1
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Ashwood B, Lewis NHC, Sanstead PJ, Tokmakoff A. Temperature-Jump 2D IR Spectroscopy with Intensity-Modulated CW Optical Heating. J Phys Chem B 2020; 124:8665-8677. [PMID: 32902979 DOI: 10.1021/acs.jpcb.0c07177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pulsed temperature-jump (T-jump) spectroscopy with infrared (IR) detection has been widely used to study biophysical processes occurring from nanoseconds to ∼1 ms with structural sensitivity. However, many systems exhibit structural dynamics on time scales longer than the millisecond barrier that is set by the time scale for thermal relaxation of the sample. We developed a linear and nonlinear infrared spectrometer coupled to an intensity-modulated continuous wave (CW) laser to probe T-jump-initiated chemical reactions from <1 ms to seconds. Time-dependent modulation of the CW laser leads to a <1 ms heating time as well as a constant final temperature (±3%) for the duration of the heating time. Temperature changes of up to 75 °C in D2O are demonstrated, allowing for nonequilibrium measurements inaccessible to standard pulsed optical T-jump setups. T-jump linear absorption, pump-probe, and two-dimensional IR (2D IR) spectroscopy are applied to the unfolding and refolding of ubiquitin and a model intercalated motif (i-motif) DNA sequence, and analysis of the observed signals is used to demonstrate the limits and utility of each method. Overall, the ability to probe temperature-induced chemical processes from <1 ms to many seconds with 2D IR spectroscopy provides multiple new avenues for time-dependent spectroscopy in chemistry and biophysics.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Nicholas H C Lewis
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Paul J Sanstead
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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2
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Lyu M, Meany B, Yang J, Li Y, Zheng M. Toward Complete Resolution of DNA/Carbon Nanotube Hybrids by Aqueous Two-Phase Systems. J Am Chem Soc 2019; 141:20177-20186. [PMID: 31783712 DOI: 10.1021/jacs.9b09953] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Sequence-dependent interactions between DNA and single-wall carbon nanotubes (SWCNTs) are shown to provide resolution for the atomic-structure-based sorting of DNA-wrapped SWCNTs. Previous studies have demonstrated that aqueous two-phase (ATP) systems are very effective for sorting DNA-wrapped SWCNTs (DNA-SWCNTs). However, most separations have been carried out with a polyethylene glycol (PEG)/polyacrylamide (PAM) ATP system, which shows severe interfacial trapping for many DNA-SWCNT dispersions, resulting in significant material loss and limiting multistage extraction. Here, we report a study of several new ATP systems for sorting DNA-SWCNTs. We have developed a convenient method to explore these systems without knowledge of the corresponding phase diagram. We further show that the molecular weight of the polymer strongly affects the partition behavior and separation results for DNA-SWCNTs in PEG/dextran (DX) ATP systems. This leads to the identification of the PEG1.5kDa/DX250kDa ATP system as an effective vehicle for the chirality separation of DNA-SWCNTs. Additionally, this ATP system exhibits greatly reduced interfacial trapping, enabling for the first time continuous multistep sorting of four species of SWCNTs from a single dispersion. Enhanced stability of DNA-SWCNTs in the PEG1.5kDa/DX250kDa ATP system also allows us to investigate pH dependent sorting of SWCNTs wrapped by C-rich sequences. Our observations suggest that hydrogen bonding may form between the DNA bases at lower pH, enabling a more ordered wrapping structure on the SWCNTs and improvement in sorting (11,0). Together, these findings reveal that the new ATP system is suitable for searching DNA sequences leading toward more complete resolution of DNA-SWCNTs. A new concept of "resolving sequences", evolved from the old notion of "recognition sequences", is proposed to describe a broader range of behaviors of DNA/SWCNT interactions and sorting.
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Affiliation(s)
- Min Lyu
- Beijing National Laboratory for Molecular Science, Key Laboratory for the Physics and Chemistry of Nanodevices, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Brendan Meany
- Materials Science and Engineering Division , National Institute of Standards and Technology , 100 Bureau Drive , Gaithersburg , Maryland 20899 , United States
| | - Juan Yang
- Beijing National Laboratory for Molecular Science, Key Laboratory for the Physics and Chemistry of Nanodevices, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Yan Li
- Beijing National Laboratory for Molecular Science, Key Laboratory for the Physics and Chemistry of Nanodevices, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Ming Zheng
- Materials Science and Engineering Division , National Institute of Standards and Technology , 100 Bureau Drive , Gaithersburg , Maryland 20899 , United States
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3
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Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles. J Biomol Struct Dyn 2018; 37:2837-2866. [PMID: 30052138 DOI: 10.1080/07391102.2018.1503972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.
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Affiliation(s)
- Margarita I Zarudnaya
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Iryna M Kolomiets
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Andriy L Potyahaylo
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Dmytro M Hovorun
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , Kyiv , Ukraine
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4
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Kumar P, Cabaj MK, Pazio A, Dominiak PM. Protonated nucleobases are not fully ionized in their chloride salt crystals and form metastable base pairs further stabilized by the surrounding anions. IUCRJ 2018; 5:449-469. [PMID: 30002846 PMCID: PMC6038959 DOI: 10.1107/s2052252518006346] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
This paper presents experimental charge-density studies of cytosinium chloride, adeninium chloride hemihydrate and guaninium dichloride crystals based on ultra-high-resolution X-ray diffraction data and extensive theoretical calculations. The results confirm that the cohesive energies of the studied systems are dominated by contributions from intermolecular electrostatic interactions, as expected for ionic crystals. Electrostatic interaction energies (Ees) usually constitute 95% of the total interaction energy. The Ees energies in this study were several times larger in absolute value when compared, for example, with dimers of neutral nucleobases. However, they were not as large as some theoretical calculations have predicted. This was because the molecules appeared not to be fully ionized in the studied crystals. Apart from charge transfer from chlorine to the protonated nucleobases, small but visible charge redistribution within the nucleobase cations was observed. Some dimers of singly protonated bases in the studied crystals, namely a cytosinium-cytosinium trans sugar/sugar edge pair and an adeninium-adeninium trans Hoogsteen/Hoogsteen edge pair, exhibited attractive interactions (negative values of Ees) or unusually low repulsion despite identical molecular charges. The pairs are metastable as a result of strong hydrogen bonding between bases which overcompensates the overall cation-cation repulsion, the latter being weakened due to charge transfer and molecular charge-density polarization.
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Affiliation(s)
- Prashant Kumar
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Malgorzata Katarzyna Cabaj
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Aleksandra Pazio
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa 02-089, Poland
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5
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Rizzo P, Lepera E, Ianniello G, Guerra G. Melt-Extruded Films of a Commercial Polymer with Intense Chiral Optical Response of Achiral Guests. Macromolecules 2014. [DOI: 10.1021/ma5000514] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paola Rizzo
- Dipartimento
di Chimica e Biologia and INSTM Research Unit, Università degli Studi di Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
| | - Eugenia Lepera
- Dipartimento
di Chimica e Biologia and INSTM Research Unit, Università degli Studi di Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
- Dipartimento
di Fisica, Università della Calabria, Ponte P. Bucci, Cubo 33B, Rende (CS) 87036, Italy
| | - Graziella Ianniello
- Dipartimento
di Chimica e Biologia and INSTM Research Unit, Università degli Studi di Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
| | - Gaetano Guerra
- Dipartimento
di Chimica e Biologia and INSTM Research Unit, Università degli Studi di Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
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6
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Rizzo P, Lepera E, Guerra G. Enantiomeric guests with the same signs of chiral optical responses. Chem Commun (Camb) 2014; 50:8185-8. [DOI: 10.1039/c4cc02853h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chiral response of non-racemic molecules, being guests of s-PS co-crystalline films, does not depend on their R or S molecular chirality but essentially only on the polymer host supramolecular chirality.
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Affiliation(s)
- Paola Rizzo
- Dipartimento di Chimica e Biologia and INSTM Research Unit
- Università degli Studi di Salerno
- 84084 Fisciano (SA), Italy
| | - Eugenia Lepera
- Dipartimento di Fisica
- Università della Calabria
- Rende (CS), Italy
| | - Gaetano Guerra
- Dipartimento di Chimica e Biologia and INSTM Research Unit
- Università degli Studi di Salerno
- 84084 Fisciano (SA), Italy
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7
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Tubbs J, Condon DE, Kennedy S, Hauser M, Bevilacqua P, Turner DH. The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics. Biochemistry 2013; 52:996-1010. [PMID: 23286901 PMCID: PMC3571207 DOI: 10.1021/bi3010347] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/27/2012] [Indexed: 12/29/2022]
Abstract
The sequence dependence of RNA energetics is important for predicting RNA structure. Hairpins with C(n) loops are consistently less stable than hairpins with other loops, which suggests the structure of C(n) regions could be unusual in the "unfolded" state. For example, previous nuclear magnetic resonance (NMR) evidence suggested that polycytidylic acid forms a left-handed helix. In this study, UV melting experiments show that the hairpin formed by r(5'GGACCCCCGUCC) is less stable than r(5'GGACUUUUGUCC). NMR spectra for single-stranded C(4) oligonucleotide, mimicking the unfolded hairpin loop, are consistent with a right-handed A-form-like helix. Comparisons between NMR spectra and molecular dynamics (MD) simulations suggest that recent reparametrizations, parm99χ_YIL and parm99TOR, of the AMBER parm99 force field improve the agreement between structural features for C(4) determined by NMR and predicted by MD. Evidently, the force field revisions to parm99 improve the modeling of RNA energetics and therefore structure.
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Affiliation(s)
- Jason
D. Tubbs
- Department
of Chemistry, University of Rochester,
Rochester, New York 14627,
United States
- Center for
RNA Biology, University of Rochester, Rochester,
New York 14642,
United States
| | - David E. Condon
- Department
of Chemistry, University of Rochester,
Rochester, New York 14627,
United States
- Center for
RNA Biology, University of Rochester, Rochester,
New York 14642,
United States
| | - Scott
D. Kennedy
- Center for
RNA Biology, University of Rochester, Rochester,
New York 14642,
United States
- Department
of Biochemistry and
Biophysics, University of Rochester, Rochester,
New York 14642, United States
| | - Melanie Hauser
- Department of Chemistry, Buena Vista University, Storm Lake, Iowa 50588, United
States
- Department of Chemistry
and
Center for RNA Molecular Biology, The Pennsylvania State
University, University Park, Pennsylvania 16802, United
States
| | - Philip
C. Bevilacqua
- Department of Chemistry
and
Center for RNA Molecular Biology, The Pennsylvania State
University, University Park, Pennsylvania 16802, United
States
| | - Douglas H. Turner
- Department
of Chemistry, University of Rochester,
Rochester, New York 14627,
United States
- Center for
RNA Biology, University of Rochester, Rochester,
New York 14642,
United States
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8
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Rizzo P, Montefusco T, Guerra G. Chiral Optical Films Based on Achiral Chromophore Guests. J Am Chem Soc 2011; 133:9872-7. [DOI: 10.1021/ja2021087] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paola Rizzo
- Dipartimento di Chimica and INSTM Research Unit, Università degli Studi di Salerno, via Ponte don Melillo, 84084 Fisciano, Salerno, Italy
| | - Tommaso Montefusco
- Dipartimento di Chimica and INSTM Research Unit, Università degli Studi di Salerno, via Ponte don Melillo, 84084 Fisciano, Salerno, Italy
| | - Gaetano Guerra
- Dipartimento di Chimica and INSTM Research Unit, Università degli Studi di Salerno, via Ponte don Melillo, 84084 Fisciano, Salerno, Italy
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9
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Rizzo P, Beltrani M, Guerra G. Induced vibrational circular dichroism and polymorphism of syndiotactic polystyrene. Chirality 2010; 22 Suppl 1:E67-73. [DOI: 10.1002/chir.20871] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Affiliation(s)
- Paola Rizzo
- Dipartimento di Chimica and INSTM Research Unit, Università di Salerno, Via Ponte Don Melillo, 84084 Fisciano (Salerno), Italy
| | - Christophe Daniel
- Dipartimento di Chimica and INSTM Research Unit, Università di Salerno, Via Ponte Don Melillo, 84084 Fisciano (Salerno), Italy
| | - Gaetano Guerra
- Dipartimento di Chimica and INSTM Research Unit, Università di Salerno, Via Ponte Don Melillo, 84084 Fisciano (Salerno), Italy
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11
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Kudo M, Hanashima T, Muranaka A, Sato H, Uchiyama M, Azumaya I, Hirano T, Kagechika H, Tanatani A. Identification of Absolute Helical Structures of Aromatic Multilayered Oligo(m-phenylurea)s in Solution. J Org Chem 2009; 74:8154-63. [DOI: 10.1021/jo901934r] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mayumi Kudo
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Takayuki Hanashima
- School of Biomedical Science, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Atsuya Muranaka
- Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hisako Sato
- Faculty of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- PRESTO, Japan Science and Technology Agency (JST), Japan
| | - Masanobu Uchiyama
- Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Isao Azumaya
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
| | - Tomoya Hirano
- School of Biomedical Science, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hiroyuki Kagechika
- School of Biomedical Science, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Aya Tanatani
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
- PRESTO, Japan Science and Technology Agency (JST), Japan
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12
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Shanmugam G, Polavarapu PL. Concentration- and dehydration-dependent structural transitions in poly-l-lysine. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.04.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Abstract
The excited-state dynamics of the RNA homopolymer of cytosine and of the 18-mer (dC)(18) were studied by steady-state and time-resolved absorption and emission spectroscopy. At pH 6.8, excitation of poly(rC) by a femtosecond UV pump pulse produces excited states that decay up to one order of magnitude more slowly than the excited states formed in the mononucleotide cytidine 5'-monophosphate under the same conditions. Even slower relaxation is observed for the hemiprotonated, self-associated form of poly(rC), which is stable at acidic pH. Transient absorption and time-resolved fluorescence signals for (dC)(18) at pH 6.8 are similar to ones observed for poly(rC) near pH 4, indicating that hemiprotonated structures are found in DNA C tracts at neutral pH. In both systems, there is evidence for two kinds of emitting states with lifetimes of ~100 ps and slightly more than 1 ns. The former states are responsible for the bulk of emission from the hemiprotonated structures. Evidence suggests that slow electronic relaxation in these self-complexes is the result of vertical base stacking. The similar signals from RNA and DNA C tracts suggest a common base-stacked structure, which may be identical with that of i-motif DNA.
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Affiliation(s)
| | | | - Bern Kohler
- Corresponding author: e-mail: , Telephone +1-614-688-3944, Fax +1-614-292-1685
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14
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Petrovic AG, Polavarapu PL. Quadruplex structure of polyriboinosinic acid: dependence on alkali metal ion concentration, pH and temperature. J Phys Chem B 2008; 112:2255-60. [PMID: 18225882 DOI: 10.1021/jp075873v] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The vibrational infrared (IR) absorption and vibrational circular dichroism (VCD) spectral changes of polyinosinic acid (polyI) as a function of alkali metal ion concentration, temperature and pH have been investigated to establish how changes in spectral features relate to the structural modifications of polyI. A single positive VCD couplet associated with the carbonyl absorption band is considered to be the signature of quadruplex structure for polyI. The disruption of the quadruplex structure with temperature increase or pH increase at low alkali metal ion concentration is evidenced by the disappearance of this positive VCD couplet. The absence of any VCD signal upon quadruplex disruption indicates that the newly formed structure lacks helical chirality and is likely to be disordered. In the presence of 1 M NaCl or 0.1 M NaCl, the heat-induced quadruplex disruption is completely reversible. A mildly alkaline environment, in the presence of 0.1 M NaCl, is not sufficient to support the quadruplex structure of polyI. Trehalose-assisted polyI film at room temperature exhibits the same quadruplex spectral signature as that seen for solution at room temperature, but the quadruplex spectral signature in the film state remains at higher temperature, unlike in solution. This indicates that the quadruplex structure of polyI in the film state resists heat-induced disruptions.
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Affiliation(s)
- Ana G Petrovic
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
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15
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Petrovic AG, Polavarapu PL. The quadruplex-duplex structural transition of polyriboguanylic acid. J Phys Chem B 2008; 112:2245-54. [PMID: 18225881 DOI: 10.1021/jp0758723] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The vibrational infrared (IR) absorption and vibrational circular dichroism (VCD) spectral changes of polyriboguanylic acid (polyG) as a function of time, temperature and pH have been investigated to establish how changes in spectral features relate to the structural modifications of polyG. From the progression of IR and VCD spectral features with respect to time, it is observed that stabilization of the quadruplex structure at pH 6.4 (near-neutral environment) takes place within 5 days. This stabilization process is most clearly evidenced by a downshift of the carbonyl absorption band and the corresponding positive VCD couplet, from 1689 to approximately 1682 cm(-1) in time. Time-induced spectral modifications also indicated that, in an acidic environment (pH 3.1) and within a 5 day waiting period, polyG develops a duplex structure. An additional positive VCD couplet associated with an absorption band at 1589 cm(-1) is identified as a marker of the polyG duplex structure. From the progression of spectral features with respect to temperature at pH 6.4, it is found that heating induces structural changes that favor the formation of a duplex structure. This duplex structure, at pH 6.4, would not form at room temperature simply by the passage of time. When polyG is in an acidic environment (pH 3.1), heating accelerates the conversion to the duplex structure that could also be obtained with passage of time at that pH. On the basis of the comparison of experimental and quantum theoretical VCD spectra for polyG, the key spectral signature for the quadruplex form is considered to be a single positive VCD couplet, while the spectral signature for a duplex form is considered to contain an additional positive VCD couplet at a lower frequency.
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Affiliation(s)
- Ana G Petrovic
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
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16
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Zarudnaya MI, Stepanyugin AV, Potyahaylo AL, Hovorun DM. Detection of two different protonated forms of poly(C) by electrophoresis method. ACTA ACUST UNITED AC 2008. [DOI: 10.7124/bc.000792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- M. I. Zarudnaya
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - A. V. Stepanyugin
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - A. L. Potyahaylo
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - D. M. Hovorun
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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