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Abstract
Stille Coupling is a versatile C-C bond forming reaction with high functional group tolerance under mild conditions. Our on column synthesis concept for RNA modification is based on the incorporation of iodo substituted nucleotide precursors to RNA during automated standard solid phase synthesis via TBDMS-, TC-, and ACE- protecting group strategies. Subsequently, the RNA, still bound on solid support, is ready for orthogonal postsynthetic functionalization via Stille cross-couplings utilizing the advantages of solid phase synthesis. Several monomer test reactions were employed with 2-iodo adenosine and 5-iodo uridine and organostannanes as coupling partners under different conditions, changing the catalyst/ligand system, temperature, and reaction time as well as conventional heating and microwave irradiation. Finally, Stille cross-couplings under optimized conditions were transferred to fully protected 5-mer and 12-mer RNA oligonucleotides on-column. Deprotection and cleavage from solid support resulted in site-specifically labeled oligonucleotides. Derivatizations via Stille cross-couplings were performed initially with vinyltributylstannane as well as later with 2-furanyl-, 2-thiophene-, and benzothiophene-2-tributylstannanes yielding fluorescently functionalized RNA.
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Affiliation(s)
- Lena Wicke
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
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52
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53
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Sau SP, Hrdlicka PJ. C2'-pyrene-functionalized triazole-linked DNA: universal DNA/RNA hybridization probes. J Org Chem 2012; 77:5-16. [PMID: 22087648 PMCID: PMC3253902 DOI: 10.1021/jo201845z] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Development of universal hybridization probes, that is, oligonucleotides displaying identical affinity toward matched and mismatched DNA/RNA targets, has been a longstanding goal due to potential applications as degenerate PCR primers and microarray probes. The classic approach toward this end has been the use of "universal bases" that either are based on hydrogen-bonding purine derivatives or aromatic base analogues without hydrogen-bonding capabilities. However, development of probes that result in truly universal hybridization without compromising duplex thermostability has proven challenging. Here we have used the "click reaction" to synthesize four C2'-pyrene-functionalized triazole-linked 2'-deoxyuridine phosphoramidites. We demonstrate that oligodeoxyribonucleotides modified with the corresponding monomers display (a) minimally decreased thermal affinity toward DNA/RNA complements relative to reference strands, (b) highly robust universal hybridization characteristics (average differences in thermal denaturation temperatures of matched vs mismatched duplexes involving monomer W are <1.7 °C), and (c) exceptional affinity toward DNA targets containing abasic sites opposite of the modification site (ΔT(m) up to +25 °C). The latter observation, along with results from absorption and fluorescence spectroscopy, suggests that the pyrene moiety is intercalating into the duplex whereby the opposing nucleotide is pushed into an extrahelical position. These properties render C2'-pyrene-functionalized triazole-linked DNA as promising universal hybridization probes for applications in nucleic acid chemistry and biotechnology.
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Affiliation(s)
- Sujay P. Sau
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA
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54
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Wu F, Shao Y, Ma K, Cui Q, Liu G, Xu S. Simultaneous fluorescence light-up and selective multicolor nucleobase recognition based on sequence-dependent strong binding of berberine to DNA abasic site. Org Biomol Chem 2012; 10:3300-7. [DOI: 10.1039/c2ob00028h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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55
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Atsumi H, Maekawa K, Nakazawa S, Shiomi D, Sato K, Kitagawa M, Takui T, Nakatani K. Tandem Arrays of TEMPO and Nitronyl Nitroxide Radicals with Designed Arrangements on DNA. Chemistry 2011; 18:178-83. [DOI: 10.1002/chem.201102693] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Indexed: 12/24/2022]
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56
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Tanabe K, Ando Y, Nishimoto SI. Reversible modification of oligodeoxynucleotides: click reaction at phosphate group and alkali treatment. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.10.109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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57
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Xia Y, Li Y, Burts AO, Ottaviani MF, Tirrell DA, Johnson JA, Turro NJ, Grubbs RH. EPR Study of Spin Labeled Brush Polymers in Organic Solvents. J Am Chem Soc 2011; 133:19953-9. [DOI: 10.1021/ja2085349] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yan Xia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Yongjun Li
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Alan O. Burts
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - M. Francesca Ottaviani
- Department of Earth, Life and Environment Sciences, University of Urbino, Loc. Crocicchia -61029 Urbino, Italy
| | - David A. Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jeremiah A. Johnson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicholas J. Turro
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Robert H. Grubbs
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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58
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Motea EA, Lee I, Berdis AJ. Development of a 'clickable' non-natural nucleotide to visualize the replication of non-instructional DNA lesions. Nucleic Acids Res 2011; 40:2357-67. [PMID: 22086959 PMCID: PMC3300027 DOI: 10.1093/nar/gkr980] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The misreplication of damaged DNA is an important biological process that produces numerous adverse effects on human health. This report describes the synthesis and characterization of a non-natural nucleotide, designated 3-ethynyl-5-nitroindolyl-2′-deoxyriboside triphosphate (3-Eth-5-NITP), as a novel chemical reagent that can probe and quantify the misreplication of damaged DNA. We demonstrate that this non-natural nucleotide is efficiently inserted opposite an abasic site, a commonly formed and potentially mutagenic non-instructional DNA lesion. The strategic placement of the ethynyl moiety allows the incorporated nucleoside triphosphate to be selectively tagged with an azide-containing fluorophore using ‘click’ chemistry. This reaction provides a facile way to quantify the extent of nucleotide incorporation opposite non-instructional DNA lesions. In addition, the incorporation of 3-Eth-5-NITP is highly selective for an abasic site, and occurs even in the presence of a 50-fold molar excess of natural nucleotides. The biological applications of using 3-Eth-5-NITP as a chemical probe to monitor and quantify the misreplication of non-instructional DNA lesions are discussed.
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Affiliation(s)
- Edward A Motea
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
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59
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Synthesis and characterization of fluorescent perylene bisimide-containing glycopolymers for Escherichia coli conjugation and cell imaging. POLYMER 2011. [DOI: 10.1016/j.polymer.2011.10.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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60
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Flaender M, Sicoli G, Aci-Seche S, Reignier T, Maurel V, Saint-Pierre C, Boulard Y, Gambarelli S, Gasparutto D. A triple spin-labeling strategy coupled with DEER analysis to detect DNA modifications and enzymatic repair. Chembiochem 2011; 12:2560-3. [PMID: 21984076 DOI: 10.1002/cbic.201100550] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Indexed: 12/20/2022]
Abstract
In a spin: Spin-labeled oligonucleotides produced by click chemistry can be studied by EPR, by using a DEER sequence. This was used to test a complex triple-labeling strategy with damaged DNA. Extensive and accurate analysis of DNA structure and enzymatic repair processes were performed after digestion by EndoIV. Modified DNA structures and DNA-protein interactions can now be readily studied.
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Affiliation(s)
- Mélanie Flaender
- Institut Nanoscience et Cryogénie, Laboratoire de Chimie Inorganique et Biologique, UMR-E n°3 CEA-UJF, CEA-Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 9, France
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61
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Xu S, Shao Y, Ma K, Cui Q, Liu G, Wu F, Li M. Fluorescence light-up recognition of DNA nucleotide based on selective abasic site binding of an excited-state intramolecular proton transfer probe. Analyst 2011; 136:4480-5. [PMID: 21946800 DOI: 10.1039/c1an15652g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation-related diseases. Various fluorescence methods for SNP detection have been proposed and many are already in use. However, fluorescence enhancement for signal-on SNP identification without label modification still remains a challenge. Here, we find that the abasic site (AP site) in a DNA duplex can be developed as a binding pocket favorable for the occurrence of the excited-state intramolecular proton transfer (ESIPT) of a 3-hydroxyflavone, fisetin, which is used as a proof of concept for effective SNP identification. Fisetin binding at the AP site is highly selective for target thymine or cytosine facing the AP site by observation of a drastic increase in the ESIPT emission band. In addition, the target recognition selectivity based on this ESIPT process is not affected by flanking bases of the AP site. The binding selectivity of fisetin at the AP site is also confirmed by measurements of fluorescence resonance energy transfer, emission lifetime and DNA melting. The fluorescent signal-on sensing for SNP based on this fluorophore is substantially advantageous over the previously used fluorophores such as the AP site-specific signal-off organic ligands with a similar fluorescing mechanism before and after binding to DNA with hydrogen bonding interaction. We expect that this approach will be employed to develop a practical SNP detection method by locating an AP site toward a target and employing an ESIPT probe as readout.
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Affiliation(s)
- Shujuan Xu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
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62
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Nguyen P, Qin PZ. RNA dynamics: perspectives from spin labels. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:62-72. [PMID: 21882345 DOI: 10.1002/wrna.104] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dynamics are important and indispensible physical attributes that play essential roles in RNA function. RNA dynamics are complex, spanning vast timescales, and encompassing a large number of physical modes. The technique of site-directed spin labeling (SDSL), which derives information on local structural and dynamic features of a macromolecule by monitoring a chemically stable nitroxide radical using electron paramagnetic resonance spectroscopy, has been applied to monitor intrinsic dynamics at defined structural states as well as to probe conformational transition dynamics of RNAs. The current state of SDSL studies of RNA dynamics is summarized here. Further development and application of SDSL promise to open up many more opportunities for probing RNA dynamics and connecting dynamics to structure and function.
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Affiliation(s)
- Phuong Nguyen
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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63
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Ma K, Cui Q, Liu G, Wu F, Xu S, Shao Y. DNA abasic site-directed formation of fluorescent silver nanoclusters for selective nucleobase recognition. NANOTECHNOLOGY 2011; 22:305502. [PMID: 21719966 DOI: 10.1088/0957-4484/22/30/305502] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation related diseases. Various methods for SNP detection have been proposed and many are already in use. Here, we find that the abasic site (AP site) in the DNA duplex can be developed as a capping scaffold for the generation of fluorescent silver nanoclusters (Ag NCs). As a proof of concept, the DNA sequences from fragments near codon 177 of cancer supression gene p53 were used as a model for SNP detection by in situ formed Ag NCs. The formation of fluorescent Ag NCs in the AP site-containing DNA duplex is highly selective for cytosine facing the AP site and guanines flanking the site and can be employed in situ as readout for SNP detection. The fluorescent signal-on sensing for SNP based on this inorganic fluorophore is substantially advantageous over the previously reported signal-off responses using low-molecular-weight organic ligands. The strong dependence of fluorescent Ag NC formation on the sequences surrounding the AP site was successfully used to identify mutations in codon 177 of cancer supression gene p53. We anticipate that this approach will be employed to develop a practical SNP detection method by locating an AP site toward the midway cytosine in a target strand containing more than three consecutive cytosines.
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Affiliation(s)
- Kun Ma
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
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64
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Pulsed electron-electron double resonance: beyond nanometre distance measurements on biomacromolecules. Biochem J 2011; 434:353-63. [PMID: 21348855 DOI: 10.1042/bj20101871] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PELDOR (or DEER; pulsed electron-electron double resonance) is an EPR (electron paramagnetic resonance) method that measures via the dipolar electron-electron coupling distances in the nanometre range, currently 1.5-8 nm, with high precision and reliability. Depending on the quality of the data, the error can be as small as 0.1 nm. Beyond mere mean distances, PELDOR yields distance distributions, which provide access to conformational distributions and dynamics. It can also be used to count the number of monomers in a complex and allows determination of the orientations of spin centres with respect to each other. If, in addition to the dipolar through-space coupling, a through-bond exchange coupling mechanism contributes to the overall coupling both mechanisms can be separated and quantified. Over the last 10 years PELDOR has emerged as a powerful new biophysical method without size restriction to the biomolecule to be studied, and has been applied to a large variety of nucleic acids as well as proteins and protein complexes in solution or within membranes. Small nitroxide spin labels, paramagnetic metal ions, amino acid radicals or intrinsic clusters and cofactor radicals have been used as spin centres.
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65
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Krstić I, Hänsel R, Romainczyk O, Engels JW, Dötsch V, Prisner TF. Long-Range Distance Measurements on Nucleic Acids in Cells by Pulsed EPR Spectroscopy. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100886] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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66
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Krstić I, Hänsel R, Romainczyk O, Engels JW, Dötsch V, Prisner TF. Long-range distance measurements on nucleic acids in cells by pulsed EPR spectroscopy. Angew Chem Int Ed Engl 2011; 50:5070-4. [PMID: 21506223 DOI: 10.1002/anie.201100886] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Indexed: 12/18/2022]
Affiliation(s)
- Ivan Krstić
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
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67
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Edwards TE, Cekan P, Reginsson GW, Shelke SA, Ferré-D'Amaré AR, Schiemann O, Sigurdsson ST. Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C. Nucleic Acids Res 2011; 39:4419-26. [PMID: 21252294 PMCID: PMC3105401 DOI: 10.1093/nar/gkr015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Previously, we developed the deoxycytosine analog Ç (C-spin) as a bi-functional spectroscopic probe for the study of nucleic acid structure and dynamics using electron paramagnetic resonance (EPR) and fluorescence spectroscopy. To understand the effect of Ç on nucleic acid structure, we undertook a detailed crystallographic analysis. A 1.7 Å resolution crystal structure of Ç within a decamer duplex A-form DNA confirmed that Ç forms a non-perturbing base pair with deoxyguanosine, as designed. In the context of double-stranded DNA Ç adopted a planar conformation. In contrast, a crystal structure of the free spin-labeled base ç displayed a ∼ 20° bend at the oxazine linkage. Density function theory calculations revealed that the bent and planar conformations are close in energy and exhibit the same frequency for bending. These results indicate a small degree of flexibility around the oxazine linkage, which may be a consequence of the antiaromaticity of a 16-π electron ring system. Within DNA, the amplitude of the bending motion is restricted, presumably due to base-stacking interactions. This structural analysis shows that the Ç forms a planar, structurally non-perturbing base pair with G indicating it can be used with high confidence in EPR- or fluorescence-based structural and dynamics studies.
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68
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Studying biomolecular complexes with pulsed electron–electron double resonance spectroscopy. Biochem Soc Trans 2011; 39:128-39. [DOI: 10.1042/bst0390128] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The function of biomolecules is intrinsically linked to their structure and the complexes they form during function. Techniques for the determination of structures and dynamics of these nanometre assemblies are therefore important for an understanding on the molecular level. PELDOR (pulsed electron–electron double resonance) is a pulsed EPR method that can be used to reliably and precisely measure distances in the range 1.5–8 nm, to unravel orientations and to determine the number of monomers in complexes. In conjunction with site-directed spin labelling, it can be applied to biomolecules of all sizes in aqueous solutions or membranes. PELDOR is therefore complementary to the methods of X-ray crystallography, NMR and FRET (fluorescence resonance energy transfer) and is becoming a powerful method for structural determination of biomolecules. In the present review, the methods of PELDOR are discussed and examples where PELDOR has been used to obtain structural information on biomolecules are summarized.
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69
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Li WT, Wu WH, Tang CH, Tai R, Chen ST. One-pot tandem copper-catalyzed library synthesis of 1-thiazolyl-1,2,3-triazoles as anticancer agents. ACS COMBINATORIAL SCIENCE 2011; 13:72-8. [PMID: 21247128 DOI: 10.1021/co1000234] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One-pot multicomponent synthesis to assemble compounds has been an efficient method for constructing a compound library. We have developed one-pot tandem copper-catalyzed azidation and CuAAC reactions that afford 1-thiazolyl-1,2,3-triazoles with anticancer activity. By utilizing this one-pot synthetic strategy, we constructed a library of 1-thiazolyl-1,2,3-triazoles in search of the potent lead compound. Furthermore, 1-thiazolyl-1,2,3-triazoles were evaluated for anticancer activity against the multidrug-resistant cancer cells MES-SA/Dx5. Most of the 1-thiazolyl-1,2,3-triazoles revealed cytotoxic effect against cancer cells at micromolar to low micromolar range. Testing some of the most potent compounds (5{4,2-4} and 5{5,1-3}) against the normal cell line Vero showed no significant toxicity (except 5{4,2}) to normal cells. This result indicates that compounds 5{4,3-4} and 5{5,1-3} possessed good potency and selectivity to cancer cells over normal cells.
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Affiliation(s)
- Wen-Tai Li
- Institute of Biological Chemistry and Genomic Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Wan-Hsun Wu
- Institute of Biological Chemistry and Genomic Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chien-Hsiang Tang
- Institute of Biological Chemistry and Genomic Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Ready Tai
- Institute of Biological Chemistry and Genomic Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shui-Tein Chen
- Institute of Biological Chemistry and Genomic Research Center, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
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70
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Krstić I, Endeward B, Margraf D, Marko A, Prisner TF. Structure and dynamics of nucleic acids. Top Curr Chem (Cham) 2011; 321:159-98. [PMID: 22160388 DOI: 10.1007/128_2011_300] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this chapter we describe the application of CW and pulsed EPR methods for the investigation of structural and dynamical properties of RNA and DNA molecules and their interaction with small molecules and proteins. Special emphasis will be given to recent applications of dipolar spectroscopy on nucleic acids.
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Affiliation(s)
- Ivan Krstić
- Goethe University Frankfurt, Frankfurt am Main, Germany
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71
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Shelke SA, Sigurdsson ST. Site-Directed Nitroxide Spin Labeling of Biopolymers. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2011. [DOI: 10.1007/430_2011_62] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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