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Ma C, Chan RCT, Chan CTL, Wong AKW, Chung BPY, Kwok WM. Fluorescence and Ultrafast Fluorescence Unveil the Formation, Folding Molecularity, and Excitation Dynamics of Homo-Oligomeric and Human Telomeric i-Motifs at Acidic and Neutral pH. Chem Asian J 2018; 13:3706-3717. [PMID: 30230251 DOI: 10.1002/asia.201801117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/28/2018] [Indexed: 01/07/2023]
Abstract
i-Motifs are tetraplex DNAs known to be stable at acidic pH. The structure of i-motifs is important in DNA nanotechnology; i-motif-forming sequences with consecutive cytosine (C) molecules are abundant throughout the human genome. There is, however, little information on the structure of C-rich DNAs under physiologically relevant neutral conditions. The electron dynamics of i-motifs, crucial to both biology and materials applications, also remains largely unexplored. In this work, we report a combined femtosecond and nanosecond broadband time-resolved fluorescence (TRF) and steady-state fluorescence investigation on homo-oligomer dC20 , a human telomeric sequence (HTS) 5'-dC3 (TA2 C3 )3 , and its analogue performed with different excitation at both acidic and neutral pH. Our study provides direct observation of intrinsic fluorescence and the first full probe of the real-time dynamics of the intrinsic fluorescence from i-motifs formed from varied sequences and pH conditions. The results obtained demonstrate concrete evidence for the existence at neutral pH of i-motifs from both dC20 and the HTS. It also identifies that, under neutral conditions, the i-motif from dC20 adopting the bimolecular folding structure is significantly more stable than the HTS i-motif featuring the unimolecular topology. Our femtosecond and nanosecond TRF study unveils excitation dynamics distinctive of the interdigitated architecture of i-motifs with the excited states involved exhibiting deactivation over a remarkably broad timescale through multiple channels involving proton-coupled electron transfer lasting tens of picoseconds, as signified by the solvent kinetic isotope effect, and structure-dependent charge recombination in the hundreds of picoseconds to tens of nanoseconds time regime.
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Affiliation(s)
- Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China
| | - Ruth Chau-Ting Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Chris Tsz-Leung Chan
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China
| | - Allen Ka-Wa Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Bowie Po-Yee Chung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
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Hou R, Wang N, Bao W, Wang Z. Mechanical transduction via a single soft polymer. Phys Rev E 2018; 97:042504. [PMID: 29758660 DOI: 10.1103/physreve.97.042504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Indexed: 06/08/2023]
Abstract
Molecular machines from biology and nanotechnology often depend on soft structures to perform mechanical functions, but the underlying mechanisms and advantages or disadvantages over rigid structures are not fully understood. We report here a rigorous study of mechanical transduction along a single soft polymer based on exact solutions to the realistic three-dimensional wormlike-chain model and augmented with analytical relations derived from simpler polymer models. The results reveal surprisingly that a soft polymer with vanishingly small persistence length below a single chemical bond still transduces biased displacement and mechanical work up to practically significant amounts. This "soft" approach possesses unique advantages over the conventional wisdom of rigidity-based transduction, and potentially leads to a unified mechanism for effective allosterylike transduction and relay of mechanical actions, information, control, and molecules from one position to another in molecular devices and motors. This study also identifies an entropy limit unique to the soft transduction, and thereby suggests a possibility of detecting higher efficiency for kinesin motor and mutants in future experiments.
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Affiliation(s)
- Ruizheng Hou
- School of Science and Institute of Quantum Optics and Quantum Information, Xi'an Jiaotong University, Shaan Xi 710049, China
| | - Nan Wang
- Department of Mathematics, National University of Singapore, Singapore 119076
| | - Weizhu Bao
- Department of Mathematics, National University of Singapore, Singapore 119076
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119076
| | - Zhisong Wang
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119076
- Department of Physics, National University of Singapore, Singapore 117542
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Benabou S, Aviñó A, Eritja R, González C, Gargallo R. Fundamental aspects of the nucleic acid i-motif structures. RSC Adv 2014. [DOI: 10.1039/c4ra02129k] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.
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Affiliation(s)
- S. Benabou
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
| | - A. Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - R. Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - C. González
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid, Spain
| | - R. Gargallo
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
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G-Quadruplex conformational change driven by pH variation with potential application as a nanoswitch. Biochim Biophys Acta Gen Subj 2013; 1830:4935-42. [DOI: 10.1016/j.bbagen.2013.06.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 06/16/2013] [Accepted: 06/19/2013] [Indexed: 12/18/2022]
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Battle C, Chu X, Jayawickramarajah J. Oligonucleotide-Based Systems for Input-Controlled and Non-Covalently Regulated Protein-Binding. Supramol Chem 2013; 25. [PMID: 24187478 DOI: 10.1080/10610278.2013.810337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Supramolecular chemists continuously take inspiration from complex biological systems to develop functional molecules involved in molecular recognition and self-assembly. In this regard, "smart" synthetic molecules that emulate allosteric proteins are both exciting and challenging, since many allosteric proteins can be considered as molecular switches that bind to other protein targets in a non-covalent fashion, and importantly, are capable of having their output activity controlled by prior binding to input molecules. This review discusses the foundations and passage toward the development of non-covalently operated oligonucleotide-based systems with protein-binding capacity that can be precisely regulated in an input-controlled manner.
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Affiliation(s)
- Cooper Battle
- Department of Chemistry, Tulane University, New Orleans, LA, USA
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Abstract
The physicochemical properties of small molecules as well as macromolecules are modulated by solution pH, and DNA is no exception. Special sequences of DNA can adopt unusual conformations e.g., triplex, i-motif and A-motif, depending on solution pH. The specific range of pH for these unusual structures is dictated by the pKa of protonation of the relevant nucleobase involved in the resultant non-canonical base pairing that is required to stabilise the structure. The biological significance of these pH-dependent structures is not yet clear. However, these non-B-DNA structures have been used to design different devices to direct chemical reactions, generate mechanical force, sense pH, etc. The performance of these devices can be monitored by a photonic signal. They are autonomous and their ‘waste free’ operation cycles makes them highly processive. Applications of these devices help to increase understanding of the structural polymorphism of the motifs themselves. The design of these devices has continuously evolved to improve their performance efficiency in different contexts. In some examples, these devices have been shown to perform inside complex living systems with similar efficiencies, to report on the chemical environment there. The robust performance of these devices opens up exciting possibilities for pH-sensitive DNA devices in the study of various pH-regulated biological events.
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Affiliation(s)
- Sonali Saha
- National Centre for Biological Sciences TIFR, GKVK, Bellary Road, Bangalore 560065 India
| | - Yamuna Krishnan*
- National Centre for Biological Sciences TIFR, GKVK, Bellary Road, Bangalore 560065 India
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Li W, Feng L, Ren J, Wu L, Qu X. Visual Detection of Glucose Using Conformational Switch of i-Motif DNA and Non-Crosslinking Gold Nanoparticles. Chemistry 2012; 18:12637-42. [DOI: 10.1002/chem.201201914] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Indexed: 11/08/2022]
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Xu W, Xie X, Li D, Yang Z, Li T, Liu X. Ultrasensitive colorimetric DNA detection using a combination of rolling circle amplification and nicking endonuclease-assisted nanoparticle amplification (NEANA). SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:1846-50. [PMID: 22461378 DOI: 10.1002/smll.201200263] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Indexed: 05/18/2023]
Abstract
A combination of rolling circle amplification and nicking endonuclease-assisted nanoparticle amplification (NEANA) is used for the rapid, colorimetric detection of DNA. The integration of rolling circle amplification into the NEANA approach allows for detection of oligonucleotides with arbitrary sequences at ultralow concentrations.
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Affiliation(s)
- Wei Xu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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Xu C, Zhao C, Ren J, Qu X. pH-controlled reversible drug binding and release using a cytosine-rich hairpin DNA. Chem Commun (Camb) 2011; 47:8043-5. [PMID: 21677978 DOI: 10.1039/c1cc12594j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we report that a cytosine-rich DNA carrier, that oscillates between a hairpin and an i-motif structure in its response to pH variation, can be used as a drug binding and release device.
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Affiliation(s)
- Can Xu
- Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Changchun, Jilin 130022, China
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