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Matsumoto S, Sugimoto N. New Insights into the Functions of Nucleic Acids Controlled by Cellular Microenvironments. Top Curr Chem (Cham) 2021; 379:17. [PMID: 33782792 DOI: 10.1007/s41061-021-00329-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/11/2021] [Indexed: 12/11/2022]
Abstract
The right-handed double-helical B-form structure (B-form duplex) has been widely recognized as the canonical structure of nucleic acids since it was first proposed by James Watson and Francis Crick in 1953. This B-form duplex model has a monochronic and static structure and codes genetic information within a sequence. Interestingly, DNA and RNA can form various non-canonical structures, such as hairpin loops, left-handed helices, triplexes, tetraplexes of G-quadruplex and i-motif, and branched junctions, in addition to the canonical structure. The formation of non-canonical structures depends not only on sequence but also on the surrounding environment. Importantly, these non-canonical structures may exhibit a wide variety of biological roles by changing their structures and stabilities in response to the surrounding environments, which undergo vast changes at specific locations and at specific times in cells. Here, we review recent progress regarding the interesting behaviors and functions of nucleic acids controlled by molecularly crowded cellular conditions. New insights gained from recent studies suggest that nucleic acids not only code genetic information in sequences but also have unknown functions regarding their structures and stabilities through drastic structural changes in cellular environments.
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Affiliation(s)
- Saki Matsumoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan. .,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
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2
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Park JJ, Han SY. Alternated Branching Ratios by Anomaly in Collision-Induced Dissociation of Proton-Bound Hoogsteen Base Pairs of 1-Methylcytosine with 1-Methylguanine and 9-Methylguanine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:846-854. [PMID: 30911905 DOI: 10.1007/s13361-019-02161-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/26/2019] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
A comparative study on the proton-bound complexes of 1-methylcytosine (1-mC) with 1-methylguanine (1-mG) and 9-methylguanine (9-mG), [1-mC:1-mG:H]+ and [1-mC:9-mG:H]+, respectively, was carried out using energy-resolved collision-induced dissociation (ER-CID) experiments in combination with quantum chemical calculations. In ER-CID experiments, the measured survival yields indicated an essentially identical stability for the two proton-bound complexes. In comparison with the lowest-energy structures and base-pairing energetics predicted at the B3LYP/6-311+G(2d,2p) theory level, both complexes produced in this study were suggested to be proton-bound Hoogsteen base pairs. Curiously, despite the similarity in structures, binding energetics, and potential energy surfaces predicted by the B3LYP theory, the fragment branching ratios exhibited an intriguing alternation between the two proton-bound Hoogsteen base pairs. The CID of [1-mC:1-mG:H]+ produced protonated cytosines, [1-mC:H]+, more abundantly than [1-mG:H]+, whereas that of [1-mC:9-mG:H]+ gave rise to a more pronounced production of protonated guanines, [9-mG:H]+. However, using the proton affinities of moieties predicted by the high-accuracy methods, including CBS-QB3 and the Guassian-4 theory, the anomaly known for [Cytosine:Guanine:H]+ (J. Am. Soc. Mass Spectrom. 29, 2368-2379 (2018)) successfully accounted for the alternated branching ratios. Thereby, the anomaly, more specifically, the production of proton-transferred fragments of O-protonated cytosines in the CID of proton-bound Hoogsteen base pairs, is indeed real, which is disclosed as the alternated branching ratios in the CID spectra of [1-mC:1-mG:H]+ and [1-mC:9-mG:H]+ in this study. Graphical Abstract .
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Affiliation(s)
- Jeong Ju Park
- Department of Nanochemistry, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea
| | - Sang Yun Han
- Department of Nanochemistry, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea.
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3
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Park JJ, Lee CS, Han SY. Proton Transfer Accounting for Anomalous Collision-Induced Dissociation of Proton-Bound Hoogsteen Base Pair of Cytosine and Guanine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2368-2379. [PMID: 30215166 DOI: 10.1007/s13361-018-2060-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/08/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
To understand the anomalous collision-induced dissociation (CID) behavior of the proton-bound Hoogsteen base pair of cytosine (C) and guanine (G), C:H+∙∙∙G, we investigated CID of a homologue series of proton-bound heterodimers of C, 1-methylcytosine, and 5-methylcytosine with G as a common base partner. The CID experiments were performed in an energy-resolved way (ER-CID) under both multiple and near-single collision conditions. The relative stabilities of the protonated complexes examined by ER-CID suggested that the proton-bound complexes produced by electrospray ionization in this study are proton-bound Hoogsteen base pairs. On the other hand, in contrast to the other base pairs, CID of C:H+∙∙∙G exhibited more abundant productions of C:H+, the fragment protonated on the moiety with a smaller proton affinity, than that of G:H+. This appeared to contradict general prediction based on the kinetic method. However, further theoretical exploration of potential energy surfaces found that there can be facile proton transfers in the proton-bound Hoogsteen base pairs during the CID process, which makes the process accessible to an additional product state of O-protonated C for C:H+ fragments. The presence of an additional dissociation channel, which in other words corresponds to twofold degeneracy in the transition state leading to C:H+ fragments, effectively doubles the apparent reaction rate for production of C:H+. In this way, the process gives rise to the anomaly, the observed pronounced formation of C:H+ in the CID of the proton-bound Hoogsteen base pair, C:H+∙∙∙G. Graphical Abstract ᅟ.
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Affiliation(s)
- Jeong Ju Park
- Department of Nanochemistry, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea
| | - Choong Sik Lee
- Scientific Investigation Laboratory, Ministry of National Defense, 22 Itaewon-ro, Yongsan-gu, Seoul, 04383, Republic of Korea
| | - Sang Yun Han
- Department of Nanochemistry, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea.
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4
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Cruz-Ortiz AF, Rossa M, Berthias F, Berdakin M, Maitre P, Pino GA. Fingerprints of Both Watson-Crick and Hoogsteen Isomers of the Isolated (Cytosine-Guanine)H + Pair. J Phys Chem Lett 2017; 8:5501-5506. [PMID: 29064704 DOI: 10.1021/acs.jpclett.7b02140] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Gas phase protonated guanine-cytosine (CGH+) pair was generated using an electrospray ionization source from solutions at two different pH (5.8 and 3.2). Consistent evidence from MS/MS fragmentation patterns and differential ion mobility spectra (DIMS) point toward the presence of two isomers of the CGH+ pair, whose relative populations depend strongly on the pH of the solution. Gas phase infrared multiphoton dissociation (IRMPD) spectroscopy in the 900-1900 cm-1 spectral range further confirms that the Watson-Crick isomer is preferentially produced (91%) at pH = 5.8, while the Hoogsteen isomer predominates (66%) at pH = 3.2). These fingerprint signatures are expected to be useful for the development of new analytical methodologies and to trigger isomer selective photochemical studies of protonated DNA base pairs.
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Affiliation(s)
- Andrés F Cruz-Ortiz
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Maximiliano Rossa
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Francis Berthias
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Matías Berdakin
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Philippe Maitre
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Gustavo A Pino
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
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D'Urso A, Randazzo R, Rizzo V, Gangemi CMA, Romanucci V, Zarrelli A, Tomaselli G, Milardi D, Borbone N, Purrello R, Piccialli G, Di Fabio G, Oliviero G. Stabilization vs. destabilization of G-quadruplex superstructures: the role of the porphyrin derivative having spermine arms. Phys Chem Chem Phys 2017. [PMID: 28650039 DOI: 10.1039/c7cp02816d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of the porphyrin derivative H2TCPPSpm4, having spermine pendants in the four meso positions, with the G-quadruplex (GQ) structure formed by the DNA aptamer TGGGAG has been investigated by means of UV, electronic circular dichroism and PAGE studies. The results reported here demonstrate that the porphyrin derivative is capable of stabilizing or destabilizing the higher-ordered structures of parallel GQs, depending on the method used to reach their relative stoichiometry (titration vs. single addition). Noteworthily, when two equivalents of H2TCPPSpm4 were mixed directly with one equivalent of the (TGGGAG)4 GQ to reach a 2 : 1 H2TCPPSpm4 : GQ ratio T1/2 higher than 80 °C was also observed confirming the presence of higher-ordered GQ structures.
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Affiliation(s)
- A D'Urso
- Department of Chemical Science, University of Catania, V.le A Doria 6, 95125, Catania, Italy.
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6
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Wen H, Zhou J, Pan W, Li Z, Liang D. Assembly and Reassembly of Polyelectrolyte Complex Formed by Poly(ethylene glycol)-block-poly(glutamate sodium) and S5R4 Peptide. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00746] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hao Wen
- Beijing National
Laboratory for Molecular Sciences and the Key Laboratory of Polymer
Chemistry and Physics of Ministry of Education, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China 100871
| | - Jihan Zhou
- Beijing National
Laboratory for Molecular Sciences and the Key Laboratory of Polymer
Chemistry and Physics of Ministry of Education, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China 100871
| | - Wei Pan
- Beijing National
Laboratory for Molecular Sciences and the Key Laboratory of Polymer
Chemistry and Physics of Ministry of Education, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China 100871
| | - Zhibo Li
- School of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong, China 266061
| | - Dehai Liang
- Beijing National
Laboratory for Molecular Sciences and the Key Laboratory of Polymer
Chemistry and Physics of Ministry of Education, College of Chemistry
and Molecular Engineering, Peking University, Beijing, China 100871
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7
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Pramanik S, Tateishi-Karimata H, Sugimoto N. Organelle-mimicking liposome dissociates G-quadruplexes and facilitates transcription. Nucleic Acids Res 2014; 42:12949-59. [PMID: 25336617 PMCID: PMC4227800 DOI: 10.1093/nar/gku998] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Important biological reactions involving nucleic acids occur near the surface of membranes such as the nuclear membrane (NM) and rough endoplasmic reticulum (ER); however, the interactions between biomembranes and nucleic acids are poorly understood. We report here that transcription was facilitated in solution with liposomes, which mimic a biomembrane surface, relative to the reaction in a homogeneous aqueous solution when the template was able to form a G-quadruplex. The G-quadruplex is known to be an inhibitor of transcription, but the stability of the G-quadruplex was decreased at the liposome surface because of unfavourable enthalpy. The destabilization of the G-quadruplex was greater at the surface of NM- and ER-mimicking liposomes than at the surfaces of liposomes designed to mimic other organelles. Thermodynamic analyses revealed that the G-rich oligonucleotides adopted an extended structure at the liposome surface, whereas in solution the compact G-quadruplex was formed. Our data suggest that changes in structure and stability of nucleic acids regulate biological reactions at membrane surfaces.
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Affiliation(s)
- Smritimoy Pramanik
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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8
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Tateishi-Karimata H, Nakano SI, Sugimoto N. Quantitative analyses of nucleic Acid stability under the molecular crowding condition induced by cosolutes. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2013; Chapter 7:7.19.1-7.19.17. [PMID: 23775810 DOI: 10.1002/0471142700.nc0719s53] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A variety of biomolecules, including nucleic acids, proteins, polysaccharides, and other soluble and insoluble low-molecular weight components, are present in living cells. These molecules occupy a significant fraction of the cellular volume (up to 40%), resulting in a highly crowded intracellular environment. This situation is referred to as molecular crowding. Although the thermodynamic stabilities of DNA structures are known to be altered in a crowded environment, less is known about the behavior of nucleic acids and their interactions with cations and water molecules under such conditions. This unit describes methods that can be used to quantitatively analyze the molecular crowding effects caused by cosolutes on the thermodynamic stability, hydration, and cation binding of nucleic acid structures.
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Affiliation(s)
- Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
| | - Shu-Ichi Nakano
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan.,Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan.,Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan
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9
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Miyoshi D, Fujimoto T, Sugimoto N. Molecular Crowding and Hydration Regulating of G-Quadruplex Formation. Top Curr Chem (Cham) 2012; 330:87-110. [DOI: 10.1007/128_2012_335] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Zhang X, Servos MR, Liu J. Ultrahigh Nanoparticle Stability against Salt, pH, and Solvent with Retained Surface Accessibility via Depletion Stabilization. J Am Chem Soc 2012; 134:9910-3. [DOI: 10.1021/ja303787e] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xu Zhang
- Department
of Chemistry and Waterloo Institute for Nanotechnology and ‡Department of
Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
| | - Mark R. Servos
- Department
of Chemistry and Waterloo Institute for Nanotechnology and ‡Department of
Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
| | - Juewen Liu
- Department
of Chemistry and Waterloo Institute for Nanotechnology and ‡Department of
Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
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11
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Pramanik S, Nagatoishi S, Sugimoto N. DNA tetraplex structure formation from human telomeric repeat motif (TTAGGG):(CCCTAA) in nanocavity water pools of reverse micelles. Chem Commun (Camb) 2012; 48:4815-7. [PMID: 22456442 DOI: 10.1039/c2cc30622k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In an equimolar ratio the human telomeric oligonucleotides d[AGGG(TTAGGG)(3)] and d[(CCCTAA)(3)CCCT] formed mixed structures of duplex and tetraplex in bis(2-ethylhexyl)sulfosuccinate reverse micelles; only the duplex was observed in aqueous buffer. This finding suggests that heterogeneous confined media in the cell nucleus might induce a significant fraction of the telomeric region of genomic DNA to adopt non-canonical tetraplex structure.
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Affiliation(s)
- Smritimoy Pramanik
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan
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12
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Yaku H, Fujimoto T, Murashima T, Miyoshi D, Sugimoto N. Phthalocyanines: a new class of G-quadruplex-ligands with many potential applications. Chem Commun (Camb) 2012; 48:6203-16. [DOI: 10.1039/c2cc31037f] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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13
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Zaki A, Dave N, Liu J. Amplifying the Macromolecular Crowding Effect Using Nanoparticles. J Am Chem Soc 2011; 134:35-8. [DOI: 10.1021/ja207661z] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Ahmed Zaki
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1,
Canada
| | - Neeshma Dave
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1,
Canada
| | - Juewen Liu
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1,
Canada
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14
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Nagatoishi S, Isono N, Tsumoto K, Sugimoto N. Hydration is required in DNA G-quadruplex-protein binding. Chembiochem 2011; 12:1822-6. [PMID: 21671334 DOI: 10.1002/cbic.201100264] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Indexed: 01/26/2023]
Affiliation(s)
- Satoru Nagatoishi
- Frontier Institute for Biomolecular Engineering Research, Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan
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