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Illangasekare M, Turk R, Peterson GC, Lladser M, Yarus M. Chiral histidine selection by D-ribose RNA. RNA 2010; 16:2370-2383. [PMID: 20940341 PMCID: PMC2995399 DOI: 10.1261/rna.2385310] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 08/27/2010] [Indexed: 05/30/2023]
Abstract
The invariant choice of L-amino acids and D-ribose RNA for biological translation requires explanation. Here we study this chiral choice using mixed, equimolar D-ribose RNAs having 15, 18, 21, 27, 35, and 45 contiguous randomized nucleotides. These are used for simultaneous affinity selection of the smallest bound and eluted RNAs using equal amounts of L- and D-His immobilized on an achiral glass support, with racemic histidine elution. The experiment as a whole therefore determines whether RNA containing D-ribose binds L-histidine or D-histidine more easily (that is, by using a site that is more abundant/requires fewer nucleotides). The most prevalent/smallest RNA sites are reproducibly and repeatedly selected and there is a four- to sixfold greater abundance of L-histidine sites. RNA's chiral D-ribose therefore yields a more frequent fit to L-histidine. Accordingly, a D-ribose RNA site for L-His is smaller by the equivalent of just over one conserved nucleotide. The most prevalent L-His site also performs better than the most frequent D-His site-but rarer D-ribose RNAs can bind D-His with excellent affinity and discrimination. The prevalent L-His site is one we have selected before under very different conditions. Thus, selection is again reproducible, as is the recurrence of cognate coding triplets in these most probable L-His sites. If our selected RNA population were equilibrated with racemic His, we calculate that L-His would participate in seven of eight His:RNA complexes, or more. Thus, if D-ribose RNA were first chosen biologically, translational L-His usage could have followed.
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Affiliation(s)
- Mali Illangasekare
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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52
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53
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Surya Prakash GK, Zibinsky M, Upton TG, Kashemirov BA, McKenna CE, Oertell K, Goodman MF, Batra VK, Pedersen LC, Beard WA, Shock DD, Wilson SH, Olah GA. Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid. Proc Natl Acad Sci U S A 2010; 107:15693-8. [PMID: 20724659 PMCID: PMC2936638 DOI: 10.1073/pnas.1007430107] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is difficult to overestimate the importance of nucleoside triphosphates in cellular chemistry: They are the building blocks for DNA and RNA and important sources of energy. Modifications of biologically important organic molecules with fluorine are of great interest to chemists and biologists because the size and electronegativity of the fluorine atom can be used to make defined structural alterations to biologically important molecules. Although the concept of nonhydrolyzable nucleotides has been around for some time, the progress in the area of modified triphosphates was limited by the lack of synthetic methods allowing to access bisCF(2)-substituted nucleotide analogs-one of the most interesting classes of nonhydrolyzable nucleotides. These compounds have "correct" polarity and the smallest possible steric perturbation compared to natural nucleotides. No other known nucleotides have these advantages, making bisCF(2)-substituted analogs unique. Herein, we report a concise route for the preparation of hitherto unknown highly acidic and polybasic bis(difluoromethylene)triphosphoric acid 1 using a phosphorous(III)/phosphorous(V) interconversion approach. The analog 1 compared to triphosphoric acid is enzymatically nonhydrolyzable due to substitution of two bridging oxygen atoms with CF(2) groups, maintaining minimal perturbations in steric bulkiness and overall polarity of the triphosphate polyanion. The fluorinated triphosphoric acid 1 was used for the preparation of the corresponding fluorinated deoxynucleotides (dNTPs). One of these dNTP analogs (dT) was demonstrated to fit into DNA polymerase beta (DNA pol beta) binding pocket by obtaining a 2.5 A resolution crystal structure of a ternary complex with the enzyme. Unexpected dominating effect of triphosphate/Mg(2+) interaction over Watson-Crick hydrogen bonding was found and discussed.
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Affiliation(s)
- G. K. Surya Prakash
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Mikhail Zibinsky
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Thomas G. Upton
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Boris A. Kashemirov
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Charles E. McKenna
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Keriann Oertell
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Myron F. Goodman
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Vinod K. Batra
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Lars C. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - William A. Beard
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - David D. Shock
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Samuel H. Wilson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - George A. Olah
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
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54
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Hou X, Wang G, Gaffney BL, Jones RA. Preparation of DNA and RNA fragments containing guanine N(2)-thioalkyl tethers. Curr Protoc Nucleic Acid Chem 2010; Chapter 5:Unit-5.8. [PMID: 20517990 PMCID: PMC2967349 DOI: 10.1002/0471142700.nc0508s41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
This unit describes procedures for preparation of deoxyguanosine and guanosine derivatives in which the guanine N(2) contains a thiopropyl tether, protected as a tert-butyl disulfide. After incorporation into a DNA or RNA fragment, this tether allows site-specific cross-linking to a thiol of a protein or another nucleic acid.
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Affiliation(s)
- Xiaorong Hou
- Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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55
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Abstract
We have used single-molecule fluorescence microscopy to study the folded state of human telomerase RNA (hTR). Here we show that hTR adopts a new conformation on binding to human telomerase reverse transcriptase (hTERT) and reconstitution of an active ribonucleoprotein complex. Our data are consistent with the formation of an RNA pseudoknot in active human telomerase.
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Affiliation(s)
- Justin A. Yeoman
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Angel Orte
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Beth Ashbridge
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - David Klenerman
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Shankar Balasubramanian
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, U.K
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56
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Abstract
The known biological functions of RNA have expanded in recent years and now include gene regulation, maintenance of sub-cellular structure, and catalysis, in addition to propagation of genetic information. As for proteins, RNA function is tightly correlated with structure. Unlike proteins, structural information for larger, biologically functional RNAs is relatively limited. NMR signal degeneracy, relaxation problems, and a paucity of long-range (1)H-(1)H dipolar contacts have limited the utility of traditional NMR approaches. Selective isotope labeling, including nucleotide-specific and segmental labeling strategies, may provide the best opportunities for obtaining structural information by NMR. Here we review methods that have been developed for preparing and purifying isotopically labeled RNAs, as well as NMR strategies that have been employed for signal assignment and structure determination.
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Affiliation(s)
- Kun Lu
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 USA
| | - Yasuyuki Miyazaki
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 USA
| | - Michael F. Summers
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 USA
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57
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Abstract
The synthesis of RNA chains from 3',5'-cAMP and 3',5'-cGMP was observed. The RNA chains formed in water, at moderate temperatures (40-90 degrees C), in the absence of enzymes or inorganic catalysts. As determined by RNase analyses, the bonds formed were canonical 3',5'-phosphodiester bonds. The polymerizations are based on two reactions not previously described: 1) oligomerization of 3', 5'-cGMP to approximately 25-nucleotide-long RNA molecules, and of 3',5'-cAMP to 4- to 8-nucleotide-long molecules. Oligonucleotide A molecules were further extended by reciprocal terminal ligation to yield RNA molecules up to >120 nucleotides long and 2) chain extension by terminal ligation of newly polymerized products of 3',5'-cGMP on preformed oligonucleotides. The enzyme- and template-independent synthesis of long oligomers in water from prebiotically affordable precursors approaches the concept of spontaneous generation of (pre)genetic information.
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Affiliation(s)
| | - Samanta Pino
- the Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza di Roma, and
| | - Fabiana Ciciriello
- the Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza di Roma, and
| | - Ernesto Di Mauro
- the Fondazione Istituto Pasteur-Fondazione Cenci-Bolognetti, c/o Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza di Roma, P. le Aldo Moro, 5, Rome 00185, Italy
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58
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Carlucci M, Kierzek E, Marciniak A, Turner DH, Kierzek R. Chemical synthesis of LNA-2-thiouridine and its influence on stability and selectivity of oligonucleotide binding to RNA. Biochemistry 2009; 48:10882-93. [PMID: 19835380 PMCID: PMC2839159 DOI: 10.1021/bi901506f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hybridization to RNA is important for many applications, including antisense therapeutics, RNA interference, and microarray screening. Similar thermodynamic stabilities of A-U and G-U base pairs result in difficulties in selective binding to RNA. Moreover, A-U pairs are weaker than G-C pairs so that binding is sometimes weak when many A-U pairs are present. It is known, however, that replacement of uridine with 2-thiouridine significantly improves binding and selectivity. To test for additional improvement of binding and of the specificity for binding A over G, LNA-2-thiouridine was synthesized for the first time and incorporated into many LNA-2'-O-methyl-RNA/RNA duplexes. UV melting was used to measure the thermodynamic effect of replacing 2'-O-methyluridine with 2'-O-methyl-2-thiouridine or LNA-2-thiouridine. The 2-thiouridine usually enhances binding and selectivity. Selectivity is optimized when a single 2-thiouridine is placed at an internal position in a duplex.
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Affiliation(s)
- Marta Carlucci
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Anna Marciniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627-0216, USA
- Center for Pediatric Biomedical Research, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
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59
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Hou X, Wang G, Gaffney BL, Jones RA. Synthesis of guanosine and deoxyguanosine phosphoramidites with cross-linkable thioalkyl tethers for direct incorporation into RNA and DNA. Nucleosides Nucleotides Nucleic Acids 2009; 28:1076-94. [PMID: 20183575 PMCID: PMC2829721 DOI: 10.1080/15257770903368385] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We describe the synthesis of protected phosphoramidites of deoxyriboguanosine and guanosine derivatives containing a thiopropyl tether at the guanine N2 (7a,b) for site-specific crosslinking from the minor groove of either DNA or RNA to a thiol of a protein or another nucleic acid. The thiol is initially protected as a tert-butyl disulfide that is stable during oligonucleotide synthesis. While the completed oligonucleotide is still attached to the support, or after purification, the tert-butyl thiol can readily be removed or replaced by thioethylamine or 5-thio-2-nitrobenzoic acid, which have more favorable crosslinking rates.
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Affiliation(s)
- Xiaorong Hou
- Department of Chemistry and Chemical Biology, 610 Taylor Road, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854
| | - Gang Wang
- Department of Chemistry and Chemical Biology, 610 Taylor Road, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854
| | - Barbara L. Gaffney
- Department of Chemistry and Chemical Biology, 610 Taylor Road, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854
| | - Roger A. Jones
- Department of Chemistry and Chemical Biology, 610 Taylor Road, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854
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60
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Morales GA. QSAR allows going a step further by measuring and quantifying cause-effect information to chemical structures. Mol Divers 2009; 13:275-6. [PMID: 19585248 DOI: 10.1007/s11030-009-9180-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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61
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Scientists playing God! Indian J Physiol Pharmacol 2009; 53:195-6. [PMID: 20329365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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62
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Fukuda M, Nakamura M, Takada T, Yamana K. Duplex formation of multiple pyrene-modified RNAs. Nucleic Acids Symp Ser (Oxf) 2009; 53:133-134. [PMID: 19749296 DOI: 10.1093/nass/nrp067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We synthesized multiple pyrene-modified RNA sequences having two kinds of consecutive sequences, U(Py)U(Py) and A(Py)A(Py), and investigated their duplex formations and the pyrene associations.
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Affiliation(s)
- Minoru Fukuda
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo 671-2280, Japan
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63
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Oeda Y, Iijima Y, Tsunoda H, Okubo A, Seio K, Sekine M. Synthesis and properties of new RNA molecules incorporating 2'-O-aryluridine derivatives. Nucleic Acids Symp Ser (Oxf) 2009; 53:117-118. [PMID: 19749288 DOI: 10.1093/nass/nrp059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A variety of 2'-O-arylnucleosides with functional groups were synthesized by the microwave-assisted reaction of 2,2'-anhydrouridine with phenol derivatives. The 2'-O-arylnucleosides thus obtained were incorporated into 2'-O-Me RNA or DNA oligomers and their hybridization properties were studied by T(m) measurements.
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Affiliation(s)
- Yusuke Oeda
- Department of Life Science, Graduate School of Bioscience and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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64
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Sheng P, Yang Z, Kim Y, Wu Y, Tan W, Benner SA. Design of a novel molecular beacon: modification of the stem with artificially genetic alphabet. Chem Commun (Camb) 2008:5128-30. [PMID: 18956044 PMCID: PMC2763601 DOI: 10.1039/b811159f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A molecular beacon that incorporates components of an artificially expanded genetic information system (Aegis) in its stem is shown not to be opened by unwanted stem invasion by adventitious standard DNA; this should improve the "darkness" of the beacon in real-world applications.
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Affiliation(s)
- Pinpin Sheng
- Department of Chemistry and UF Genetics Institute, Shands Cancer Center, Center for Research at Bio/nano Interface and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
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65
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Alldred MJ, Che S, Ginsberg SD. Terminal continuation (TC) RNA amplification without second strand synthesis. J Neurosci Methods 2008; 177:381-5. [PMID: 19026688 DOI: 10.1016/j.jneumeth.2008.10.027] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 10/21/2008] [Indexed: 02/07/2023]
Abstract
Terminal continuation (TC) RNA amplification was developed originally to reproducibly and inexpensively amplify RNA. The TC RNA amplification method has been improved further by obviating second strand DNA synthesis, a cost-effective protocol that takes less time to perform with fewer manipulations required for RNA amplification. Results demonstrate that TC RNA amplification without second strand synthesis does not differ from the original protocol using RNA harvested from mouse brain and from hippocampal neurons obtained via laser capture microdissection from postmortem human brains. The modified TC RNA amplification method can discriminate single cell gene expression profiles between normal control and Alzheimer's disease hippocampal neurons indistinguishable from the original protocol. Thus, TC RNA amplification without second strand synthesis is a reproducible, time- and cost-effective method for RNA amplification from minute amounts of input RNA, and is compatible with microaspiration strategies and subsequent microarray analysis as well as quantitative real-time PCR.
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Affiliation(s)
- Melissa J Alldred
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, United States
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66
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Iwase R, Toyama T. Synthesis of a guanosine phosphoramidite derivative containing a photocleavable protecting group at the O6 position via regioselective protection of the 2'-hydroxy group with a TBDMS group. ACTA ACUST UNITED AC 2008:135-6. [PMID: 18029623 DOI: 10.1093/nass/nrm068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
To construct modified RNA that form A-type duplex with photo-irradiation, a photocleavable a-methyl-2-nitropiperonyl (MeNP) group was introduced at O(6) position of guanosine. A guanosine phosphoramidite derivative containing the MeNP group was synthesized via regioselective 2'-O-protection of 3',5'-O-di(t-butyl)silanediylguanosine with TBDMS group. The MeNP group was found to be stable under conditions of solid-phase synthesis of RNA. The MeNP group was also found to be removable by UV irradiation at wavelength of 365 nm for 10 min.
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Affiliation(s)
- Reiko Iwase
- Department of Biosciences, Teikyo University of Science and Technology, 2525 Yatsusawa, Uenohara, Yamanashi 409-0193, Japan.
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67
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Puffer B, Moroder H, Aigner M, Micura R. 2'-Methylseleno-modified oligoribonucleotides for X-ray crystallography synthesized by the ACE RNA solid-phase approach. Nucleic Acids Res 2008; 36:970-83. [PMID: 18096613 PMCID: PMC2241898 DOI: 10.1093/nar/gkm880] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 10/01/2007] [Accepted: 10/01/2007] [Indexed: 11/15/2022] Open
Abstract
Site-specifically modified 2'-methylseleno RNA represents a valuable derivative for phasing of X-ray crystallographic data. Several successful applications in three-dimensional structure determination of nucleic acids, such as the Diels-Alder ribozyme, have relied on this modification. Here, we introduce synthetic routes to 2'-methylseleno phosphoramidite building blocks of all four standard nucleosides, adenosine, cytidine, guanosine and uridine, that are tailored for 2'-O-bis(acetoxyethoxy)methyl (ACE) RNA solid-phase synthesis. We additionally report on their incorporation into oligoribonucleotides including deprotection and purification. The methodological expansion of 2'-methylseleno labeling via ACE RNA chemistry is a major step to make Se-RNA generally accessible and to receive broad dissemination of the Se-approach for crystallographic studies on RNA. Thus far, preparation of 2'-methylseleno-modified oligoribonucleotides has been restricted to the 2'-O-[(triisopropylsilyl)oxy]methyl (TOM) and 2'-O-tert-butyldimethylsilyl (TBDMS) RNA synthesis methods.
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Affiliation(s)
| | | | | | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens University, Innrain 52a, 6020 Innsbruck, Austria
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68
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Rajamani S, Vlassov A, Benner S, Coombs A, Olasagasti F, Deamer D. Lipid-assisted synthesis of RNA-like polymers from mononucleotides. ORIGINS LIFE EVOL B 2008; 38:57-74. [PMID: 18008180 DOI: 10.1007/s11084-007-9113-2] [Citation(s) in RCA: 200] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Accepted: 09/27/2007] [Indexed: 11/24/2022]
Abstract
A fundamental problem in research on the origin of life is the process by which polymers capable of catalysis and replication were produced on the early Earth. Here we show that RNA-like polymers can be synthesized non-enzymatically from mononucleotides in lipid environments. The RNA-like polymers were initially identified by nanopore analysis, a technique with single molecule sensitivity. To our knowledge, this is the first such application of a nanopore instrument to detect RNA synthesis under simulated prebiotic conditions. The synthesis of the RNA-like polymers was confirmed by standard methods of enzymatic end labeling followed by gel electrophoresis. Chemical activation of the mononucleotides is not required. Instead, synthesis of phosphodiester bonds is driven by the chemical potential of fluctuating anhydrous and hydrated conditions, with heat providing activation energy during dehydration. In the final hydration step, the RNA-like polymer is encapsulated within lipid vesicles. This process provides a laboratory model of an early stage of evolution toward an RNA World.
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Affiliation(s)
- Sudha Rajamani
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
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69
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Abstract
Studies of catalytically active DNA sequences have expanded considerably since the first artificial deoxyribozyme was identified in 1994. Nevertheless, the field is still quite young, and advances in both fundamental understanding and practical applications of deoxyribozymes are still developing. Deoxyribozymes that either cleave or ligate two RNA substrates have been most widely investigated, and this review describes recent advances in the fundamental studies and applications of these DNA enzymes. Deoxyribozymes with catalytic activities other than RNA ligation and cleavage are also increasingly pursued, and this review covers several key examples.
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Affiliation(s)
- Claudia Höbartner
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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70
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Abstract
Discoveries demonstrating that RNA can serve genetic, catalytic, structural, and regulatory roles have provided strong support for the existence of an RNA World that preceded the origin of life as we know it. Despite the appeal of this idea, it has been difficult to explain how macromolecular RNAs emerged from small molecules available on the early Earth. We propose here a mechanism by which mutual catalysis in a pre-biotic network initiated a progression of stages characterized by ever larger and more effective catalysts supporting a proto-metabolic network, and the emergence of RNA as the dominant macromolecule due to its ability to both catalyze chemical reactions and to be copied in a template-directed manner. This model suggests that many features of modern life, including the biosynthetic pathways leading to simple metabolites, the structures of organic and metal ion cofactors, homochirality, and template-directed replication of nucleic acids, arose long before the RNA World and were retained as pre-biotic systems became more sophisticated.
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Affiliation(s)
- Shelley D Copley
- University of Colorado at Boulder, CIRES, Campus Box 216, Boulder, CO 80309, USA.
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71
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Halamikova A, Vrana O, Kasparkova J, Brabec V. Biochemical Studies of the Thermal Effects on DNA Modifications by the Antitumor Cisplatin and Their Repair. Chembiochem 2007; 8:2008-15. [PMID: 17868156 DOI: 10.1002/cbic.200700288] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Using biochemical methods, we have examined the effect of two factors that might play a role in the mechanism of the biological activity of cisplatin at elevated temperatures (>37 degrees C). We show that increased temperatures result in distinct alterations in the modification of the target DNA by cisplatin, and in the repair of these modifications. Our in vitro results support the view that the enhanced DNA-cross-linking efficiency of cisplatin and the lower efficiency of native DNA repair mechanisms at higher temperature play at least a partial role in the potentiation of the antitumor effects of cisplatin under conditions of mild hyperthermia.
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Affiliation(s)
- Anna Halamikova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i
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72
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Semenyuk A, Földesi A, Johansson T, Estmer-Nilsson C, Blomgren P, Brännvall M, Kirsebom LA, Kwiatkowski M. Synthesis of RNA using 2'-O-DTM protection. J Am Chem Soc 2007; 128:12356-7. [PMID: 16984152 DOI: 10.1021/ja0636587] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
tert-Butyldithiomethyl (DTM), a novel hydroxyl protecting group, cleavable under reductive conditions, was developed and applied for the protection of 2'-OH during solid-phase RNA synthesis. This function is compatible with all standard protecting groups used in oligonucleotide synthesis, and allows for fast and high-yield synthesis of RNA. Oligonucleotides containing the 2'-O-DTM groups can be easily deprotected under the mildest possible aqueous and homogeneous conditions. The preserved 5'-O-DMTr function can be used for high-throughput cartridge RNA purification.
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Affiliation(s)
- Andrey Semenyuk
- Department of Genetics and Pathology, Uppsala University, Sweden
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73
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Abstract
5'-Nucleotides of A and U with the phosphate activated with 1-methyladenine generate RNA oligomers containing 40-50 monomers in 1 day in reactions catalyzed by montmorillonite. The corresponding monomers of C give oligomers that are 20-25-mers in length after a 9-day reaction. It was not possible to determine the chain lengths of the oligomers of G since they did not give well-defined bands on gel electrophoresis. Co-oligomers of A and U as well as A, U, G, and C were also prepared. The oligo(A)s formed were separated by gel electrophoresis, and the bands of the 7-39-mers were isolated, the 3',5'-phosphodiester bonds were cleaved by RNase T(2), and the terminal phosphate groups were cleaved with alkaline phosphatase. HPLC analysis revealed that the proportions of A(5)'pp(5)'A, A, A(2)'pA, and A(2)'pA(2)'pA formed were almost the same for the long and shorter oligomers. A similar structure analysis performed on the oligo(U)s established that the proportions of U(5)'pp(5)'U, U, U(2)'pU, U(2)'pU(2)'pU, U(2)'pU(2)'pU(2)'pU, and U(2)'pU(2)'pU(2)'pU(2)'pU did not vary with chain length. The structural analysis of the oligomers of A revealed that 74% of the phosphodiester bonds were 3',5'-linked a value slightly greater than 67% observed when imidazole was the activating group. 61% of the bonds in the U oligomers were 3',5'-linked, which is almost 3 times greater than the 20% measured when imidazole was the activating group. The potential significance of these data to the origin and early evolution of life is discussed.
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Affiliation(s)
- Wenhua Huang
- Department of Chemistry and Chemical Biology and New York Center for Studies on the Origins of Life and Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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74
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Yang YW, Zhang S, McCullum EO, Chaput JC. Experimental Evidence That GNA and TNA Were Not Sequential Polymers in the Prebiotic Evolution of RNA. J Mol Evol 2007; 65:289-95. [PMID: 17828568 DOI: 10.1007/s00239-007-9017-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Accepted: 04/25/2007] [Indexed: 10/22/2022]
Abstract
Systematic investigation into the chemical etiology of ribose has led to the discovery of glycerol nucleic acid (GNA) and threose nucleic acid (TNA) as possible progenitor candidates of RNA in the origins of life. Coupled with their chemical simplicity, polymers for both systems are capable of forming stable Watson-Crick antiparallel duplex structures with themselves and RNA, thereby providing a mechanism for the transfer of genetic information between successive genetic systems. Investigation into whether both polymers arose independently or descended from a common evolutionary pathway would provide additional constraints on models that describe the emergence of a hypothetical RNA world. Here we show by thermal denaturation that complementary GNA and TNA mixed sequence polymers are unable, even after prolonged incubation times, to adopt stable helical structures by intersystem cross-pairing. This experimental observation suggests that GNA and TNA, whose structures derive from one another, were not consecutive polymers in the same evolutionary pathway to RNA.
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Affiliation(s)
- Ying-Wei Yang
- The Center for BioOptical Nanotechnology, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
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75
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Shiba Y, Kitagawa H, Masutomi Y, Ishiyama K, Ohgi T, Yano J. A novel RNA synthetic method with a 2'-O-(2-cyanoethoxymethyl) protecting group. ACTA ACUST UNITED AC 2007:11-2. [PMID: 17150792 DOI: 10.1093/nass/nrl006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
A novel method for the synthesis of RNA oligomers with 2-cyanoethoxymethyl (CEM) as the 2'-hydroxyl protecting group has been developed. The new method allows the synthesis of oligonucleotides with an efficiency and final purity comparable to that obtained in DNA synthesis.(1) In addition, the CEM method has the potential for application to the synthesis of very long RNA oligonucleotides.
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Affiliation(s)
- Yoshinobu Shiba
- Discovery Research Laboratories, Nippon Shinyaku Co. Ltd., 3-14-1 Sakura, Tsukuba City, Ibaraki 305-0003, Japan
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76
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Abstract
Recently, a novel base-modified uridine derivative, 5-taurinomethyluridine (taum(5)U) was discovered from bovine and human mitochondrial tRNAs, and this modified ribonucleoside was found to existed at the first position of the anti-codon. We report efficient reactions for the synthesis of RNA oligomers including this base-modified ribonucleotide.
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Affiliation(s)
- Toshihiko Ogata
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The Universitiy of Tokyo, Bioscience Bldg 702, Kashiwa, Chiba 277-8562, Japan
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77
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Abstract
Synthetic biology has a promising outlook in biotechnology and for understanding the self-organizing principle of biological molecules in life. However, synthetic biologists have been looking for new molecular "parts" that function as modular units required in designing and constructing new "devices" and "systems" for regulating cell function because the number of such parts is strictly limited at present. In this review, we focus on RNA/ribonucleoprotein (RNP) architectures that hold promise as new "parts" for synthetic biology. They are constructed with molecular design and an experimental evolution technique. So far, designed self-folding RNAs, RNA (RNP) enzymes, and nanoscale RNA architectures have been successfully constructed by utilizing Watson-Crick base-pairs together with specific RNA-RNA or RNA-protein binding motifs of known defined 3D structures. Riboregulators for regulating targeted gene expression have also been designed and produced in vitro as well as in vivo. Lately, RNA and ribonucleoprotein complexes have been strongly attracting the attention of molecular biologists because a variety of noncoding RNAs discovered in nature perform spatiotemporal gene expressions. Thus we hope that newly accumulating knowledge on naturally occurring RNAs and RNP complexes will provide a variety of new parts, devices and systems for synthetic biology.
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Affiliation(s)
- Hirohide Saito
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; ICORP, Japan Science and Technology Corporation (JST), Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.
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78
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Wada T, Hashimoto Y, Sato H, Inoue Y. Synthesis of peptide ribonucleic acid consisting of D- and L-gamma-glutamic acid as a backbone structure. ACTA ACUST UNITED AC 2007:27-8. [PMID: 17150461 DOI: 10.1093/nass/48.1.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A novel nucleic acid model using peptide ribonucleic acid (PRNA), which contains 5-amino-5-deoxyribonucleoside as a recognition site for nucleic acids and consists D-glutamic acid (D-PRNA) instead of L-glutamic acid (L-PRNA) as a backbone structure, has been designed and synthesized. Difference between D-PRNA and L-PRNA oligomers was elucidated on the basis of the effects of chirality of gamma-glutamic acid backbone upon structure elucidated by CD spectra.
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79
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Abstract
Stereoregulated diribonucleoside phosphorothioates were synthesized by the use of 2'-O-TBDMS-protected ribonucleoside 3'-O-oxazaphospholidine derivatives as monomers and N-(cyanomethyl)ammonium salts as activators. Diastereoselectivity of the condensation reaction was found to be highly dependent on the substituent groups of the oxazaphospnolidine ring as well as the structure of the activators. By the use of the optimized oxazaphospholidine monomers and activators, diastereopure diribonucleoside phosphorothioate bearing Rp and Sp configurations were obtained in good yields.
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Affiliation(s)
- Takeshi Wada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Bldg 702, Kashiwa, Chiba 277-8562, Japan
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80
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Tanaka Y, Akagi K, Nakamura Y, Kozu T. RNA aptamers targeting the carboxyl terminus of KRAS oncoprotein generated by an improved SELEX with isothermal RNA amplification. Oligonucleotides 2007; 17:12-21. [PMID: 17461759 DOI: 10.1089/oli.2006.0035r1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mutations in the KRAS gene occur frequently in various human tumors and are known to lead to malignant transformation. We isolated RNA aptamers targeting activated mutant KRAS proteins using an improved SELEX method by isothermal RNA amplification. RNA aptamers were selected against mutant KRAS (G12V) proteins, as well as a biotinylated 15-amino-acid peptide from the carboxyl terminal of KRAS that contains a farnesylation site. All the selected RNA aptamers bound to the basic carboxy-terminal region of KRAS protein and the highest K(D) value was 2.3 microM. By an in vitro scintillation proximity assay, we demonstrated that KRAS aptamers inhibited farnesylation moderately. From these aptamers, we determined a consensus sequence (U)CCAAGCAC(AC) that, when concatamerized, exhibited higher binding affinity to the carboxy-terminal region of KRAS protein. Further improvement of binding affinity between aptamers and KRAS protein might provide a new therapeutic approach for activated mutant KRAS proteins.
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Affiliation(s)
- Yoichiro Tanaka
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama 362-0806, Japan., Department of Basic Medical Science, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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81
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Abstract
We report on the formation of novel RNA molecules in a recombination-like, nonenzymatic reaction proceeding in the complex of partially complementary RNA-oligonucleotides under very simple conditions. Analysis of the isolated products demonstrated that at least 5% of the formed linkages are of the (natural) 3',5'-phosphodiester type. We suggest that similar reactions could contribute to the development of the 'RNA world', but could also proceed in vivo within variously structured RNA or RNA complexes containing loops, bulges, or dangling ends, providing an emergence of novel RNA sequences.
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Affiliation(s)
- Alexei V Lutay
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev Ave, 8, Novosibirsk, 630090, Russian Federation.
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82
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Shibamiya A, Muhl L, Tannert-Otto S, Preissner K, Kanse S. Nucleic acids potentiate Factor VII-activating protease (FSAP)-mediated cleavage of platelet-derived growth factor-BB and inhibition of vascular smooth muscle cell proliferation. Biochem J 2007; 404:45-50. [PMID: 17300216 PMCID: PMC1868837 DOI: 10.1042/bj20070166] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
FSAP (Factor VII-activating protease) can cleave and inactivate PDGF-BB (platelet-derived growth factor-BB) and thereby inhibits VSMC (vascular smooth-muscle cell) proliferation. The auto-activation of FSAP is facilitated by negatively charged polyanions such as heparin, dextransulfate or extracellular ribonucleic acids. Since auto-activation is essential for the anti-proliferative function of FSAP, the influence of nucleic acids as cofactors for the FSAP-mediated inhibition of PDGF-BB was investigated. Natural or artificial RNA was an effective cofactor for FSAP mediated PDGF-BB degradation, whereas the effect of DNA was weak. RNA-induced cleavage of PDGF-BB was inhibited by serine protease inhibitors. The pattern of PDGF-BB cleavage was identical with either heparin or RNA as a cofactor. One of the cleavage sites in PDGF-BB was at the positions 160-162 (R160KK162), which is an important region for receptor binding and activation. In VSMCs, PDGF-BB-stimulated DNA synthesis was inhibited by FSAP in the presence of RNA. RNA was more effective than DNA and the cofactor activity of RNA was neutralized after pretreatment with RNase. FSAP binding to RNA protected the nucleic acid from degradation by RNase. These data are relevant to situations where extracellular nucleic acids released from necrotic or apoptotic cells could activate local FSAP, leading to inhibition of PDGF-BB.
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Affiliation(s)
- Aya Shibamiya
- *Institute for Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, Germany
- †Graduate School of Health Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Lars Muhl
- *Institute for Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, Germany
| | - Susanne Tannert-Otto
- *Institute for Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, Germany
| | - Klaus T. Preissner
- *Institute for Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, Germany
| | - Sandip M. Kanse
- *Institute for Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, Germany
- To whom correspondence should be addressed (email )
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83
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Grant GPG, Qin PZ. A facile method for attaching nitroxide spin labels at the 5' terminus of nucleic acids. Nucleic Acids Res 2007; 35:e77. [PMID: 17517787 PMCID: PMC1904292 DOI: 10.1093/nar/gkm240] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 03/21/2007] [Accepted: 04/02/2007] [Indexed: 01/02/2023] Open
Abstract
In site-directed spin labeling (SDSL), a nitroxide moiety containing a stable, unpaired electron is covalently attached to a specific site within a macromolecule, and structural and dynamic information at the labeling site is obtained via electron paramagnetic resonance (EPR) spectroscopy. Successful SDSL requires efficient site-specific incorporation of nitroxides. Work reported here presents a new method for facile nitroxide labeling at the 5' terminus of nucleic acids of arbitrary sizes. T4-polynucleotide kinase was used to enzymatically substitute a phosphorothioate group at the 5' terminus of a nucleic acid, and the resulting phosphorothioate was then reacted with an iodomethyl derivative of a nitroxide. The method was successfully demonstrated on both chemically synthesized and naturally occurring nucleic acids. The attached nitroxides reported duplex formation as well as tertiary folding of nucleic acids, indicating that they serve as a valid probe in nucleic acid studies.
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Affiliation(s)
- Gian Paola G. Grant
- Department of Chemistry and Department of Biological Sciences, University of Southern California, LJS-251, 840 Downey Way, Los Angeles, CA 90089-0744, USA
| | - Peter Z. Qin
- Department of Chemistry and Department of Biological Sciences, University of Southern California, LJS-251, 840 Downey Way, Los Angeles, CA 90089-0744, USA
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84
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Abstract
This protocol describes a general method for the preparation of RNAs in which the reactivity or hydrogen-bonding properties of the molecule are modified in a photoreversible fashion by use of a caging strategy. A single caged adenosine, modified at the 2' position as a nitro-benzyl ether, can be incorporated into short RNAs by chemical synthesis or into long RNAs by a combination of chemical and enzymatic synthesis. The modified RNAs can be uncaged by photolysis under a variety of conditions including the use of a laser or xenon lamp, and the course of this uncaging reaction may be readily followed by HPLC or thin-layer chromatography.
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Affiliation(s)
- Steven G Chaulk
- Department of Biochemistry, University of Alberta Edmonton, Alberta, Canada T6G 2H7
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85
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Abstract
An enzyme family known as adenosine deaminases that act on RNA (ADARs) catalyzes adenosine deamination in RNA. ADARs act on RNA that is largely double-stranded and convert adenosine to inosine, resulting, in many cases, in an I x U pair. Thermodynamic parameters derived from optical melting studies are reported for a series of 14 oligoribonucleotides containing single I x U pairs adjacent to Watson-Crick pairs. In order to determine unique linearly independent nearest neighbor parameters for I x U pairs, four duplexes containing 3'-terminal I x U pairs and four duplexes containing 5'-terminal I x U pairs have also been thermodynamically characterized. This data was combined with previously published data of seven duplexes containing internal, terminal, or tandem I x U pairs from Strobel et al. [Strobel, S. A., Cech, T. R., Usman, N., and Beigelman, L. (1994) Biochemistry 33, 13824-13838] and Serra et al. [Serra, M. J., Smolter, P. E., and Westhof, E. (2004) Nucleic Acids Res. 32, 1824-1828]. On average, a duplex with an internal I x U pair is 2.3 kcal/mol less stable than the same duplex with an A-U pair, however, a duplex with a terminal I x U pair is 0.8 kcal/mol more stable than the same duplex with an A-U pair. Although isosteric with a G-U pair, on average, a duplex with an internal I x U pair is 1.9 kcal/mol less stable than the same duplex with a G-U pair, however, a duplex with a terminal I x U pair is 0.9 kcal/mol more stable than the same duplex with a G-U pair. Duplexes with tandem I x U pairs are on average 5.9 and 3.8 kcal/mol less stable than the same duplex with tandem A-U or tandem G-U pairs, respectively. Using the combined thermodynamic data and a complete linear least-squares fitting routine, nearest neighbor parameters for all nearest neighbor combinations of I x U pairs and an additional parameter for terminal I x U pairs have been derived.
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Affiliation(s)
- Daniel J Wright
- Department of Chemistry, Saint Louis University, Saint Louis, Missouri 63103, USA
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86
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Mikhailov SN, Efimtseva EV, Rodionov AA, Shelkunova AA, Rozenski J, Emmerechts G, Schepers G, Van Aerschot A, Herdewijn P. Synthesis of RNA containing O-beta-D-ribofuranosyl-(1''-2')-adenosine-5''-phosphate and 1-methyladenosine, minor components of tRNA. Chem Biodivers 2007; 2:1153-63. [PMID: 17193197 DOI: 10.1002/cbdv.200590085] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
tRNA is best known for its function as amino acid carrier in the translation process, using the anticodon loop in the recognition process with mRNA. However, the impact of tRNA on cell function is much wider, and mutations in tRNA can lead to a broad range of diseases. Although the cloverleaf structure of tRNA is well-known based on X-ray-diffraction studies, little is known about the dynamics of this fold, the way structural dynamics of tRNA is influenced by the modified nucleotides present in tRNA, and their influence on the recognition of tRNA by synthetases, ribosomes, and other biomolecules. One of the reasons for this is the lack of good synthetic methods to incorporate modified nucleotides in tRNA so that larger amounts become available for NMR studies. Except of 2'-O-methylated nucleosides, only one other sugar-modified nucleoside is present in tRNA, i.e., 2'-O-beta-D-ribofuranosyl nucleosides. The T loop of tRNA often contains charged modified nucleosides, of which 1-methyladenosine and phosphorylated disaccharide nucleosides are striking examples. A protecting-group strategy was developed to introduce 1-methyladenosine and 5''-O-phosphorylated 2'-O-(beta-D-ribofuranosyl)-beta-D-ribofuranosyladenine in the same RNA fragment. The phosphorylation of the disaccharide nucleoside was performed after the assembly of the RNA on solid support. The modified RNA was characterized by mass-spectrometry analysis from the RNase T1 digestion fragments. The successful synthesis of this T loop of the tRNA of Schizosaccharomyces pombe initiator tRNA(Met) will be followed by its structural analysis by NMR and by studies on the influence of these modified nucleotides on dynamic interactions within the complete tRNA.
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Affiliation(s)
- Sergey N Mikhailov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow, 119991, Russia.
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87
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Lackey JG, Sabatino D, Damha MJ. Solid-phase synthesis and on-column deprotection of RNA from 2'- (and 3'-) O-levulinated (Lv) ribonucleoside monomers. Org Lett 2007; 9:789-92. [PMID: 17279762 DOI: 10.1021/ol0629521] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
[reaction: see text] The solid-phase synthesis of oligoribonucleotides derived from ribonucleosides esterified at the 2'- (or 3'-) position with the levulinyl (Lv) group is described. The oligomers can be released from the solid support as 2'-O-Lv ester derivatives or fully deprotected while still attached to the solid support.
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Affiliation(s)
- Jeremy G Lackey
- Department of Chemistry, McGill University, Montreal, QC, Canada
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88
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Cieślak J, Kauffman JS, Kolodziejski MJ, Lloyd JR, Beaucage SL. Assessment of 4-Nitrogenated Benzyloxymethyl Groups for 2‘-Hydroxyl Protection in Solid-Phase RNA Synthesis. Org Lett 2007; 9:671-4. [PMID: 17256869 DOI: 10.1021/ol0629824] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The search for a 2'-OH protecting group that would impart ribonucleoside phosphoramidites with coupling kinetics and coupling efficiencies comparable to those of deoxyribonucleoside phosphoramidites led to an assessment of 2'-O-(4-nitrogenated benzyloxy)methyl groups through solid-phase RNA synthesis using phosphoramidites 2a-d, 12a, and 14a. These phosphoramidites exhibited rapid and efficient coupling properties. Particularly noteworthy is the cleavage of the 2'-O-[4-(N-methylamino)benzyloxy]methyl groups in 0.1 M AcOH, which led to U19dT within 15 min at 90 degrees C. [reaction: see text]
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Affiliation(s)
- Jacek Cieślak
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, Maryland 20892, USA
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89
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Abstract
One of the hallmarks of DNA and RNA structures is their elegant chirality. Using these chiral structures to induce enantioselectivity in chemical synthesis is as enticing as it is challenging. In recent years, three general approaches have been developed to achieve this, including chirality transfer by nucleotide templated synthesis, enantioselective catalysis by RNA/DNAzymes and DNA-based asymmetric catalysis. In this article the concepts behind these strategies as well as the important achievements in this field will be discussed.
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Affiliation(s)
- Gerard Roelfes
- Department of Organic Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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90
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Abstract
The field of RNA structure has exploded in recent years, in part owing to advances in crystallography of RNA molecules. This phenomenon can largely be attributed to the development of three modern methods: (1) large-scale in vitro RNA synthesis, (2) cryocrystallography, and (3) high-intensity synchrotron beamlines. Milligram quantities of RNA can be routinely synthesized using either chemical or enzymatic syntheses, making it feasible to carry out routine crystallization experiments on RNA. This has allowed crystals of RNA to be readily obtained. Generally, RNA crystals tend to be susceptible to radiation damage and to diffract X-rays more weakly than their protein counterparts. However, cryocrystallography and the high-intensity X-ray sources have overcome many of the difficulties involved in solving crystal structures of RNA. As a result of these advances, we now have a database of RNA structures that span from simple duplexes and hairpins to complex ribozymes and ribosomes. The protocols presented here describe methods to synthesize, purify, crystallize, and derivatize RNA for use in crystallographic studies.
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Affiliation(s)
- Barbara L Golden
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
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91
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Ohgi T, Yano J, Saneyoshi H, Seio K, Sekine M. [RNA chemistry]. Tanpakushitsu Kakusan Koso 2006; 51:2502-8. [PMID: 17471970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- Tadaaki Ohgi
- Center for Cancer Research NCI-Frederick NIH, USA.
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92
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Harada K. [Tailor-made RNAs: from self-folding RNAs to RNA-polypeptide complexes]. Tanpakushitsu Kakusan Koso 2006; 51:2489-95. [PMID: 17471968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
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93
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Crowe MA, Sutherland JD. Reaction of cytidine nucleotides with cyanoacetylene: support for the intermediacy of nucleoside-2',3'-cyclic phosphates in the prebiotic synthesis of RNA. Chembiochem 2006; 7:951-6. [PMID: 16642527 DOI: 10.1002/cbic.200600024] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A robust and prebiotically plausible synthesis of RNA is a key requirement of the "RNA World" hypothesis, but, to date, no such synthesis has been demonstrated. Monomer synthesis strategies involving attachment of preformed nucleobases to sugars have failed, and, even if activated 5'-nucleotides could be made, the hydrolysis of these intermediates in water makes their efficient oligomerisation appear unlikely. We recently reported a synthesis of cytidine-2',3'-cyclic phosphate 1 (C>p) in which the nucleobase was assembled in stages on a sugar-phosphate template. However, 2',3'-cyclic nucleotides (N>p's) also undergo hydrolysis, in this case giving a mixture of the 2'- and 3'-monophosphates. This hydrolysis has previously been seen as making the, otherwise promising, oligomerisation of N>p's seem as unlikely as that of the 5'-activated nucleotides. We now find that cyanoacetylene, the reagent used for the second stage of nucleobase assembly in the synthesis of C>p, also reverses the effect of the hydrolysis by driving efficient cyclisation of C2'p and C3'p back to C>p. Excess cyanoacetylene also derivatises the nucleobase, but this modification is reversible at neutral pH. These findings significantly strengthen the case for N>p's in a prebiotic synthesis of RNA.
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Affiliation(s)
- Michael A Crowe
- School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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94
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Abstract
The most challenging step in protein microarray fabrication is high-throughput production of proteins. Here we report two similar strategies to fabricate protein chips through capture onto a solid surface of the nascent polypeptides during translation of synthetic or in vitro-transcribed RNAs. Using these approaches, we efficiently fabricated both peptide and protein microarrays at relatively high density. We further demonstrated that such protein chips can be used to analyze protein activity.
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Affiliation(s)
- Sheng-Ce Tao
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Affiliation(s)
| | - Scott K. Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801 (USA), Phone: (+1) 217-244-4489, Fax: (+1) 217-244-8024, E-mail:
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Hirao I, Kimoto M, Mitsui T, Fujiwara T, Kawai R, Sato A, Harada Y, Yokoyama S. An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA. Nat Methods 2006; 3:729-35. [PMID: 16929319 DOI: 10.1038/nmeth915] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Accepted: 07/10/2006] [Indexed: 11/08/2022]
Abstract
Methods for the site-specific incorporation of extra components into nucleic acids can be powerful tools for creating DNA and RNA molecules with increased functionality. We present an unnatural base pair system in which DNA containing an unnatural base pair can be amplified and function as a template for the site-specific incorporation of base analog substrates into RNA via transcription. The unnatural base pair is formed by specific hydrophobic shape complementation between the bases, but lacks hydrogen bonding interactions. In replication, this unnatural base pair exhibits high selectivity in combination with the usual triphosphates and modified triphosphates, gamma-amidotriphosphates, as substrates of 3' to 5' exonuclease-proficient DNA polymerases, allowing PCR amplification. In transcription, the unnatural base pair complementarity mediates the incorporation of these base substrates and their analogs, such as a biotinylated substrate, into RNA by T7 RNA polymerase (RNAP). With this system, functional components can be site-specifically incorporated into a large RNA molecule.
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Affiliation(s)
- Ichiro Hirao
- Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Ikawa Y. [A promising strategy to generate artificial RNA catalysts: the marriage of de novo design and directed evolution]. Tanpakushitsu Kakusan Koso 2006; 51:950-7. [PMID: 16838669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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Abstract
Recent discovery of RNA interference has reinvigorated the interest in chemically modified RNA. Chemical approaches may be used to optimize properties of small interfering RNAs, such as thermal stability, cellular delivery, in vivo half-life, and pharmacokinetics. From this perspective, amides as neutral and hydrophobic internucleoside linkages in RNA are highly interesting modifications that so far have not been tested in RNA interference. Amides are remarkably good mimics of the phosphodiester backbone of RNA and can be prepared using a relatively straightforward peptide coupling chemistry. The synthetic challenge that has hampered the progress in this field has been preparation of monomeric building blocks for such couplings, the nucleoside amino acid equivalents. Herein, we report two synthetic routes to enantiomerically pure 3'-aminomethyl-5'-carboxy-3',5'-dideoxy nucleosides, monomers for preparation of amide-modified RNA. Modification of uridine, a representative of natural nucleosides, using nitroaldol chemistry gives the target amino acid in 16 steps and 9% overall yield. The alternative synthesis starting from glucose is somewhat less efficient (17 steps and 6% yield of 3'-azidomethyl-5'-carboxy-3',5'-dideoxy uridine), but provides easier access to modified nucleosides having other heterocyclic bases. The syntheses developed herein will allow preparation of amide-modified RNA analogues and exploration of their potential as tools and probes for RNA interference, fundamental biochemistry, and bio- and nanotechnology.
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Affiliation(s)
- Qun Xu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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Abstract
A novel method for the synthesis of RNA oligomers with 2-cyanoethoxymethyl (CEM) as the 2'-hydroxyl protecting group has been developed. The new method allows the synthesis of oligoribonucleotides with an efficiency and final purity comparable to that obtained in DNA synthesis. [structure: see text]
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Affiliation(s)
- Tadaaki Ohgi
- Discovery Research Laboratories, Nippon Shinyaku Co. Ltd., 3-14-1 Sakura, Tsukuba City, Ibaraki 305-0003, Japan.
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