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Yuan D, Du X, Shi J, Zhou N, Baoum AA, Al Footy KO, Badahdah KO, Xu B. Synthesis and evaluation of the biostability and cell compatibility of novel conjugates of nucleobase, peptidic epitope, and saccharide. Beilstein J Org Chem 2015; 11:1352-9. [PMID: 26425189 PMCID: PMC4578436 DOI: 10.3762/bjoc.11.145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/16/2015] [Indexed: 11/23/2022] Open
Abstract
This article reports the synthesis of a new class of conjugates containing a nucleobase, a peptidic epitope, and a saccharide and the evalution of their gelation, biostability, and cell compatibility. We demonstrate a facile synthetic process, based on solid-phase peptide synthesis of nucleopeptides, to connect a saccharide with the nucleopeptides for producing the target conjugates. All the conjugates themselves (1-8) display excellent solubility in water without forming hydrogels. However, a mixture of 5 and 8 self-assembles to form nanofibers and results in a supramolecular hydrogel. The proteolytic stabilities of the conjugates depend on the functional peptidic epitopes. We found that TTPV is proteolytic resistant and LGFNI is susceptible to proteolysis. In addition, all the conjugates are compatible to the mammalian cells tested.
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Affiliation(s)
- Dan Yuan
- Department of Chemistry, Brandeis University, 415 South Street, MS015, Waltham, MA 02453, USA
| | - Xuewen Du
- Department of Chemistry, Brandeis University, 415 South Street, MS015, Waltham, MA 02453, USA
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, 415 South Street, MS015, Waltham, MA 02453, USA
| | - Ning Zhou
- Department of Chemistry, Brandeis University, 415 South Street, MS015, Waltham, MA 02453, USA
| | | | | | | | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, MS015, Waltham, MA 02453, USA
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2
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Egetenmeyer S, Richert C. Synthesis of oligodeoxynucleotides with 5'-caps binding RNA targets. ACTA ACUST UNITED AC 2013; Chapter 4:Unit4.53. [PMID: 23255203 DOI: 10.1002/0471142700.nc0453s51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protocols for the synthesis of oligodeoxynucleotides with a short peptidyl substituent linked to the 5'-O-terminus through a phosphodiester bond are presented. The example given is a peptidyl cap consisting of the residues of L-prolinol, glycine, and the acyl residue of oxolinic acid. DNA probes with this cap, also known as ogOA cap, give melting point increases for duplexes with RNA targets and improve mismatch discrimination at the terminus. The cap is either introduced in one step, using a newly developed phosphoramidite reagent, or assembled on the DNA chain. The step-wise assembly of the peptidyl chain is advantageous for combinatorial studies aimed at the optimization of a cap structure. The block coupling method, introducing the preassembled cap in one step, is attractive for routine use of a cap already optimized for a given application. Cap-bearing probes can increase fidelity of hybridization in a genomic context. They can be synthesized by automated DNA synthesis.
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Affiliation(s)
- Simone Egetenmeyer
- Institute for Organic Chemistry, University of Stuttgart, Stuttgart, Germany
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3
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Criton M, Dewynter G, Montero JL. Regioselective synthesis of nucleopeptidic bioconjugates enzymatic catalysis with ultrasonic irradiation. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19911101007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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4
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Sauerbrei B, Kappes T, Waldmann H. Enzymatic synthesis of peptide conjugates — Tools for the study of biological signal transduction. Top Curr Chem (Cham) 2008. [DOI: 10.1007/bfb0119220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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5
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Slaitas A, Yeheskiely E. SYNTHESIS AND REACTIVITY OF NUCLEOSIDE SULFILIMINES. PHOSPHORUS SULFUR 2004. [DOI: 10.1080/10426500490257113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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6
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Stepwise solid phase synthesis of uridylylated viral genome-linked peptides using uridylylated amino acid building blocks. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00042-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Slaitas A, Yeheskiely E. Fast and efficient peptide bond formation using bis-[alpha,alpha-bis(trifluoromethyl)-benzyloxy]diphenylsulfur. Part I. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2002; 60:283-91. [PMID: 12383118 DOI: 10.1034/j.1399-3011.2002.21015.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This study towards the development of sulfurane-based coupling agents shows that bis-[alpha,alpha-bis(trifluoromethyl)-benzyloxy]diphenylsulfur (BTBDS) can facilitate rapid amide bond formation between Nalpha-urethane-protected l-amino acids and l-phenylalanine ethyl ester in the absence of an external base. The corresponding dipeptide esters were obtained in excellent yields and with no detectable racemization, as judged by analysis of the formed dipeptides by chiral-phase HPLC. In addition, BTBDS-mediated condensation of benzoyl-l-phenylalanine with l-phenylalanine ethyl ester was also investigated. The results indicate that sulfuranes can be useful for application in racemization-sensitive systems, such as segment condensation.
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Affiliation(s)
- A Slaitas
- Division of Organic and Bioorganic Chemistry, MBB, Scheele Laboratory, Karolinska Institute, Stockholm, Sweden
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8
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Debéthune L, Marchán V, Fàbregas G, Pedroso E, Grandas A. Towards nucleopeptides containing any trifunctional amino acid (II). Tetrahedron 2002. [DOI: 10.1016/s0040-4020(02)00793-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Hayakawa Y. Toward an Ideal Synthesis of Oligonucleotides: Development of a Novel Phosphoramidite Method with High Capability. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2001. [DOI: 10.1246/bcsj.74.1547] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Jeyaraj DA, Waldmann H. Synthesis of nucleopeptides by an enzyme labile urethane protecting group. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(00)02121-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Moriguchi T, Yanagi T, Kunimori M, Wada T, Sekine M. Synthesis and properties of aminoacylamido-AMP: chemical optimization for the construction of an N-acyl phosphoramidate linkage. J Org Chem 2000; 65:8229-38. [PMID: 11101378 DOI: 10.1021/jo0008338] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes the design and synthesis of a new type of aminoacyl-adenylate analogue (aa-AMPN) having an N-acyl phosphoramidate linkage where the oxygen atom of the mixed anhydride bond of aminoacyl-adenylate (aa-AMP) is replaced by an amino group. This new type of aa-AMP analogue is expected to be useful as material for studies on the recognition mechanism of the aminoacylation of tRNA and other biochemical reactions. The condensation of phosphoramidite derivatives of carboxamides with nucleoside derivatives failed, because the activated phosphoramidite derivatives reacted with not only the hydroxyl groups but also another reactive species. An alternative approach was examined by the reaction of 5'-O-phosphoramidite adenosine derivatives with carboxamide derivatives. The TBTr and TSE groups were chosen for protection of the amino group of amino acid amides and the phosphate group, respectively. Detailed studies revealed that the use of 5-(3,5-dinitrophenyl)-1H-tetrazole as an activating catalyst of phosphoramidites resulted in rapid condensation within 10 min to give fully protected aa-AMPN derivatives. No side reaction occurred. Deprotection of these products via a two-step procedure gave aa-AMPN derivatives in good yields. It also turned out that aa-AMPNs thus obtained are stable under both acidic and basic conditions, such as 0.1 M HCl (pH 1.0) and 0.1 M NaOH (pH 13.0).
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Affiliation(s)
- T Moriguchi
- Faculty of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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12
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Marchán V, Rodríguez-Tanty C, Estrada M, Pedroso E, Grandas A. Alternative Procedures for the Synthesis of Methionine-Containing Peptide−Oligonucleotide Hybrids. European J Org Chem 2000. [DOI: 10.1002/1099-0690(200007)2000:13<2495::aid-ejoc2495>3.0.co;2-t] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Robles J, Beltrán M, Marchán V, Pérez Y, Travesset I, Pedroso E, Grandas A. Towards nucleopeptides containing any trifunctional amino acid. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00815-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Schwope I, Bleczinski CF, Richert C. Synthesis of 3',5'-Dipeptidyl Oligonucleotides. J Org Chem 1999; 64:4749-4761. [PMID: 11674548 DOI: 10.1021/jo990036d] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptide-DNA hybrids are richly functionalized analogues of biomolecules that may have applications as hybridization probes and antisense agents with tunable binding and targeting properties. So far, synthetic efforts have mainly focused on hybrids bearing a single peptide chain, either at the 5'- or the 3'-terminus. Such singly modified analogues are vulnerable to nuclease attack at the unmodified terminus. Here we report a convenient and high-yielding solid-phase synthesis of 3'- and 5'-modified analogues of DNA with aminoacyl and peptidyl appendages at both termini. Using MALDI-TOF mass spectra of crude products as the criterion, serine, glycolic acid, hydroxylauric acid, and dimethyl hydroxypropionic acid were tested as 3'-linker residues. The latter, together with a direct amide link at the 5'-terminus, gave the highest yields of hybrids. The optimized procedure assembles hybrids on a controlled pore glass support bearing three consecutive omega-hydroxy lauric acid linkers. This support greatly reduces side reactions observed with conventional supports, probably due to its ability to increase steric accessibility during coupling ("swelling") and its rapid hydrolysis during deprotection with ammonium hydroxide. Dihybrids with aromatic, basic, and acidic amino acid residues were prepared, including H-Phe-Gly-TGCGCA-DP-Phe-OH, where DP denotes the dimethyl hydroxypropionic acid linker, whose structure was confirmed via mass spectrometry and one- and two-dimensional NMR. Further, a mixed coupling with seven Fmoc-protected amino acids was shown to produce a combinatorial library of dipeptidyl DNA hybrids.
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Affiliation(s)
- Ina Schwope
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155
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15
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Eisele F, Owen DJ, Waldmann H. Peptide conjugates as tools for the study of biological signal transduction. Bioorg Med Chem 1999; 7:193-224. [PMID: 10218812 DOI: 10.1016/s0968-0896(98)00204-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Today, many biological phenomena are being investigated and understood in molecular detail, and organic chemistry is increasingly being directed towards biological phenomena. This review is intended to highlight this interplay of organic chemistry and biology, using biological signal transduction as an example. Lipo-, glyco-, phospho- and nucleoproteins play key roles in the processes whereby chemical signals are passed across cell membranes and further to the cell nucleus. For the study of the biological phenomena associated with these protein conjugates, structurally well-defined peptides containing the characteristic linkage region of the peptide backbone with the lipid, the carbohydrate or the phosphoric acid ester can provide valuable tools. The multi-functionality and pronounced acid- and base-lability of such compounds renders their synthesis a formidable challenge to conventional organic synthesis. However, the recent development of enzymatic protecting groups, provides one of the central techniques which, when coupled with classic chemical synthesis, can provide access to these complex and sensitive biologically relevant peptide conjugates under particularly mild conditions and with high selectivity.
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Affiliation(s)
- F Eisele
- Universität Karlsruhe, Institut für Organische Chemie, Germany
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16
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17
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Jungmann V, Waldmann H. An enzymatic protecting group strategy for the synthesis of nucleopeptides. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(97)10873-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Kappes T, Waldmann H. Enzymatic Synthesis of Peptide Conjugates: Tools for the Study of Biological Signal Transduction. ACTA ACUST UNITED AC 1997. [DOI: 10.1002/jlac.199719970504] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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20
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Lawrence AJ, Pavey JBJ, Cosstick R, O'Neil IA. Synthesis and Properties of 2‘-Deoxy-2‘-α-C-branched Nucleosides and Nucleotides. J Org Chem 1996. [DOI: 10.1021/jo9614607] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anthony J. Lawrence
- Robert Robinson Laboratories, Department of Chemistry, University of Liverpool, P.O. Box 147, Liverpool L69 3BX, U.K
| | - John B. J. Pavey
- Robert Robinson Laboratories, Department of Chemistry, University of Liverpool, P.O. Box 147, Liverpool L69 3BX, U.K
| | - Richard Cosstick
- Robert Robinson Laboratories, Department of Chemistry, University of Liverpool, P.O. Box 147, Liverpool L69 3BX, U.K
| | - Ian A. O'Neil
- Robert Robinson Laboratories, Department of Chemistry, University of Liverpool, P.O. Box 147, Liverpool L69 3BX, U.K
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21
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Lawrence AJ, Pavey JB, O'Neil IA, Cosstick R. Sunthesis of functionalised 2′-C-branched nucleosides via their γ-butyrolactones. Tetrahedron Lett 1995. [DOI: 10.1016/0040-4039(95)01226-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Bergmann F, Bannwarth W. Solid phase synthesis of directly linked peptide-oligodeoxynucleotide hybrids using standard synthesis protocols. Tetrahedron Lett 1995. [DOI: 10.1016/0040-4039(95)00155-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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Lloyd-Williams P, Merzouk A, Guibé F, Albericio F, Giralt E. Solid-phase synthesis of peptides using allylic anchoring groups 2. Palladium-catalysed cleavage of Fmoc-protected peptides. Tetrahedron Lett 1994. [DOI: 10.1016/s0040-4039(00)73378-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Beaucage SL, Iyer RP. The synthesis of specific ribonucleotides and unrelated phosphorylated biomolecules by the phosphoramidite method. Tetrahedron 1993. [DOI: 10.1016/s0040-4020(01)81543-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Kuyl-Yeheskiely E, Lodder M, van der Marel G, van Boom J. One-step synthesis of optically active benzyl N-trityl-L-aziridine-2-carboxylic esters. Tetrahedron Lett 1992. [DOI: 10.1016/s0040-4039(00)79586-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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26
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Zeng W, Hemmasi B. Solution Synthesis of Phytochelatins, Isopeptides from the Plant Kingdom. ACTA ACUST UNITED AC 1992. [DOI: 10.1002/jlac.199219920157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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27
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Robles J, Pedroso E, Grandas A. Solid phase synthesis of a model nucleopeptide with a phosphodiester bond between the 5′ end of a trinucleotide and a serine residue. Tetrahedron Lett 1991. [DOI: 10.1016/s0040-4039(00)92178-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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