1
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Hoeher JE, Sande NE, Widom JR. Probing and perturbing riboswitch folding using a fluorescent base analogue. Photochem Photobiol 2024; 100:419-433. [PMID: 38098287 PMCID: PMC10950518 DOI: 10.1111/php.13896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 03/20/2024]
Abstract
Riboswitches are mRNA segments that regulate gene expression in response to ligand binding. The Class I preQ1 riboswitch consists of a stem-loop and an adenine-rich single-stranded tail ("L3"), which adopt a pseudoknot structure upon binding of the ligand preQ1 . We inserted 2-aminopurine (2-AP), a fluorescent analogue of adenine (A), into the riboswitch at six different positions within L3. Here, 2-AP functions both as a spectroscopic probe and as a "mutation" that reveals how alteration of specific A residues impacts the riboswitch. Using fluorescence and circular dichroism spectroscopy, we found that 2-AP decreases the affinity of the riboswitch for preQ1 at all labeling positions tested, although modified and unmodified variants undergo the same global conformational changes at sufficiently high preQ1 concentration. 2-AP substitution is most detrimental to ligand binding at sites proximal to the ligand-binding pocket, while distal labeling sites exhibit the largest impacts on the stability of the L3 domain in the absence of ligand. Insertion of multiple 2-AP residues does not induce significant additional disruptions. Our results show that interactions involving the A residues in L3 play a critical role in ligand recognition by the preQ1 riboswitch and that 2-AP substitution exerts complex and varied impacts on this riboswitch.
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Affiliation(s)
- Janson E. Hoeher
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR
| | - Natalie E. Sande
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR
| | - Julia R. Widom
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR
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2
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Zhang J. Probing RNA Structures and Interactions Using Fluorescence Lifetime Analyses. Methods Mol Biol 2023; 2568:13-23. [PMID: 36227559 PMCID: PMC11268537 DOI: 10.1007/978-1-0716-2687-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Structural analyses of large, complex noncoding RNAs continue to lag behind their rapid discovery and functional descriptions. Site-specifically incorporated, minimally invasive fluorescent probes such as 2-aminopurine (2AP) and pyrrolo-cytosine (PyC) have provided essential complementary information about local RNA structure, conformational dynamics, and interactions. Here I describe a protocol that benchmarks and correlates local RNA conformations with their respective fluorescence lifetimes, as a general technique that confers key advantages over fluorescence intensity-based methods. The observation that fluorescence lifetimes are more sensitive to local structures than sequence contexts suggests broad utility across diverse RNA and ribonucleoprotein systems.
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Affiliation(s)
- Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
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3
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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4
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McGovern-Gooch KR, Baird NJ. Fluorescence-based investigations of RNA-small molecule interactions. Methods 2019; 167:54-65. [PMID: 31129289 DOI: 10.1016/j.ymeth.2019.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/08/2019] [Accepted: 05/20/2019] [Indexed: 12/17/2022] Open
Abstract
Interrogating non-coding RNA structures and functions with small molecules is an area of rapidly increasing interest among biochemists and chemical biologists. However, many biochemical approaches to monitoring RNA structures are time-consuming and low-throughput, and thereby are only of limited utility for RNA-small molecule studies. Fluorescence-based techniques are powerful tools for rapid investigation of RNA conformations, dynamics, and interactions with small molecules. Many fluorescence methods are amenable to high-throughput analysis, enabling library screening for small molecule binders. In this review, we summarize numerous fluorescence-based approaches for identifying and characterizing RNA-small molecule interactions. We describe in detail a high-information content dual-reporter FRET assay we developed to characterize small molecule-induced conformational and stability changes. Our assay is uniquely suited as a platform for both small molecule discovery and thorough characterization of RNA-small molecule binding mechanisms. Given the growing recognition of non-coding RNAs as attractive targets for therapeutic intervention, we anticipate our FRET assay and other fluorescence-based techniques will be indispensable for the development of potent and specific small molecule inhibitors targeting RNA.
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Affiliation(s)
- Kayleigh R McGovern-Gooch
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19104 United States
| | - Nathan J Baird
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19104 United States.
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5
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Cho SJ, Ghorbani-Choghamarani A, Saito Y, Hudson RHE. 6-Phenylpyrrolocytidine: An Intrinsically Fluorescent, Environmentally Responsive Nucleoside Analogue. ACTA ACUST UNITED AC 2019; 76:e75. [PMID: 30725523 DOI: 10.1002/cpnc.75] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The detailed synthetic protocols for the preparation of phosphoramidite reagents compatible with standard, automated oligonucleotide synthesis for the 2'-deoxy- and ribo-6-phenylpyrrolocyitidine are reported. Each protocol starts with the parent nucleoside and prepares the 5'-O-dimethoxytrityl-N4 -benzoyl-5-iodocytosine derivative for the nucleobase modification chemistry. The key step is the direct formation of 6-phenylpyrrolocytosine aglycon via a sequential, one-pot Pd-catalyzed Sonogashira-type cross- coupling followed by a 5-endo-dig cyclization. Subsequent standard transformations provide the deoxy- and 2'-O-tert-butyldimethysilyl protected ribo- nucleoside phosphoramidite reagents. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Sung Ju Cho
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Arash Ghorbani-Choghamarani
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada.,Department of Chemistry, Faculty of Science, Ilam University, Ilam, Iran
| | - Yoshio Saito
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada.,Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima, Japan
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
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6
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Bull GD, Thompson KC. Proton Transfer and Tautomerism in 2-Aminopurine-Thymine and Pyrrolocytosine-Guanine Base Pairs. Biochemistry 2018; 57:4547-4561. [PMID: 30024730 DOI: 10.1021/acs.biochem.8b00521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Pyrrolocytosine (PC) and 2-aminopurine (2AP) are fluorescent nucleobase analogues of the DNA nucleobases cytosine and adenine, respectively, and form base pairs with guanine and thymine. Both fluorescent nucleobases are used extensively as probes for local structure in nucleic acids as the fluorescence properties of PC and 2AP are very sensitive to changes such as helix formation, although the reasons for this sensitivity are not clear. To address this question, ab initio calculations have been used to calculate energies, at the MP2 and CIS level, of three different tautomer pairings of PC-G, and two of 2AP-T, which can potentially be interconverted by double proton transfer between the bases. Potential energy curves linking the different tautomer pairs have been calculated. For both PC-G and 2AP-T, the most stable tautomer pair in the electronic ground state is that analogous to the natural C-G and A-T base pair. In the case of 2AP-T, an alternative, stable, tautomer base pair was located in the first electronically excited state; however, it lies higher in energy than the tautomer pair analogous to A-T, making conversion to the alternative form unlikely. In contrast, in the case of PC-G, an alternative tautomer base pair is found to be the most stable form in the first electronically excited state, and this form is accessible following initial excitation from the ground state tautomer pair, thus suggesting an alternative deactivation route via double proton transfer may be possible when PC is involved in hydrogen bonding, such as occurs in helical conformations.
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Affiliation(s)
- Graham D Bull
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck , University of London , Malet Street , Bloomsbury, London WC1E 7HX , U.K
| | - Katherine C Thompson
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck , University of London , Malet Street , Bloomsbury, London WC1E 7HX , U.K
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7
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Trachsel MA, Lobsiger S, Schär T, Blancafort L, Leutwyler S. Planarizing cytosine: The S 1 state structure, vibrations, and nonradiative dynamics of jet-cooled 5,6-trimethylenecytosine. J Chem Phys 2018; 146:244308. [PMID: 28668059 DOI: 10.1063/1.4989465] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We measure the S0 → S1 spectrum and time-resolved S1 state nonradiative dynamics of the "clamped" cytosine derivative 5,6-trimethylenecytosine (TMCyt) in a supersonic jet, using two-color resonant two-photon ionization (R2PI), UV/UV holeburning, and ns time-resolved pump/delayed ionization. The experiments are complemented with spin-component scaled second-order approximate coupled cluster (SCS-CC2), time-dependent density functional theory, and multi-state second-order perturbation-theory (MS-CASPT2) ab initio calculations. While the R2PI spectrum of cytosine breaks off ∼500 cm-1 above its 000 band, that of TMCyt extends up to +4400 cm-1 higher, with over a hundred resolved vibronic bands. Thus, clamping the cytosine C5-C6 bond allows us to explore the S1 state vibrations and S0 → S1 geometry changes in detail. The TMCyt S1 state out-of-plane vibrations ν1', ν3', and ν5' lie below 420 cm-1, and the in-plane ν11', ν12', and ν23' vibrational fundamentals appear at 450, 470, and 944 cm-1. S0 → S1 vibronic simulations based on SCS-CC2 calculations agree well with experiment if the calculated ν1', ν3', and ν5' frequencies are reduced by a factor of 2-3. MS-CASPT2 calculations predict that the ethylene-type S1 ⇝ S0 conical intersection (CI) increases from +366 cm-1 in cytosine to >6000 cm-1 in TMCyt, explaining the long lifetime and extended S0 → S1 spectrum. The lowest-energy S1 ⇝ S0 CI of TMCyt is the "amino out-of-plane" (OPX) intersection, calculated at +4190 cm-1. The experimental S1 ⇝ S0 internal conversion rate constant at the S1(v'=0) level is kIC=0.98-2.2⋅108 s-1, which is ∼10 times smaller than in 1-methylcytosine and cytosine. The S1(v'=0) level relaxes into the T1(3ππ*) state by intersystem crossing with kISC=0.41-1.6⋅108 s-1. The T1 state energy is measured to lie 24 580±560 cm-1 above the S0 state. The S1(v'=0) lifetime is τ=2.9 ns, resulting in an estimated fluorescence quantum yield of Φfl=24%. Intense two-color R2PI spectra of the TMCyt amino-enol tautomers appear above 36 000 cm-1. A sharp S1 ionization threshold is observed for amino-keto TMCyt, yielding an adiabatic ionization energy of 8.114±0.002 eV.
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Affiliation(s)
- Maria A Trachsel
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Simon Lobsiger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Tobias Schär
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Facultat de Ciències, Universitat de Girona, C/M. A. Campmany 69, 17003 Girona, Spain
| | - Samuel Leutwyler
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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8
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Nguyen QL, Spata VA, Matsika S. Photophysical properties of pyrrolocytosine, a cytosine fluorescent base analogue. Phys Chem Chem Phys 2018; 18:20189-98. [PMID: 27251599 DOI: 10.1039/c6cp01559j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The photophysical behavior of pyrrolocytosine (PC), a fluorescent base analogue of cytosine, has been investigated using theoretical approaches. The similarities between the PC and cytosine structures allow PC to maintain the pseudo-Watson-Crick base-pairing arrangement with guanine. Cytosine, similar to the other natural nucleobases, is practically non-fluorescent, because of ultrafast radiationless decay occurring through conical intersections. PC displays a much higher fluorescence quantum yield than cytosine, making it an effective fluorescent marker to study the structure, function, and dynamics of DNA/RNA complexes. Similar to 2-aminopurine, a constitutional isomer of adenine that base-pairs with thymine, PC's fluorescence is quenched when it is incorporated into a dinucleotide or a trinucleotide. In this work we examine the photophysical properties of isolated PC, microhydrated PC, as well as, complexes where PC is either base-stacked or hydrogen-bonded with guanine. Our results indicate that hydration affects the radiationless decay pathways in PC by destabilizing conical intersections. The calculations of dimers and trimers show that the radiative decay is affected by π stacking, while the presence of charge transfer states between PC and guanine may contribute to radiationless decay.
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9
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Fluorescent nucleobases as tools for studying DNA and RNA. Nat Chem 2017; 9:1043-1055. [PMID: 29064490 DOI: 10.1038/nchem.2859] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023]
Abstract
Understanding the diversity of dynamic structures and functions of DNA and RNA in biology requires tools that can selectively and intimately probe these biomolecules. Synthetic fluorescent nucleobases that can be incorporated into nucleic acids alongside their natural counterparts have emerged as a powerful class of molecular reporters of location and environment. They are enabling new basic insights into DNA and RNA, and are facilitating a broad range of new technologies with chemical, biological and biomedical applications. In this Review, we will present a brief history of the development of fluorescent nucleobases and explore their utility as tools for addressing questions in biophysics, biochemistry and biology of nucleic acids. We provide chemical insights into the two main classes of these compounds: canonical and non-canonical nucleobases. A point-by-point discussion of the advantages and disadvantages of both types of fluorescent nucleobases is made, along with a perspective into the future challenges and outlook for this burgeoning field.
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10
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Freeman NS, Moore CE, Wilhelmsson LM, Tor Y. Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes. J Org Chem 2016; 81:4530-9. [PMID: 27128151 PMCID: PMC5493935 DOI: 10.1021/acs.joc.6b00310] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nucleodyes, visibly colored chromophoric nucleoside analogues, are reported. Design criteria are outlined and the syntheses of cytidine and uridine azo dye analogues derived from 6-aminouracil are described. Structural analysis shows that the nucleodyes are sound structural analogues of their native nucleoside counterparts, and photophysical studies demonstrate that the nucleodyes are sensitive to microenvironmental changes. Quantum chemical calculations are presented as a valuable complementary tool for the design of strongly absorbing nucleodyes, which overlap with the emission of known fluorophores. Förster critical distance (R0) calculations determine that the nucleodyes make good FRET pairs with both 2-aminopurine (2AP) and pyrrolocytosine (PyC). Additionally, unique tautomerization features exhibited by 5-(4-nitrophenylazo)-6-oxocytidine (8) are visualized by an extraordinary crystal structure.
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Affiliation(s)
- Noam S. Freeman
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
| | - Curtis E. Moore
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
| | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry
and Biochemistry, Chalmers University of Technology, Gothenburg 41296, Sweden
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
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11
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Elmehriki AAH, Suchý M, Chicas KJ, Wojciechowski F, Hudson RHE. Synthesis and spectral characterization of environmentally responsive fluorescent deoxycytidine analogs. ARTIFICIAL DNA, PNA & XNA 2015; 5:e29174. [PMID: 25483932 DOI: 10.4161/adna.29174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Herein, we describe the synthesis and spectroscopic properties of five novel pyrrolodeoxycytidine analogs, and the related 5-(1-pyrenylethynyl)-2'-deoxycytidine analog; as well as fluorescence characterization of 5-(p-methoxyphenylethynyl)-2'-deoxyuridine. Within this series of compounds, rigidification of the structure from 6-phenylpyrrolodeoxycytidine to 5,6-benzopyrroldeoxycytidine made remarkable improvement of the fluorescence quantum yield (Φ ~1, EtOH) and substantially increased the Stokes shift. Exchange of the phenyl group of 6-phenylpyrrolodeoxycytidine for other heterocycles (benzofuryl or indolyl) produced an increase in the extinction coefficient at the excitation wavelength while preserving high quantum yields. The steady-state fluorescence response to the environment was determined by sensitivity of Stokes shift to solvent polarity. The effect of solvent polarity on fluorescence emission intensity was concurrently examined and showed that 5,6-benzopyrrolodeoxycytidine is highly sensitive to the presence of water. On the other hand, the previously synthesized 5-(p-methoxyphenylethynyl)-2'-deoxyuridine was found to be sensitive to solvent viscosity indicating molecular rotor behavior.
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Affiliation(s)
- Adam A H Elmehriki
- a Department of Chemistry; The University of Western Ontario; London, ON Canada
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12
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Yang H, Mei H, Seela F. Pyrrolo-dC Metal-Mediated Base Pairs in the Reverse Watson-Crick Double Helix: Enhanced Stability of Parallel DNA and Impact of 6-Pyridinyl Residues on Fluorescence and Silver-Ion Binding. Chemistry 2015; 21:10207-19. [PMID: 26096946 DOI: 10.1002/chem.201500582] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Indexed: 11/11/2022]
Abstract
Reverse Watson-Crick DNA with parallel-strand orientation (ps DNA) has been constructed. Pyrrolo-dC (PyrdC) nucleosides with phenyl and pyridinyl residues linked to the 6 position of the pyrrolo[2,3-d]pyrimidine base have been incorporated in 12- and 25-mer oligonucleotide duplexes and utilized as silver-ion binding sites. Thermal-stability studies on the parallel DNA strands demonstrated extremely strong silver-ion binding and strongly enhanced duplex stability. Stoichiometric UV and fluorescence titration experiments verified that a single (2py) PyrdC-(2py) PyrdC pair captures two silver ions in ps DNA. A structure for the PyrdC silver-ion base pair that aligns 7-deazapurine bases head-to-tail instead of head-to-head, as suggested for canonical DNA, is proposed. The silver DNA double helix represents the first example of a ps DNA structure built up of bidentate and tridentate reverse Watson-Crick base pairs stabilized by a dinuclear silver-mediated PyrdC pair.
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Affiliation(s)
- Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany)
| | - Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany)
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857. .,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany).
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13
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Zhang J, Ferré-D'Amaré AR. Direct evaluation of tRNA aminoacylation status by the T-box riboswitch using tRNA-mRNA stacking and steric readout. Mol Cell 2014; 55:148-55. [PMID: 24954903 DOI: 10.1016/j.molcel.2014.05.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/28/2014] [Accepted: 04/08/2014] [Indexed: 01/01/2023]
Abstract
T-boxes are gene-regulatory mRNA elements with which Gram-positive bacteria sense amino acid availability. T-boxes have two functional domains. Stem I recognizes the overall shape and anticodon of tRNA, while a 3' domain evaluates its aminoacylation status, overcoming an otherwise stable transcriptional terminator if the bound tRNA is uncharged. Although T-boxes are believed to evaluate tRNA charge status without using any proteins, this has not been demonstrated experimentally because of the instability of aminoacyl-tRNA. Using a simple method to prepare homogeneous aminoacyl-tRNA, we show that the Bacillus subtilis glyQS T-box functions independently of any tRNA-binding protein. Comparison of aminoacyl-tRNA analogs demonstrates that the T-box detects the molecular volume of tRNA 3'-substituents. Calorimetry and fluorescence lifetime analysis of labeled RNAs shows that the tRNA acceptor end coaxially stacks on a helix in the T-box 3' domain. This intimate intermolecular association, selective for uncharged tRNA, stabilizes the antiterminator conformation of the T-box.
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Affiliation(s)
- Jinwei Zhang
- National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA.
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14
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15
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Dyakonova ES, Koval VV, Ishchenko AA, Saparbaev MK, Kaptein R, Fedorova OS. Kinetic mechanism of the interaction of Saccharomyces cerevisiae AP-endonuclease 1 with DNA substrates. BIOCHEMISTRY (MOSCOW) 2012; 77:1162-71. [DOI: 10.1134/s0006297912100082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Ming X, Seela F. A Nucleobase-Discriminating Pyrrolo-dC Click Adduct Designed for DNA Fluorescence Mismatch Sensing. Chemistry 2012; 18:9590-600. [DOI: 10.1002/chem.201103385] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 04/17/2012] [Indexed: 11/10/2022]
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17
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Völker J, Gindikin V, Klump HH, Plum GE, Breslauer KJ. Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states. J Am Chem Soc 2012; 134:6033-44. [PMID: 22397401 PMCID: PMC3318849 DOI: 10.1021/ja3010896] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Indexed: 11/30/2022]
Abstract
DNA repeat domains can form ensembles of canonical and noncanonical states, including stable and metastable DNA secondary structures. Such sequence-induced structural diversity creates complex conformational landscapes for DNA processing pathways, including those triplet expansion events that accompany replication, recombination, and/or repair. Here we demonstrate further levels of conformational complexity within repeat domains. Specifically, we show that bulge loop structures within an extended repeat domain can form dynamic ensembles containing a distribution of loop positions, thereby yielding families of positional loop isomers, which we designate as "rollamers". Our fluorescence, absorbance, and calorimetric data are consistent with loop migration/translocation between sites within the repeat domain ("rollamerization"). We demonstrate that such "rollameric" migration of bulge loops within repeat sequences can invade and disrupt previously formed base-paired domains via an isoenthalpic, entropy-driven process. We further demonstrate that destabilizing abasic lesions alter the loop distributions so as to favor "rollamers" with the lesion positioned at the duplex/loop junction, sites where the flexibility of the abasic "universal hinge" relaxes unfavorable interactions and/or facilitates topological accommodation. Another strategic siting of an abasic site induces directed loop migration toward denaturing domains, a phenomenon that merges destabilizing domains. In the aggregate, our data reveal that dynamic ensembles within repeat domains profoundly impact the overall energetics of such DNA constructs as well as the distribution of states by which they denature/renature. These static and dynamic influences within triplet repeat domains expand the conformational space available for selection and targeting by the DNA processing machinery. We propose that such dynamic ensembles and their associated impact on DNA properties influence pathways that lead to DNA expansion.
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Affiliation(s)
- Jens Völker
- Department
of Chemistry and
Chemical Biology, Rutgers, The State University of New
Jersey, 610 Taylor Road, Piscataway, New Jersey 08854,
United States
| | - Vera Gindikin
- Department
of Chemistry and
Chemical Biology, Rutgers, The State University of New
Jersey, 610 Taylor Road, Piscataway, New Jersey 08854,
United States
| | - Horst H. Klump
- Department
of Molecular and
Cell Biology, University of Cape Town,
Private Bag, Rondebosch 7800, South Africa
| | - G. Eric Plum
- IBET Inc., 1507 Chambers
Road, Suite 301, Columbus, Ohio 43212, United States
| | - Kenneth J. Breslauer
- Department
of Chemistry and
Chemical Biology, Rutgers, The State University of New
Jersey, 610 Taylor Road, Piscataway, New Jersey 08854,
United States
- The Cancer Institute
of New Jersey, New Brunswick, New Jersey 08901, United
States
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18
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Huang W, Kim J, Jha S, Aboul-Ela F. Conformational heterogeneity of the SAM-I riboswitch transcriptional ON state: a chaperone-like role for S-adenosyl methionine. J Mol Biol 2012; 418:331-49. [PMID: 22425639 DOI: 10.1016/j.jmb.2012.02.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 02/09/2012] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
Abstract
Riboswitches are promising targets for the design of novel antibiotics and engineering of portable genetic regulatory elements. There is evidence that variability in riboswitch properties allows tuning of expression for genes involved in different stages of biosynthetic pathways by mechanisms that are not currently understood. Here, we explore the mechanism for tuning of S-adenosyl methionine (SAM)-I riboswitch folding. Most SAM-I riboswitches function at the transcriptional level by sensing the cognate ligand SAM. SAM-I riboswitches orchestrate the biosynthetic pathways of cysteine, methionine, SAM, and so forth. We use base-pair probability predictions to examine the secondary-structure folding landscape of several SAM-I riboswitch sequences. We predict different folding behaviors for different SAM-I riboswitch sequences. We identify several "decoy" base-pairing interactions involving 5' riboswitch residues that can compete with the formation of a P1 helix, a component of the ligand-bound "transcription OFF" state, in the absence of SAM. We hypothesize that blockage of these interactions through SAM contacts contributes to stabilization of the OFF state in the presence of ligand. We also probe folding patterns for a SAM-I riboswitch RNA using constructs with different 3' truncation points experimentally. Folding was monitored through fluorescence, susceptibility to base-catalyzed cleavage, nuclear magnetic resonance, and indirectly through SAM binding. We identify key decision windows at which SAM can affect the folding pathway towards the OFF state. The presence of decoy conformations and differential sensitivities to SAM at different transcript lengths is crucial for SAM-I riboswitches to modulate gene expression in the context of global cellular metabolism.
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Affiliation(s)
- Wei Huang
- Department of Biological Science, Louisiana State University, Baton Rouge, LA 70803, USA
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19
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Buskiewicz IA, Burke JM. Folding of the hammerhead ribozyme: pyrrolo-cytosine fluorescence separates core folding from global folding and reveals a pH-dependent conformational change. RNA (NEW YORK, N.Y.) 2012; 18:434-448. [PMID: 22274955 PMCID: PMC3285932 DOI: 10.1261/rna.030999.111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 11/09/2011] [Indexed: 05/30/2023]
Abstract
The catalytic activity of the hammerhead ribozyme is limited by its ability to fold into the native tertiary structure. Analysis of folding has been hampered by a lack of assays that can independently monitor the environment of nucleobases throughout the ribozyme-substrate complex in real time. Here, we report the development and application of a new folding assay in which we use pyrrolo-cytosine (pyC) fluorescence to (1) probe active-site formation, (2) examine the ability of peripheral ribozyme domains to support native folding, (3) identify a pH-dependent conformational change within the ribozyme, and (4) explore its influence on the equilibrium between the folded and unfolded core of the hammerhead ribozyme. We conclude that the natural ribozyme folds in two distinct noncooperative steps and the pH-dependent correlation between core folding and activity is linked to formation of the G8-C3 base pair.
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Affiliation(s)
- Iwona A Buskiewicz
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA.
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20
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Gray RD, Petraccone L, Buscaglia R, Chaires JB. 2-aminopurine as a probe for quadruplex loop structures. Methods Mol Biol 2010; 608:121-36. [PMID: 20012419 DOI: 10.1007/978-1-59745-363-9_8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescent reporter groups have served for many years as sensitive probes of macromolecular structure. Such probes can be especially useful in comparative studies such as detection of conformational changes and discrimination among structural models. Spectroscopic methods such as fluorescence are attractive because they are rapid, require small amounts of material, are nondestructive, can be carried out with commonly available equipment, and are relatively inexpensive. In addition, there is a rich library of theoretical and practical materials available to aid in data interpretation.The intrinsic fluorescence of most nucleic acids is too low to be useful in structural studies. Thus, it is necessary to incorporate a suitable reporter group to utilize fluorescence methods involving polynucleotide structure. A highly fluorescent adenine analog, 2-aminopurine, has long served in this capacity. The present article describes our use of 2-aminopurine as a probe of loop structures in quadruplex DNA. In particular, we show how knowledge of the relative intensity of 2-aminopurine emission as well as its sensitivity to exogenous quenching molecules such as acrylamide can aid in comparing crystal and solution structures of an oligonucleotide model of the human telomere and in discrimination among models containing tandem repeats of the telomeric quadruplex.
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Affiliation(s)
- Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
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21
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Wahba AS, Esmaeili A, Damha MJ, Hudson RHE. A single-label phenylpyrrolocytidine provides a molecular beacon-like response reporting HIV-1 RT RNase H activity. Nucleic Acids Res 2010; 38:1048-56. [PMID: 19933258 PMCID: PMC2817455 DOI: 10.1093/nar/gkp1022] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2009] [Revised: 10/19/2009] [Accepted: 10/19/2009] [Indexed: 12/12/2022] Open
Abstract
6-Phenylpyrrolocytidine (PhpC), a structurally conservative and highly fluorescent cytidine analog, was incorporated into oligoribonucleotides. The PhpC-containing RNA formed native-like duplex structures with complementary DNA or RNA. The PhpC-modification was found to act as a sensitive reporter group being non-disruptive to structure and the enzymatic activity of RNase H. A RNA/DNA hybrid possessing a single PhpC insert was an excellent substrate for HIV-1 RT Ribonuclease H and rapidly reported cleavage of the RNA strand with a 14-fold increase in fluorescence intensity. The PhpC-based assay for RNase H was superior to the traditional molecular beacon approach in terms of responsiveness, rapidity and ease (single label versus dual). Furthermore, the PhpC-based assay is amenable to high-throughput microplate assay format and may form the basis for a new screen for inhibitors of HIV-RT RNase H.
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Affiliation(s)
- Alexander S. Wahba
- Department of Chemistry, McGill University, Montreal, QC, H3A 2K6 Canada, Department of Chemistry, University of Birjand, Birjand, Iran and Department of Chemistry, University of Western Ontario, London, ON, N6A 5B7 Canada
| | - Abbasali Esmaeili
- Department of Chemistry, McGill University, Montreal, QC, H3A 2K6 Canada, Department of Chemistry, University of Birjand, Birjand, Iran and Department of Chemistry, University of Western Ontario, London, ON, N6A 5B7 Canada
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montreal, QC, H3A 2K6 Canada, Department of Chemistry, University of Birjand, Birjand, Iran and Department of Chemistry, University of Western Ontario, London, ON, N6A 5B7 Canada
| | - Robert H. E. Hudson
- Department of Chemistry, McGill University, Montreal, QC, H3A 2K6 Canada, Department of Chemistry, University of Birjand, Birjand, Iran and Department of Chemistry, University of Western Ontario, London, ON, N6A 5B7 Canada
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22
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Wojciechowski F, Hudson RHE. Peptide nucleic acid containing a meta-substituted phenylpyrrolocytosine exhibits a fluorescence response and increased binding affinity toward RNA. Org Lett 2009; 11:4878-81. [PMID: 19788268 DOI: 10.1021/ol9019474] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Peptide nucleic acids (PNA) containing meta-substituted 6-phenylpyrrolocytosine (PhpC), [mono-m-(aminoethoxy)phenyl]pyrrolocytosine (mmePhpC), [mono-m-(aminopropoxy)phenyl]pyrrolocytosine (mmpPhpC), and [mono-m-(guanidinoethoxy)phenyl]pyrrolocytosine (mmguaPhpC), have been synthesized. Meta-substituted PhpCs have been hybridized with overall higher binding affinity toward DNA and RNA than previously synthesized moePhpC or newly synthesized mopPhpC. The guanidinium-containing nucleobase, mmguaPhpC, exhibited the highest increase in binding affinity toward RNA while fluorometrically responding on the state of hybridization.
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Affiliation(s)
- Filip Wojciechowski
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
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23
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Baase WA, Jose D, Ponedel BC, von Hippel PH, Johnson NP. DNA models of trinucleotide frameshift deletions: the formation of loops and bulges at the primer-template junction. Nucleic Acids Res 2009; 37:1682-9. [PMID: 19155277 PMCID: PMC2655659 DOI: 10.1093/nar/gkn1042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although mechanisms of single-nucleotide residue deletion have been investigated, processes involved in the loss of longer nucleotide sequences during DNA replication are poorly understood. Previous reports have shown that in vitro replication of a 3′-TGC TGC template sequence can result in the deletion of one 3′-TGC. We have used low-energy circular dichroism (CD) and fluorescence spectroscopy to investigate the conformations and stabilities of DNA models of the replication intermediates that may be implicated in this frameshift. Pyrrolocytosine or 2-aminopurine residues, site-specifically substituted for cytosine or adenine in the vicinity of extruded base sequences, were used as spectroscopic probes to examine local DNA conformations. An equilibrium mixture of four hybridization conformations was observed when template bases looped-out as a bulge, i.e. a structure flanked on both sides by duplex DNA. In contrast, a single-loop structure with an unusual unstacked DNA conformation at its downstream edge was observed when the extruded bases were positioned at the primer–template junction, showing that misalignments can be modified by neighboring DNA secondary structure. These results must be taken into account in considering the genetic and biochemical mechanisms of frameshift mutagenesis in polymerase-driven DNA replication.
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Affiliation(s)
- Walter A Baase
- Department of Chemistry and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1229, USA
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