1
|
Shiekh S, Kodikara SG, Balci H. Structure, Topology, and Stability of Multiple G-quadruplexes in Long Telomeric Overhangs. J Mol Biol 2024; 436:168205. [PMID: 37481156 PMCID: PMC10799177 DOI: 10.1016/j.jmb.2023.168205] [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: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Telomeres and their single stranded overhangs gradually shorten with successive cell divisions, as part of the natural aging process, but can be elongated by telomerase, a nucleoprotein complex which is activated in the majority of cancers. This prominent implication in cancer and aging has made the repetitive telomeric sequences (TTAGGG repeats) and the G-quadruplex structures that form in their overhangs the focus of intense research in the past several decades. However, until recently most in vitro efforts to understand the structure, stability, dynamics, and interactions of telomeric overhangs had been focused on short sequences that are not representative of longer sequences encountered in a physiological setting. In this review, we will provide a broad perspective about telomeres and associated factors, and introduce the agents and structural characteristics involved in organizing, maintaining, and protecting telomeric DNA. We will also present a summary of recent research performed on long telomeric sequences, nominally defined as those that can form two or more tandem G-quadruplexes, i.e., which contain eight or more TTAGGG repeats. Results of experimental studies using a broad array of experimental tools, in addition to recent computational efforts will be discussed, particularly in terms of their implications for the stability, folding topology, and compactness of the tandem G-quadruplexes that form in long telomeric overhangs.
Collapse
Affiliation(s)
- Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA.
| |
Collapse
|
2
|
Kristoffersen E, Coletta A, Lund L, Schiøtt B, Birkedal V. Inhibited complete folding of consecutive human telomeric G-quadruplexes. Nucleic Acids Res 2023; 51:1571-1582. [PMID: 36715345 PMCID: PMC9976873 DOI: 10.1093/nar/gkad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 12/24/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Noncanonical DNA structures, termed G-quadruplexes, are present in human genomic DNA and are important elements in many DNA metabolic processes. Multiple sites in the human genome have G-rich DNA stretches able to support formation of several consecutive G-quadruplexes. One of those sites is the telomeric overhang region that has multiple repeats of TTAGGG and is tightly associated with both cancer and aging. We investigated the folding of consecutive G-quadruplexes in both potassium- and sodium-containing solutions using single-molecule FRET spectroscopy, circular dichroism, thermal melting and molecular dynamics simulations. Our observations show coexistence of partially and fully folded DNA, the latter consisting of consecutive G-quadruplexes. Following the folding process over hours in sodium-containing buffers revealed fast G-quadruplex folding but slow establishment of thermodynamic equilibrium. We find that full consecutive G-quadruplex formation is inhibited by the many DNA structures randomly nucleating on the DNA, some of which are off-path conformations that need to unfold to allow full folding. Our study allows describing consecutive G-quadruplex formation in both nonequilibrium and equilibrium conditions by a unified picture, where, due to the many possible DNA conformations, full folding with consecutive G-quadruplexes as beads on a string is not necessarily achieved.
Collapse
Affiliation(s)
- Emil Laust Kristoffersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Andrea Coletta
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Line Mørkholt Lund
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Birgit Schiøtt
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | | |
Collapse
|
3
|
Elgar C, Yusoh NA, Tiley PR, Kolozsvári N, Bennett LG, Gamble A, Péan EV, Davies ML, Staples CJ, Ahmad H, Gill MR. Ruthenium(II) Polypyridyl Complexes as FRET Donors: Structure- and Sequence-Selective DNA-Binding and Anticancer Properties. J Am Chem Soc 2023; 145:1236-1246. [PMID: 36607895 PMCID: PMC9853847 DOI: 10.1021/jacs.2c11111] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ruthenium(II) polypyridyl complexes (RPCs) that emit from metal-to-ligand charge transfer (MLCT) states have been developed as DNA probes and are being examined as potential anticancer agents. Here, we report that MLCT-emissive RPCs that bind DNA undergo Förster resonance energy transfer (FRET) with Cy5.5-labeled DNA, forming mega-Stokes shift FRET pairs. Based on this discovery, we developed a simple and rapid FRET binding assay to examine DNA-binding interactions of RPCs with diverse photophysical properties, including non-"light switch" complexes [Ru(dppz)2(5,5'dmb)]2+ and [Ru(PIP)2(5,5'dmb)]2+ (dppz = dipyridophenazine, 5,5'dmb = 5,5'-dimethyl-2,2'-bipyridine, PIP = 2-phenyl-imidazo[4,5-f][1,10]phenanthroline). Binding affinities toward duplex, G-quadruplex, three-way junction, and mismatch DNA were determined, and derived FRET donor-acceptor proximities provide information on potential binding sites. Molecules characterized by this method demonstrate encouraging anticancer properties, including synergy with the PARP inhibitor Olaparib, and mechanistic studies indicate that [Ru(PIP)2(5,5'dmb)]2+ acts to block DNA replication fork progression.
Collapse
Affiliation(s)
- Christopher
E. Elgar
- Department
of Chemistry, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, U.K.
| | - Nur Aininie Yusoh
- UPM-MAKNA
Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Paul R. Tiley
- Department
of Chemistry, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, U.K.
| | - Natália Kolozsvári
- Department
of Chemistry, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, U.K.
| | - Laura G. Bennett
- North
West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor LL57 2DG, U.K.
| | - Amelia Gamble
- North
West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor LL57 2DG, U.K.
| | - Emmanuel V. Péan
- SPECIFIC
IKC, Materials Science and Engineering, Faculty of Science and Engineering, Swansea University, Swansea SA1 8EN, U.K.
| | - Matthew L. Davies
- SPECIFIC
IKC, Materials Science and Engineering, Faculty of Science and Engineering, Swansea University, Swansea SA1 8EN, U.K.
| | - Christopher J. Staples
- North
West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor LL57 2DG, U.K.
| | - Haslina Ahmad
- UPM-MAKNA
Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia,Department
of Chemistry, Faculty of Science, Universiti
Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Martin R. Gill
- Department
of Chemistry, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, U.K.,
| |
Collapse
|
4
|
Vinayagamurthy S, Bagri S, Mergny JL, Chowdhury S. Telomeres expand sphere of influence: emerging molecular impact of telomeres in non-telomeric functions. Trends Genet 2023; 39:59-73. [PMID: 36404192 PMCID: PMC7614491 DOI: 10.1016/j.tig.2022.10.002] [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: 06/05/2022] [Revised: 09/12/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022]
Abstract
Although the impact of telomeres on physiology stands well established, a question remains: how do telomeres impact cellular functions at a molecular level? This is because current understanding limits the influence of telomeres to adjacent subtelomeric regions despite the wide-ranging impact of telomeres. Emerging work in two distinct aspects offers opportunities to bridge this gap. First, telomere-binding factors were found with non-telomeric functions. Second, locally induced DNA secondary structures called G-quadruplexes are notably abundant in telomeres, and gene regulatory regions genome wide. Many telomeric factors bind to G-quadruplexes for non-telomeric functions. Here we discuss a more general model of how telomeres impact the non-telomeric genome - through factors that associate at telomeres and genome wide - and influence cell-intrinsic functions, particularly aging, cancer, and pluripotency.
Collapse
Affiliation(s)
- Soujanya Vinayagamurthy
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sulochana Bagri
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jean-Louis Mergny
- Institute of Biophysics of the CAS, v.v.i. Královopolská 135, 612 65 Brno, Czech Republic; Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; GNR Knowledge Centre for Genome and Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India.
| |
Collapse
|
5
|
Abstract
We present single-molecule experimental and computational modeling studies investigating the accessibility of human telomeric overhangs of physiologically relevant lengths. We studied 25 different overhangs that contain 4-28 repeats of GGGTTA (G-Tract) sequence and accommodate one to seven tandem G-quadruplex (GQ) structures. Using the FRET-PAINT method, we probed the distribution of accessible sites via a short imager strand, which is complementary to a G-Tract and transiently binds to available sites. We report accessibility patterns that periodically change with overhang length and interpret these patterns in terms of the underlying folding landscape and folding frustration. Overhangs that have [4n]G-Tracts, (12, 16, 20…) demonstrate the broadest accessibility patterns where the peptide nucleic acid probe accesses G-Tracts throughout the overhang. On the other hand, constructs with [4n+2]G-Tracts, (14, 18, 22…) have narrower patterns where the neighborhood of the junction between single- and double-stranded telomeres is most accessible. We interpret these results as the folding frustration being higher in [4n]G-Tract constructs compared to [4n+2]G-Tract constructs. We also developed a computational model that tests the consistency of different folding stabilities and cooperativities between neighboring GQs with the observed accessibility patterns. Our experimental and computational studies suggest the neighborhood of the junction between single- and double-stranded telomeres is least stable and most accessible, which is significant as this is a potential site where the connection between POT1/TPP1 (bound to single-stranded telomere) and other shelterin proteins (localized on double-stranded telomere) is established.
Collapse
|
6
|
Marquevielle J, De Rache A, Vialet B, Morvan E, Mergny JL, Amrane S. G-quadruplex structure of the C. elegans telomeric repeat: a two tetrads basket type conformation stabilized by a non-canonical C-T base-pair. Nucleic Acids Res 2022; 50:7134-7146. [PMID: 35736226 PMCID: PMC9262591 DOI: 10.1093/nar/gkac523] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 05/07/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022] Open
Abstract
The Caenorhabditis elegans model has greatly contributed to the understanding of the role of G-quadruplexes in genomic instability. The GGCTTA repeats of the C. elegans telomeres resemble the GGGTTA repeats of the human telomeres. However, the comparison of telomeric sequences (Homo sapiens, Tetrahymena, Oxytricha, Bombyx mori and Giardia) revealed that small changes in these repeats can drastically change the topology of the folded G-quadruplex. In the present work we determined the structure adopted by the C. elegans telomeric sequence d[GG(CTTAGG)3]. The investigated C. elegans telomeric sequence is shown to fold into an intramolecular two G-tetrads basket type G-quadruplex structure that includes a C-T base pair in the diagonal loop. This work sheds light on the telomeric structure of the widely used C. elegans animal model.
Collapse
Affiliation(s)
| | | | - Brune Vialet
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA laboratory, 146 rue Léo Saignat F-33000 Bordeaux, France
| | - Estelle Morvan
- Institut Européen de Chimie et Biologie, UMS 3033 US001, CNRS-Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Jean-Louis Mergny
- Correspondence may also be addressed to Jean-Louis Mergny. Tel: + 33 1 69 33 50 01;
| | - Samir Amrane
- To whom correspondence should be addressed. Tel: +33 5 40 00 22 24;
| |
Collapse
|
7
|
Frasson I, Pirota V, Richter SN, Doria F. Multimeric G-quadruplexes: A review on their biological roles and targeting. Int J Biol Macromol 2022; 204:89-102. [PMID: 35124022 DOI: 10.1016/j.ijbiomac.2022.01.197] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/20/2022] [Accepted: 01/31/2022] [Indexed: 12/12/2022]
Abstract
In human cells, nucleic acids adopt several non-canonical structures that regulate key cellular processes. Among them, G-quadruplexes (G4s) are stable structures that form in guanine-rich regions in vitro and in cells. G4 folded/unfolded state shapes numerous cellular processes, including genome replication, transcription, and translation. Moreover, G4 folding is involved in genomic instability. G4s have been described to multimerize, forming high-order structures in both DNA and/or RNA strands. Multimeric G4s can be formed by adjacent intramolecular G4s joined by stacking interactions or connected by short loops. Multimeric G4s can also originate from the assembly of guanines embedded on independent DNA or RNA strands. Notably, crucial regions of the human genome, such as the 3'-terminal overhang of the telomeric DNA as well as the open reading frame of genes involved in the preservation of neuron viability in the human central and peripheral nervous system are prone to form multimeric G4s. The biological importance of such structures has been recently described, with multimeric G4s playing potentially protective or deleterious effects in the pathogenic cascade of various diseases. Here, we portray the multifaceted scenario of multimeric G4s, in terms of structural properties, biological roles, and targeting strategies.
Collapse
Affiliation(s)
- Ilaria Frasson
- Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy
| | - Valentina Pirota
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100 Pavia, Italy; G4-INTERACT, USERN, v. le Taramelli 10, 27100 Pavia, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy.
| | - Filippo Doria
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100 Pavia, Italy.
| |
Collapse
|
8
|
Zhou X, Zhang JL, Chang MH, Fan GT, Liu XZ, Wu SJ, Shi X. Sensitive osteosarcoma diagnosis through five-base telomerase product-triggered CRISPR-Cas12a enhanced rolling circle amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:4063-4068. [PMID: 34555130 DOI: 10.1039/d1ay00952d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Osteosarcoma is the most frequent primary malignant bone tumor, composed of mesenchymal cells producing osteoid and immature bone. The sensitive detection of telomerase plays a pivotal role in the early diagnosis and therapeutic treatment of osteosarcoma. We report here an in vitro strategy for sensitive telomerase activity detection through the integration of rolling circle amplification (RCA) and a clustered regularly spaced short palindrome repeats (CRISPR)-Cas12a system. In the proposed strategy, telomerase substrate (TS) primers are easily controlled to extend five bases (GGGTT) to give short telomerase extension products (TEP) with definite lengths without adding dATP. The resulting short TEPs can then cyclize the padlock through hybridizing with its two terminals and thus initiate the following RCA. To obtain an improved sensitivity, the CRISPR-Cas12a system is attached to collaterally cut surrounding DNA reporter probes after recognizing the target single strand DNA sequence in the RCA products. The highlights of this strategy are as follows: (i) the short TEP triggered strategy is excellent at detecting low telomerase activity and thus contributes to the early diagnosis of malignant tumors; (ii) highly sensitive telomerase activity detection which is easy to operate from RCA initiated CRISPR-Cas12a; (iii) opening up of a new avenue for telomerase activity detection with a CRISPR-Cas12a system. Finally, the proposed strategy exhibited sensitive telomerase activity detection under optimized experimental parameters and has great application potential for the clinical diagnosis of malignant tumors and the development of anti-cancer drugs.
Collapse
Affiliation(s)
- Xing Zhou
- Department of Orthopaedics, Jinling Hospital, School of Medicine, Nanjing University, 305 Zhongshan East Road, Nanjing, 210002, China.
| | - Jun-Liang Zhang
- Department of Orthopaedics, Jinling Hospital, School of Medicine, Nanjing University, 305 Zhongshan East Road, Nanjing, 210002, China.
| | - Meng-Han Chang
- Department of Orthopaedics, Jinling Hospital, School of Medicine, Nanjing University, 305 Zhongshan East Road, Nanjing, 210002, China.
| | - Gen-Tao Fan
- Department of Orthopaedics, Jinling Hospital, School of Medicine, Nanjing University, 305 Zhongshan East Road, Nanjing, 210002, China.
| | - Xiao-Zhou Liu
- Department of Orthopaedics, Jinling Hospital, School of Medicine, Nanjing University, 305 Zhongshan East Road, Nanjing, 210002, China.
| | - Su-Jia Wu
- Department of Orthopaedics, Jinling Hospital, School of Medicine, Nanjing University, 305 Zhongshan East Road, Nanjing, 210002, China.
| | - Xin Shi
- Department of Orthopaedics, Jinling Hospital, School of Medicine, Nanjing University, 305 Zhongshan East Road, Nanjing, 210002, China.
| |
Collapse
|
9
|
Mustafa G, Shiekh S, Gc K, Abeysirigunawardena S, Balci H. Interrogating accessibility of telomeric sequences with FRET-PAINT: evidence for length-dependent telomere compaction. Nucleic Acids Res 2021; 49:3371-3380. [PMID: 33693934 PMCID: PMC8034622 DOI: 10.1093/nar/gkab067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/23/2021] [Accepted: 03/08/2021] [Indexed: 12/25/2022] Open
Abstract
Single-stranded telomeric overhangs are ∼200 nucleotides long and can form tandem G-quadruplex (GQ) structures, which reduce their accessibility to nucleases and proteins that activate DNA damage response. Whether these tandem GQs further stack to form compact superstructures, which may provide better protection for longer telomeres, is not known. We report single-molecule measurements where the accessibility of 24-144 nucleotide long human telomeric DNA molecules is interrogated by a short PNA molecule that is complementary to a single GGGTTA repeat, as implemented in the FRET-PAINT method. Binding of the PNA strand to available GGGTTA sequences results in discrete FRET bursts which were analyzed in terms of their dwell times, binding frequencies, and topographic distributions. The binding frequencies were greater for binding to intermediate regions of telomeric DNA compared to 3'- or 5'-ends, suggesting these regions are more accessible. Significantly, the binding frequency per telomeric repeat monotonically decreased with increasing telomere length. These results are consistent with telomeres forming more compact structures at longer lengths, reducing accessibility of these critical genomic sites.
Collapse
Affiliation(s)
- Golam Mustafa
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Keshav Gc
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | | | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA
| |
Collapse
|
10
|
Noh G, Benetatos P. Tensile elasticity of a freely jointed chain with reversible hinges. SOFT MATTER 2021; 17:3333-3345. [PMID: 33630011 DOI: 10.1039/d1sm00053e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Many biopolymers exhibit reversible conformational transitions within the chain, which affect their bending stiffness and their response to a stretching force. For example, double stranded DNA may have denatured "bubbles" of unzipped single strands which open and close randomly. In other polymers, the transitions may be due to the reversible attachment and detachment of ligands on ligand-receptor complexes along the backbone. Semiflexible bundles under tension formed by the reversible attachment of cross-linkers, on a coarse-grained level, exhibit similar behaviour. The simplest theoretical model which captures what the above mentioned systems have in common is a freely jointed chain (FJC) with reversible hinges. Each hinge can be open, as in the usual FJC, or closed forcing the adjacent segments to align (stretch). In this article, we analyse it in the Gibbs ensemble. Remarkably, even though the usual FJC in the thermodynamic limit exhibits ensemble equivalence, the reversible FJC exhibits ensemble inequivalence. Even though a mean field treatment suggests a continuous phase transition to a fully hinged state at a certain force, the generating function method ("necklace model") shows that there is no phase transition. However, there is a crossover between the two states with clearly different responses. In the low force (linear response) regime, the reversible FJC has higher tensile compliance than its usual counterpart. In contrast, in the strong force regime, the tensile compliance of the reversible FJC is much lower than that of the usual FJC.
Collapse
Affiliation(s)
- Geunho Noh
- Department of Physics, Kyungpook National University, Bukgu, 80 Daehakro, Daegu 41566, Korea.
| | | |
Collapse
|
11
|
Monsen RC, Chakravarthy S, Dean WL, Chaires JB, Trent JO. The solution structures of higher-order human telomere G-quadruplex multimers. Nucleic Acids Res 2021; 49:1749-1768. [PMID: 33469644 PMCID: PMC7897503 DOI: 10.1093/nar/gkaa1285] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/21/2020] [Accepted: 01/13/2021] [Indexed: 12/17/2022] Open
Abstract
Human telomeres contain the repeat DNA sequence 5′-d(TTAGGG), with duplex regions that are several kilobases long terminating in a 3′ single-stranded overhang. The structure of the single-stranded overhang is not known with certainty, with disparate models proposed in the literature. We report here the results of an integrated structural biology approach that combines small-angle X-ray scattering, circular dichroism (CD), analytical ultracentrifugation, size-exclusion column chromatography and molecular dynamics simulations that provide the most detailed characterization to date of the structure of the telomeric overhang. We find that the single-stranded sequences 5′-d(TTAGGG)n, with n = 8, 12 and 16, fold into multimeric structures containing the maximal number (2, 3 and 4, respectively) of contiguous G4 units with no long gaps between units. The G4 units are a mixture of hybrid-1 and hybrid-2 conformers. In the multimeric structures, G4 units interact, at least transiently, at the interfaces between units to produce distinctive CD signatures. Global fitting of our hydrodynamic and scattering data to a worm-like chain (WLC) model indicates that these multimeric G4 structures are semi-flexible, with a persistence length of ∼34 Å. Investigations of its flexibility using MD simulations reveal stacking, unstacking, and coiling movements, which yield unique sites for drug targeting.
Collapse
Affiliation(s)
- Robert C Monsen
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - William L Dean
- James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA
| | - Jonathan B Chaires
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA.,James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA.,Department of Medicine, University of Louisville Medical School, Louisville, KY 40202, USA
| | - John O Trent
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA.,James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA.,Department of Medicine, University of Louisville Medical School, Louisville, KY 40202, USA
| |
Collapse
|
12
|
Zhang X, Zhang Y, Zhang W. Dynamic topology of double-stranded telomeric DNA studied by single-molecule manipulation in vitro. Nucleic Acids Res 2020; 48:6458-6470. [PMID: 32496520 PMCID: PMC7337930 DOI: 10.1093/nar/gkaa479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to synthesize long-chain double-stranded tandem repeats of telomeric DNA. Using mechanical manipulation assays based on single-molecule atomic force microscopy, we found that mechanical force can trigger the melting of double-stranded telomeric DNA and the formation of higher-order structures (G-quadruplexes or i-motifs). Our results show that only when both the G-strand and C-strand of double-stranded telomeric DNA form higher-order structures (G-quadruplexes or i-motifs) at the same time (e.g. in the presence of 100 mM KCl under pH 4.7), that the higher-order structure(s) can remain after the external force is removed. The presence of monovalent K+, single-wall carbon nanotubes (SWCNTs), acidic conditions, or short G-rich fragments (∼30 nt) can shift the transition from dsDNA to higher-order structures. Our results provide a new way to regulate the topology of telomeric DNA.
Collapse
Affiliation(s)
- Xiaonong Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Yingqi Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| |
Collapse
|
13
|
Bryan TM. G-Quadruplexes at Telomeres: Friend or Foe? Molecules 2020; 25:molecules25163686. [PMID: 32823549 PMCID: PMC7464828 DOI: 10.3390/molecules25163686] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/28/2022] Open
Abstract
Telomeres are DNA-protein complexes that cap and protect the ends of linear chromosomes. In almost all species, telomeric DNA has a G/C strand bias, and the short tandem repeats of the G-rich strand have the capacity to form into secondary structures in vitro, such as four-stranded G-quadruplexes. This has long prompted speculation that G-quadruplexes play a positive role in telomere biology, resulting in selection for G-rich tandem telomere repeats during evolution. There is some evidence that G-quadruplexes at telomeres may play a protective capping role, at least in yeast, and that they may positively affect telomere maintenance by either the enzyme telomerase or by recombination-based mechanisms. On the other hand, G-quadruplex formation in telomeric DNA, as elsewhere in the genome, can form an impediment to DNA replication and a source of genome instability. This review summarizes recent evidence for the in vivo existence of G-quadruplexes at telomeres, with a focus on human telomeres, and highlights some of the many unanswered questions regarding the location, form, and functions of these structures.
Collapse
Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| |
Collapse
|
14
|
Li N, Wang J, Ma K, Liang L, Mi L, Huang W, Ma X, Wang Z, Zheng W, Xu L, Chen JH, Yu Z. The dynamics of forming a triplex in an artificial telomere inferred by DNA mechanics. Nucleic Acids Res 2019; 47:e86. [PMID: 31114915 PMCID: PMC6735771 DOI: 10.1093/nar/gkz464] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 05/06/2019] [Accepted: 05/15/2019] [Indexed: 11/21/2022] Open
Abstract
A telomere carrying repetitive sequences ends with a single-stranded overhang. The G-rich overhang could fold back and bind in the major groove of its upstream duplex, forming an antiparallel triplex structure. The telomeric triplex has been proposed to function in protecting chromosome ends. However, we lack strategies to mechanically probe the dynamics of a telomeric triplex. Here, we show that the topological dynamics of a telomeric triplex involves 3' overhang binding at the ds/ssDNA junction inferred by DNA mechanics. Assisted by click chemistry and branched polymerase chain reaction, we developed a rescue-rope-strategy for mechanically manipulating an artificial telomeric DNA with a free end. Using single-molecule magnetic tweezers, we identified a rarely forming (5%) telomeric triplex which pauses at an intermediate state upon unzipping the Watson-Crick paired duplex. Our findings revealed that a mechanically stable triplex formed in a telomeric DNA can resist a force of 20 pN for a few seconds in a physiological buffer. We also demonstrated that the rescue-rope-strategy assisted mechanical manipulation can directly rupture the interactions between the third strand and its targeting duplex in a DNA triplex. Our single-molecule rescue-rope-strategy will serve as a general tool to investigate telomere dynamics and further develop triplex-based biotechnologies.
Collapse
Affiliation(s)
- Ning Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Junli Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Kangkang Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Lin Liang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Lipei Mi
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Wei Huang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Xiaofeng Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Zeyu Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Wei Zheng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Linyan Xu
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai 200025, China
| | - Zhongbo Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| |
Collapse
|
15
|
Paul A, Musetti C, Nanjunda R, Wilson WD. Biosensor-Surface Plasmon Resonance: Label-Free Method for Investigation of Small Molecule-Quadruplex Nucleic Acid Interactions. Methods Mol Biol 2019; 2035:63-85. [PMID: 31444744 DOI: 10.1007/978-1-4939-9666-7_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023]
Abstract
Biosensor-surface plasmon resonance (SPR) technology is now well established as a quantitative approach for the study of nucleic acid interactions in real time, without the need for labeling any components of the interaction. The method provides real-time equilibrium and kinetic characterization for quadruplex DNA interactions and requires small amounts of materials and no external probe. A detailed protocol for quadruplex-DNA interaction analyses with a variety of binding molecules using biosensor-SPR methods is presented. Explanations of the SPR method with basic fundamentals for use and analysis of results are described with recommendations on the preparation of the SPR instrument, sensor chips, and samples. Details of experimental design, quantitative and qualitative data analyses, and presentation are described. Some specific examples of small molecule-DNA quadruplex interactions are presented with results evaluated by both kinetic and steady-state SPR methods.
Collapse
Affiliation(s)
- Ananya Paul
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Caterina Musetti
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.,Department of Screening, Profiling and Mechanistic Biology, Platform Technology and Science, Glaxo Smith Kline, Collegeville, PA, USA
| | - Rupesh Nanjunda
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.,Janssen Research and Development, Spring House, PA, USA
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.
| |
Collapse
|
16
|
Kolesnikova S, Curtis EA. Structure and Function of Multimeric G-Quadruplexes. Molecules 2019; 24:molecules24173074. [PMID: 31450559 PMCID: PMC6749722 DOI: 10.3390/molecules24173074] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes are noncanonical nucleic acid structures formed from stacked guanine tetrads. They are frequently used as building blocks and functional elements in fields such as synthetic biology and also thought to play widespread biological roles. G-quadruplexes are often studied as monomers, but can also form a variety of higher-order structures. This increases the structural and functional diversity of G-quadruplexes, and recent evidence suggests that it could also be biologically important. In this review, we describe the types of multimeric topologies adopted by G-quadruplexes and highlight what is known about their sequence requirements. We also summarize the limited information available about potential biological roles of multimeric G-quadruplexes and suggest new approaches that could facilitate future studies of these structures.
Collapse
Affiliation(s)
- Sofia Kolesnikova
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Edward A Curtis
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic.
| |
Collapse
|
17
|
Lukášová E, Řezáčová M, Bačíková A, Šebejová L, Vávrová J, Kozubek S. Distinct cellular responses to replication stress leading to apoptosis or senescence. FEBS Open Bio 2019; 9:870-890. [PMID: 30982228 PMCID: PMC6487726 DOI: 10.1002/2211-5463.12632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 01/09/2019] [Accepted: 01/25/2019] [Indexed: 12/12/2022] Open
Abstract
Replication stress (RS) is a major driver of genomic instability and tumorigenesis. Here, we investigated whether RS induced by the nucleotide analog fludarabine and specific kinase inhibitors [e.g. targeting checkpoint kinase 1 (Chk1) or ataxia telangiectasia and Rad3‐related (ATR)] led to apoptosis or senescence in four cancer cell lines differing in TP53 mutation status and expression of lamin A/C (LA/C). RS resulted in uneven chromatin condensation in all cell types, as evidenced by the presence of metaphasic chromosomes with unrepaired DNA damage, as well as detection of less condensed chromatin in the same nucleus, frequent ultrafine anaphase bridges, and micronuclei. We observed that responses to these chromatin changes may be distinct in individual cell types, suggesting that expression of lamin A/C and lamin B1 (LB1) may play an important role in the transition of damaged cells to senescence. MCF7 mammary carcinoma cells harboring wild‐type p53 (WT‐p53) and LA/C responded to RS by transition to senescence with a significant reduction of lamin B receptor and LB1 proteins. In contrast, a lymphoid cancer cell line WSU‐NHL (WT‐p53) lacking LA/C and expressing low levels of LB1 died after several hours, while lines MEC‐1 and SU‐DHL‐4, both with mutated p53, and SU‐DHL‐4 with mutations in LA/C, died at different rates by apoptosis. Our results show that, in addition to being influenced by p53 mutation status, the response to RS (apoptosis or senescence) may also be influenced by lamin A/C and LB1 status.
Collapse
Affiliation(s)
- Emilie Lukášová
- Department of Cell Biology and Radiobiology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic
| | - Martina Řezáčová
- Department of Medical Biochemistry, Faculty of Medicine in Hradec Králové, Charles University in Prague, Hradec Králové, Czech Republic
| | - Alena Bačíková
- Department of Cell Biology and Radiobiology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic
| | - Ludmila Šebejová
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiřina Vávrová
- Department of Radiobiology, Faculty of Military Health Sciences Hradec Králové, University of Defence Brno, Hradec Králové, Czech Republic
| | - Stanislav Kozubek
- Department of Cell Biology and Radiobiology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic
| |
Collapse
|
18
|
Abstract
DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.
Collapse
Affiliation(s)
- Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering , Nanjing University , Nanjing 210023 , China.,ARNA Laboratory , Université de Bordeaux, Inserm U 1212, CNRS UMR5320, IECB , Pessac 33600 , France.,Institute of Biophysics of the CAS , v.v.i., Královopolská 135 , 612 65 Brno , Czech Republic
| | - Dipankar Sen
- Department of Molecular Biology & Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada
| |
Collapse
|