation(s)
- Noelia Ruiz
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí I Franqués 1-11, E-08028 Barcelona, Spain
| | - Petra Jarosova
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Petr Taborsky
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí I Franqués 1-11, E-08028 Barcelona, Spain.
| |
Collapse
|