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Hayashi Y, Sun Y. Overcoming Challenges in Oligonucleotide Therapeutics Analysis: A Novel Nonion Pair Approach. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2034-2037. [PMID: 39157887 PMCID: PMC11378278 DOI: 10.1021/jasms.4c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Oligonucleotide therapeutics (OT) have emerged as promising drug modality for various intractable diseases. Recently, liquid chromatography-mass spectrometry (LC-MS) has been commonly employed for characterizing and quantifying OT in biological samples. Traditionally, the ion pairing-reverse phase (IP-RP) LC-MS method has been utilized in OT bioanalyses; however, this approach is associated with several limitations, including the memory effect and ion suppression effect of IP reagents. Therefore, this study aimed to develop a new RP-LC-MS method that eliminates the need for IP reagents. Our investigation revealed that ammonium bicarbonate was essential for the successful implementation of this nonIP-RP-LC-MS-based bioanalysis of OT. Moreover, the developed method demonstrated high versatility, accommodating the analysis of various natural or chemically modified oligonucleotides. The sensitivity of the method was further assessed using reconstituted plasma samples (the lower limit of quantification in this experiment was 0.5-1 ng/mL). In summary, the developed nonIP-RP-LC-MS method offers an easy, reliable, and cost-effective approach to the bioanalysis of OT.
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Affiliation(s)
- Yoshiharu Hayashi
- Bioanalysis Research Department, CMIC Pharma Science Co., Ltd., Hyogo 677-0032, Japan
| | - Yuchen Sun
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kanagawa 210-9501, Japan
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2
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Fioretti I, Müller-Späth T, Aumann L, Sponchioni M. UV-based dynamic control improves the robustness of multicolumn countercurrent solvent gradient purification of oligonucleotides. Biotechnol J 2024; 19:e2400170. [PMID: 39014932 DOI: 10.1002/biot.202400170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/18/2024]
Abstract
Therapeutic oligonucleotides (ONs) have great potential to treat many diseases due to their ability to regulate gene expression. However, the inefficiency of standard purification techniques to separate the target sequence from molecularly similar variants is hindering development of large scale ON manufacturing at a reasonable cost. Multicolumn Countercurrent Solvent Gradient Purification (MCSGP) is a valuable process able to bypass the purity-yield tradeoff typical of single-column operations, and hence to make the ON production more sustainable from both an economic and environmental point of view. However, operating close to the optimum of MCSGP can be challenging, resulting in unstable process performance and in a drift in product quality, especially when running a continuous process for extended periods where process parameters such as temperature are prone to variation. In this work, we demonstrate how greater process robustness is introduced in the design and execution of MCSGP for the purification of a 20mer single-stranded DNA sequence through the implementation of UV-based dynamic control. With this novel approach, the cyclic steady state was reached already in the third cycle and disturbances coming from fluctuations in the feed quality, loading amount and temperature were effectively compensated allowing a stable operation close to the optimum. In response to the perturbations, the controlled process kept the standard deviation on product recovery below 3.4%, while for the non-controlled process it increased up to 27.5%.
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Affiliation(s)
- Ismaele Fioretti
- Department of Chemistry, Materials and Chemical Engineering, Politecnico di Milano, Milano, Italy
| | | | | | - Mattia Sponchioni
- Department of Chemistry, Materials and Chemical Engineering, Politecnico di Milano, Milano, Italy
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3
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Culver HR, Sinha J, Prieto TR, Calo CJ, Fairbanks BD, Bowman CN. Click Nucleic Acid–DNA Binding Behavior: Dependence on Length, Sequence, and Ionic Strength. Biomacromolecules 2020; 21:4205-4211. [DOI: 10.1021/acs.biomac.0c00996] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Heidi R. Culver
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Jasmine Sinha
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Tania R. Prieto
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Christopher J. Calo
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Benjamin D. Fairbanks
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Christopher N. Bowman
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Materials Science and Engineering Program, University of Colorado Boulder, Boulder, Colorado 80309, United States
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4
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Ultra-High-Performance Reversed-Phase Liquid Chromatography Hyphenated with ESI-Q-TOF-MS for the Analysis of Unmodified and Antisense Oligonucleotides. Chromatographia 2019. [DOI: 10.1007/s10337-019-03844-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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5
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Gajria S, Neumann T, Tirrell M. Self‐assembly and applications of nucleic acid solid‐state films. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2011; 3:479-500. [DOI: 10.1002/wnan.148] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Surekha Gajria
- Department of Chemistry, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Thorsten Neumann
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Matthew Tirrell
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
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6
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Neumann T, Gajria S, Tirrell M, Jaeger L. Reversible structural switching of a DNA-DDAB film. J Am Chem Soc 2009; 131:3440-1. [PMID: 19275252 DOI: 10.1021/ja809349m] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the novel structure and behavior of a DNA-DDAB complex film cast from an organic solvent and exhibiting a structural switching transition as it is dried or wetted with water. The film was easily prepared by formation of a complex between the negatively charged phosphate groups of DNA and the positively charged headgroup of the surfactant DDAB. This complex was then purified, dried, dissolved in 2-propanol, and cast onto a glass slide to form a self-standing film by means of slow evaporation. While the structure of the dried film was found to be composed of single-stranded DNA and a monolayer of DDAB, upon hydration of the film, the structure switched to double-stranded DNA complexed to a bilayer of DDAB. We expect this phenomenon to serve as a useful model for the design of new responsive materials and programmable self-assembly.
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Affiliation(s)
- Thorsten Neumann
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA
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7
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Rodríguez M, Moussaoui M, Benito A, Cuchillo CM, Nogués MV, Vilanova M. Human pancreatic ribonuclease presents higher endonucleolytic activity than ribonuclease A. Arch Biochem Biophys 2008; 471:191-7. [PMID: 18191631 DOI: 10.1016/j.abb.2007.12.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Revised: 12/14/2007] [Accepted: 12/15/2007] [Indexed: 11/17/2022]
Abstract
Analyzing the pattern of oligonucleotide formation induced by HP-RNase cleavage shows that the enzyme does not act randomly and follows a more endonucleolytic pattern when compared to RNase A. The enzyme prefers the binding and cleavage of longer substrate molecules, especially when the phosphodiester bond that is broken is 8-11 nucleotides away from at least one of the ends of the substrate molecule. This more endonucleolytic pattern is more appropriate for an enzyme with a regulatory role. Deleting two positive charges on the N-terminus (Arg4 and Lys6) modifies this pattern of external/internal phosphodiester bond cleavage preference, and produces a more exonucleolytic enzyme. These residues may reinforce the strength of a non-catalytic secondary phosphate binding (p2) or, alternatively, constitute a new non-catalytic phosphate binding subsite (p3).
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Affiliation(s)
- M Rodríguez
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi s/n, 17071 Girona, Spain
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8
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Cuchillo CM, Moussaoui M, Barman T, Travers F, Nogués MV. The exo- or endonucleolytic preference of bovine pancreatic ribonuclease A depends on its subsites structure and on the substrate size. Protein Sci 2002; 11:117-28. [PMID: 11742128 PMCID: PMC2368780 DOI: 10.1110/ps.13702] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The cleavage pattern of oligocytidylic acid substrates by bovine pancreatic ribonuclease A (RNase A) was studied by means of reversed-phase HPLC. Oligocytidylic acids, ranging from dinucleotides to heptanucleotides, were obtained by RNase A digestion of poly(C). They were identified by MALDI-TOF mass spectrometry; it was confirmed that all of them corresponded to the general structure (Cp)(n)C>p, in which C>p indicates a 2',3'-cyclic phosphate. This is a confirmation of the proposed mechanism for RNase A, wherein the so-called hydrolytic (or second) step is in fact a special case of the reverse of transphosphorylation (first step). The patterns of cleavage for the oligonucleotide substrates show that the native enzyme has no special preference for endonucleolytic or exonucleolytic cleavage, whereas a mutant of the enzyme (K7Q/R10Q-RNase A) lacking p(2) (a phosphate binding subsite adjacent, on the 3' side, to the main phosphate binding site p(1)) shows a clear exonucleolytic pattern; a mutant (K66Q-RNase A) lacking p(0) (a phosphate binding subsite adjacent, on the 5' side, to the main phosphate binding site p(1)) shows a more endonucleolytic pattern. This indicates the important role played by the subsites on the preference for the bond cleaved. Molecular modeling shows that, in the case of the p(2) mutant, the amide group of glutamine can form a hydrogen bond with the 2',3'-cyclic terminal phosphate, whereas the distance to a 3',5'-phosphodiester bond is too long to form such a hydrogen bond. This could explain the preference for exonucleolytic cleavage shown by the p(2) mutant.
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Affiliation(s)
- Claudi M Cuchillo
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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9
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Alberghina G, Fisichella S, Renda E. Separation of G structures formed by a 27-mer guanosine-rich oligodeoxyribonucleotide by dye-ligand affinity chromatography. J Chromatogr A 1999; 840:51-8. [PMID: 10335611 DOI: 10.1016/s0021-9673(99)00196-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
G-DNA structures, formed by a 27-mer guanosine-rich oligodeoxyribonucleotide, AACCCGGCGTTCGGGGGGTACCGGGTT, were isolated and studied by dye-ligand affinity chromatography, using a Reactive Green 19-agarose resin (RG19-aga) and gel electrophoresis. The experiments were performed in the presence of Li+, Na+ and K+, which are able to stabilise the G structures to different extents. Desalting procedures followed by affinity chromatography, performed in the presence of Li+, gave us information on the relationships among the species isolated and their stability. The results show that the more stable species were those obtained in the presence of K+, while in the presence of Li+, the formation of G structures was negligible and the oligonucleotide was almost exclusively present as a stem-loop structure recognised by the RG19-aga affinity resin. Electrophoretic and denaturation and renaturation experiments supported the affinity chromatography results.
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Affiliation(s)
- G Alberghina
- Dipartimento di Scienze Chimiche, Università di Catania, Italy
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10
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Moussaoui M, Guasch A, Boix E, Cuchillo C, Nogués M. The role of non-catalytic binding subsites in the endonuclease activity of bovine pancreatic ribonuclease A. J Biol Chem 1996; 271:4687-92. [PMID: 8617733 DOI: 10.1074/jbc.271.9.4687] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Bovine pancreatic ribonuclease A catalyzes the depolymerization of RNA. There is much evidence that several subsites, in addition to the main catalytic site, are involved in the formation of the enzyme-substrate complex. This work analyzes the pattern of oligonucleotide formation by ribonuclease A using poly(C) as substrate. The poly(C) cleavage shows that the enzyme does not act in a random fashion but rather prefers the binding and cleavage of the longer substrate molecules and that the phosphodiester bond broken should be 6-7 residues apart from the end of the chain to be preferentially cleaved by ribonuclease A. The results demonstrate the model of the cleavage of an RNA chain based on the cooperative binding between the multisubsite binding structure of ribonuclease A and the phosphates of the polynucleotide (Parés, X., Nogués, M. V., de Llorens, R., and Cuchillo, C. M. (1991) in Essays in Biochemistry (Tipton, K. F., ed) Vol. 26, pp. 89-103, Portland Press Ltd., London). The contribution to the enzymatic process of the non-catalytic phosphate-binding subsite (p2) adjacent to the catalytic center has been analyzed in p2 chemically modified ribonuclease A or by means of site-directed mutagenesis. In both cases deletion of p2 abolishes the endonuclease activity of ribonuclease A, which is substituted by an exonuclease activity. All these results support the role of the multisubsite structure of the enzyme in the endonuclease activity and in the catalytic mechanism.
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Affiliation(s)
- M Moussaoui
- Departament de Bioquímica i Biologia Molecular, Facultat de Ciències and Institut de Biologia Fonamental V. Villar-Palasí, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain Spain Spain
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11
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Baba Y. Prediction of the behaviour of oligonucleotides in high-performance liquid chromatography and capillary electrophoresis. JOURNAL OF CHROMATOGRAPHY 1993; 618:41-55. [PMID: 8227264 DOI: 10.1016/0378-4347(93)80026-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The present state of studies on prediction of the chromatographic and electrophoretic behaviour of oligonucleotides is reviewed; particular emphasis is given to high-performance liquid chromatographic and capillary electrophoretic separations. Attention is paid to fundamental theory for the prediction of retention and migration times, and bandwidths. The article also deals with the applicability of the theory to the computer-assisted prediction and the computer simulation for these two types of separation of oligonucleotides. Optimization of separation conditions using the computer simulation system is briefly described.
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Affiliation(s)
- Y Baba
- Kobe Women's College of Pharmacy, Japan
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12
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Yashima E, Shiiba T, Sawa T, Miyauchi N, Akashi M. High-performance affinity chromatography of oligonucleotides on nucleic acid analogue immobilized silica gel columns. J Chromatogr A 1992; 603:111-9. [PMID: 1322922 DOI: 10.1016/0021-9673(92)85351-s] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The nucleic acid analogues poly(9-vinyladenine) (PVAd), poly(9-adenylethyl methacrylate) and poly(thymylethyl methacrylate) (PTM) were chemically bonded to porous silica gel, which had been pretreated with 3-trimethoxysilylpropyl methacrylate, by free radical copolymerization to produce novel packing materials for affinity chromatographic columns. The columns separated nucleosides and nucleotide dimers on the basis of hydrophobic interaction using an aqueous buffer and complementary hydrogen bonding interaction in methanol as an eluent. The PVAd- and PTM-silica gel columns gave a nucleobase-selective separation of oligonucleotides differing in length from mixtures of oligoadenylic and oligouridylic acids. On the PVAd-silica gel column terminal phosphate isomers of oligouridylic acid up to seven mer were resolved and the elution order of the isomers was different from that on an ODS column.
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Affiliation(s)
- E Yashima
- Department of Applied Chemistry and Chemical Engineering, Faculty of Engineering, Kagoshima University, Japan
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13
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Baba Y, Matsuura T, Wakamoto K, Tsu-Hako M. Comparison of high-performance liquid chromatography with capillary gel electrophoresis in single-base resolution of polynucleotides. J Chromatogr A 1991. [DOI: 10.1016/0021-9673(91)80133-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Use of the 4-methoxy-4′-octyloxytrityl groups as an affinity handle for the purification of synthetic oligonucleotides. J Chromatogr A 1991. [DOI: 10.1016/s0021-9673(01)96005-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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Hill TL, Mayhew JW. Convenient purification of tritylated and detritylated oligonucleotides up to 100-mer. J Chromatogr A 1990; 512:415-31. [PMID: 2229236 DOI: 10.1016/s0021-9673(01)89508-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Oligomers from crude phosphoramidite synthesis mixtures have been purified by reversed-phased high-performance liquid chromatography by exploiting the chromatographic variables of stationary phase pore size, chain length, and gradient shape. Chromatography was performed on oligomers up to 100-mer with mobile phases containing triethylammonium acetate/acetonitrile mixtures. Convenient guidelines are offered to enrich or purify synthetic oligomers. Tritylated oligomers up to 25 bases in length are best purified on C8 or C18, 80 A columns with moderate strength mobile phases using a combination of isocratic delays and shallow gradients. For oligomers longer than 25-mer, C3, 300 A columns provide adequate fast purification in as little as 5 min, while 300 A, C8 columns with long, slow gradients gave substantially increased purity. Chromatography of detritylated oligomers requires a modified approach. Up to 25-mer they are best purified on 80 A, C18 columns with much lower organic concentrations and shallower gradients than those used for tritylated oligomers. Detrytilated oligomers greater than 25-mer can be enriched on both C3 and C8, 300 A columns using the same conditions described for shorter detritylated oligomers.
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Affiliation(s)
- T L Hill
- Beckman Instruments, Altex Division, San Ramon, CA 94583
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16
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Baba Y, Fukuda M, Yoza N. Computer-assisted retention prediction system for oligonucleotides in gradient anion-exchange chromatography. J Chromatogr A 1988; 458:385-94. [PMID: 3235640 DOI: 10.1016/s0021-9673(00)90580-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A technique is presented for the retention prediction of single-stranded homo-oligonucleotides under gradient elution conditions in anion-exchange chromatography. The prediction system is based on the theory proposed by Jandera and Churacek. In the present system, the theory was modified by the extrapolation method, utilizing the linear relationship between the log of the capacity factor and the number of nucleotides. The modified theory allowed the prediction of retention times for high-molecular-weight oligonucleotides, which could not be calculated from the original theory. Oligoadenylate was used as a standard oligonucleotide to demonstrate the accuracy of the prediction system. By use of this system, the retention times of oligoadenylates up to 25-35 bases in chain length were predicted within 8% errors under both binary-linear and binary-convex gradient shapes.
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Affiliation(s)
- Y Baba
- Department of Chemistry, Faculty of Education, Oita University, Japan
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17
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Chapter 10 Nucleic Acids, Polynucleotides and Oligonucleotides. ACTA ACUST UNITED AC 1988. [DOI: 10.1016/s0301-4770(08)61450-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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18
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Birsner U, Gilles U, Nielsen P, McMaster GK. Reversed-phase high-performance liquid chromatographic system for the rapid, automated purification of oligonucleotides. J Chromatogr A 1987; 402:381-6. [PMID: 3654875 DOI: 10.1016/0021-9673(87)80043-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- U Birsner
- Max-Planck-Institut für Immunbiologie, Freiburg, F.R.G
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19
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Carbon P, Ebel JP. In vitro construction of yeast tRNAAsp variants: nucleotide substitutions and additions in T-stem and T-loop. Nucleic Acids Res 1987; 15:1933-50. [PMID: 3550694 PMCID: PMC340609 DOI: 10.1093/nar/15.5.1933] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A procedure for the construction of 3'-end labelled yeast tRNAAsp harboring substitutions or additions of any desired nucleotide in T-stem and T-loop (position 57 to 61) has been developed. This was done by in vitro enzymatic manipulations of the yeast tRNAAsp involving specific hydrolysis with RNases, phosphorylation and dephosphorylation with T4 polynucleotide kinase and ligation with T4 RNA ligase. Using this procedure we have replaced conserved or semi-conserved nucleotides located in position 57 to 61 of yeast tRNAAsp. We have also constructed different yeast tRNAAsp with eight bases instead of seven in T-loop. Further use of these tRNAAsp variants will be discussed with the help of the crystallographic three-dimensional structure.
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20
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Hydrophilic silica-based anion exchanger with adjustable cabacity for HPLC of nucleotides. Chromatographia 1986. [DOI: 10.1007/bf02268804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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22
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Drager RR, Regnier FE. Application of the stoichiometric displacement model of retention to anion-exchange chromatography of nucleic acids. J Chromatogr A 1986; 359:147-55. [PMID: 3637180 DOI: 10.1016/0021-9673(86)80069-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The stoichiometric displacement model has been refined in its application to anion-exchange chromatography. The revised stoichiometric displacement model has been shown to be valid for anion-exchange chromatography with respect to all particulars of the model tested. It has been shown that the use of displacing agent activity is not a necessary condition for valid application of the stoichiometric displacement model to anion-exchange chromatography. While the cation of the displacing salt can influence anion-exchange chromatography, the data indicate that the displacing anion is of primary importance. It has been shown that solutes with three-dimensional structure have Zn value to solute charge ratios less than unity, and that the stoichiometric displacement model may be useful as a probe of solute three-dimensional structure.
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23
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Floyd TR, Cicero SE, Fazio SD, Raglione TV, Hsu SH, Winkle SA, Hartwick RA. Mixed-mode hydrophobic ion exchange for the separation of oligonucleotides and DNA fragments using HPLC. Anal Biochem 1986; 154:570-7. [PMID: 3014917 DOI: 10.1016/0003-2697(86)90031-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydrophobic anion exchangers were formed by cobonding both ionic and hydrophobic ligands to silica gel. These phases were used to separate single-stranded oligonucleotides and double-stranded DNA restriction fragments. By varying the ratio of n-octyldimethylsilane and either 3-chloropropyldimethylsilane or 4-chlorobutyldimethylsilane added during silanization a series of mixed-ligand or mixed-mode stationary phases was created. Concentration and ratio of bonded ligands were determined using a new gas chromatography fluorination method. Total ligand coverage was found to approach 2.1 ligands nm-2 for n-octyldimethylsilane. Bonding reproducibility for mixed-mode phases was good. Nucleic acid separations were achieved under gentle mobile phase conditions by using the stationary phase as an easily modifiable variable.
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24
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Bischoff R, McLaughlin LW. Isolation of specific tRNAs using an ionic-hydrophobic mixed-mode chromatographic matrix. Anal Biochem 1985; 151:526-33. [PMID: 3913336 DOI: 10.1016/0003-2697(85)90215-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The coating of a C18-reversed-phase high performance liquid chromatography support (octadecylsilyl-Hypersil) with a tetraalkylammonium salt (methyltrioctylammonium chloride) produces a chromatographic matrix with both ionic and hydrophobic character. Using this material oligonucleotides and tRNAs can be separated with high resolution. The observed resolution is in part due to the apparent lack of diffusion processes occurring during chromatography with this matrix. Some tRNAs can be obtained in high purity from a bulk tRNA mixture after a single chromatographic step. In general it is more efficient to use the matrix as the last step of a purification procedure for a particular tRNA. A two-step procedure is described which allows, in some cases, the isolation of small quantities of specific tRNA isoacceptors.
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25
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Stone MP, Winkle SA, McFarland GD, Yoo MC, Borer PN. 13C-NMR of ribosyl A-A-A, A-A-G, and A-U-G. Synthesis and assignment. Biophys Chem 1985; 23:129-38. [PMID: 4092078 DOI: 10.1016/0301-4622(85)80071-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The three RNA trinucleotides; ApApA, ApApG, and ApUpG, have been synthesized in sufficient quantity to obtain natural abundance 13C(1H)-NMR spectra at strand concentrations between 4 and 100 mM. Comparisons between 70 degrees C spectra of the three trimers and their consistuent dimers ApA, ApG, ApU, and UpG allow secure assignments to be made for most of the resonances. This paper describes the syntheses and 13C assignments of the oligomers.
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26
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Becker CR, Efcavitch J, Heiner CR, Kaiser NF. Use of a C4 column for reversed-phase high-performance liquid chromatographic purification of synthetic oligonucleotides. J Chromatogr A 1985. [DOI: 10.1016/s0021-9673(01)87454-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Drager RR, Regnier FE. High-performance anion-exchange chromatography of oligonucleotides. Anal Biochem 1985; 145:47-56. [PMID: 2988370 DOI: 10.1016/0003-2697(85)90324-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Several types of high-performance silica-based supports have been found to be effective in the separation of polynucleotides. The principal difference in these materials is the type of bonded phase and the method by which it is attached to the silica support. One approach is the coupling of stationary-phase groups to the surface through siloxane bonding. This technique is simple and produces a material of high capacity and resolution, but it suffers from poor bonded-phase stability. An alternative approach is the adsorption of low-molecular-weight polyethylene imines (PEI) that are crosslinked into a surface film. The stationary phase is held in place by adsorption of the film at multiple sites. A previous report on this material showed the resolution of oligonucleotides containing up to 30 bases. This paper reports further optimization of the PEI bonding chemistry in the preparation of HP-IEC columns for oligonucleotides and tRNA species. Quaternization of the ion-exchange matrix was found to increase resolution of oligonucleotides from 30 to 50 bases. The same support was found to be capable of resolving multiple tRNA species. Separations were achieved on small (0.42 X 5 cm) columns, using a 60- to 120-min ammonium sulfate gradient. The initial solvent was 15% acetonitrile in 0.05 M potassium phosphate (pH 5.9). The addition of 1 M ammonium sulfate to the initial solvent was used to prepare the final solvent.
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28
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Middleton T, Herlihy WC, Schimmel PR, Munro HN. Synthesis and purification of oligoribonucleotides using T4 RNA ligase and reverse-phase chromatography. Anal Biochem 1985; 144:110-7. [PMID: 3985307 DOI: 10.1016/0003-2697(85)90091-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
T4 RNA ligase has been used to construct a series of defined oligoribonucleotides. Hexamer or pentamer blocks were synthesized first by multiple additions of mononucleotide diphosphates to trimers with T4 RNA ligase and removal of the terminal phosphate with alkaline phosphatase; inhibitors of the ligase were removed by passing the sample over a 1-ml reverse-phase octadecasilyl column. The two nucleotide blocks were then ligated to give undecamers. Yields for the individual ligations ranged from 85 to 100% for acceptors lacking uridines and at least 70% for those containing uridines. The overall yield of the undecamer relative to the starting trimers was about 10%. Each round of ligation averaged about 8 h; the time required to synthesize each undecamer was 1 to 2 weeks. Optimization of the steps to achieve this is described in detail.
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29
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Wulfson AN, Yakimov SA. HPLC of nucleotides. II. General methods and their development for analysis and preparative separation. An approach to selectivity control. ACTA ACUST UNITED AC 1984. [DOI: 10.1002/jhrc.1240070802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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30
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Garcia S, Liautard JP. Separation of macromolecular RNAs by reversed-phase high-performance liquid chromatography. J Chromatogr A 1984; 296:355-62. [PMID: 6207189 DOI: 10.1016/s0021-9673(01)96429-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The reversed-phase high-performance liquid chromatography of synthetic and natural RNAs was studied. The results show that base composition alone cannot explain the retention characteristics of natural RNAs; secondary structures are probably involved. However, under the conditions described, the separation was independent of the sizes of the molecules. 18S and 28S ribosomal RNAs were eluted after tRNAs but before 9S globin mRNA. Furthermore, globin mRNA was resolved into two species, one containing and the other lacking poly(A). When applied to the separation of HeLa cell poly(A)-containing RNA, an heterogeneous pattern was obtained. Analysis of peptides synthesized by the mRNA showed that the separation is independent of size.
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31
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High-performance liquid chromatography of high-molecular-weight nucleic acids on the macroporous ion exchanger, nucleogen. J Chromatogr A 1984. [DOI: 10.1016/s0021-9673(01)96428-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Liautard JP. Rapid separation of single-stranded DNA from double-stranded DNA by reversed-phase high-performance liquid chromatography. J Chromatogr A 1984; 285:221-5. [PMID: 6707132 DOI: 10.1016/s0021-9673(01)87756-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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33
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Panabières F, Piechaczyk M, Rainer B, Dani C, Fort P, Riaad S, Marty L, Imbach JL, Jeanteur P, Blanchard JM. Complete nucleotide sequence of the messenger RNA coding for chicken muscle glyceraldehyde-3-phosphate dehydrogenase. Biochem Biophys Res Commun 1984; 118:767-73. [PMID: 6322764 DOI: 10.1016/0006-291x(84)91461-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The complete nucleotide sequence for chicken glyceraldehyde-3-phosphate dehydrogenase mRNA has been determined, thereby extending the longest such sequence previously reported (Dugaiczyk et al. Biochemistry, 1983, 22, 1605-1613) by 27 nucleotides. The complete mRNA with the exclusion of poly(A) is 1284 nucleotides long and contains 56 nucleotides of 5' non coding sequence and 229 nucleotides of 3' non coding region. Knowledge of the complete sequence allows us to propose secondary structures models which may be of biological significance.
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34
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Demidov V, Potaman V. High-performance liquid chromatography of the photo-products of nucleic acid components. J Chromatogr A 1984. [DOI: 10.1016/s0021-9673(01)87743-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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High-performance liquid chromatography of nucleic acid constituents: Chromatographic examination of novel stationary phases. Chromatographia 1984. [DOI: 10.1007/bf02687714] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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36
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Use of reversed-phase high-performance liquid chromatography for the purification of 5′-phosphorylated oligonucleotides. J Chromatogr A 1984. [DOI: 10.1016/s0021-9673(00)96293-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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37
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Ogilvie KK, Nemer MJ, Gillen MF. Large scale bench-top synthesis of a nineteen unit ribonucleotide on silica gel. Tetrahedron Lett 1984. [DOI: 10.1016/s0040-4039(01)81140-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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38
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High-performance liquid chromatographic separation of oligonucleotides and other nucleic acid constituents on multifunctional stationary phases. J Chromatogr A 1983. [DOI: 10.1016/s0021-9673(00)91639-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Abstract
The ability to separate biological macromolecules with good resolution on liquid chromatographic columns has depended on the development of suitable packing materials. In size exclusion chromatography, molecules are separated by size on the basis of differential permeation of the packing. Ion exchange, hydrophobic interaction (or reversed-phase), and affinity chromatography are all surface-mediated separation methods, although they depend on different retention mechanisms. High-performance liquid chromatographic columns designed for biopolymers offer major advantages over conventional columns in both speed and resolving power. The exponential growth of literature on the high-performance separation of peptides and proteins in particular indicates that the technique will become the dominant form of column liquid chromatography.
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40
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Lawson TG, Regnier FE, Weith HL. Separation of synthetic oligonucleotides on columns of microparticulate silica coated with crosslinked polyethylene imine. Anal Biochem 1983; 133:85-93. [PMID: 6314842 DOI: 10.1016/0003-2697(83)90225-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A rapid and effective method for separating oligonucleotides using high-performance ion-exchange chromatography is described. Columns were prepared by adsorbing a layer of polyethylene imine on 5-micron-diameter porous silica followed by crosslinking with a multifunctional oxirane. This weak anion-exchange matrix was found to be useful in the separation of mononucleotides and oligonucleosides containing up to 20 residues in either homo- or heteropolymers. Small analytical columns (4.2 X 150 mm) had a capacity ranging from less than a microgram in analytical separations to several milligrams in the preparative mode. The columns have proven to be especially useful in assessing the purity of precursor blocks, monitoring the chemical synthesis of oligonucleotides, and isolating reaction products after the synthesis.
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41
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Haupt W, Pingoud A. Comparison of several high-performance liquid chromatography techniques for the separation of oligodeoxynucleotides according to their chain lengths. J Chromatogr A 1983. [DOI: 10.1016/0021-9673(83)80049-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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42
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43
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Kempe T, Chow F, Sundquist WI, Nardi TJ, Paulson B, Peterson SM. Selective 2'-benzoylation at the cis 2',3'-diols of protected ribonucleosides. New solid phase synthesis of RNA and DNA-RNA mixtures. Nucleic Acids Res 1982; 10:6695-714. [PMID: 6184676 PMCID: PMC326958 DOI: 10.1093/nar/10.21.6695] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
5'-0-(Dimethoxytrityl)-2'-0-(benzoyl or 3,4,5-trimethoxybenzoyl)-base protected ribonucleosides have been prepared by selective benzoylation of the 2'-hydroxyl group. The isomerization of the 2'-benzoates to the 3'-benzoates was studied. The protected ribonucleosides have been converted to either methylphosphochloridites or methylphosphoamidites and used to synthesize oligoribonucleotides on silica gel solid support. The synthetic RNA were deprotected and isolated using conditions that minimize internucleotide cleavage. The use of 2'-benzoates as protecting groups for ribonucleosides has made it possible to easily prepare and isolate mixtures of DNA and RNA.
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44
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Crowther JB, Caronia JP, Hartwick RA. An improved method for the determination of oligonucleotide chain length using phosphodiesterase hydrolysis and ion-pair high-performance liquid chromatography. Anal Biochem 1982; 124:65-73. [PMID: 6289698 DOI: 10.1016/0003-2697(82)90220-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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45
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46
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Holbrook SR, Tinoco I, Young TS, Kim SH, Martin FH. Crystallization and preliminary crystallographic investigation of a DNA-RNA hybrid. J Mol Biol 1981; 153:837-40. [PMID: 6175761 DOI: 10.1016/0022-2836(81)90423-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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47
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Stone MP, Borer PN. H-NMR of G-U-C and G-U-C-C in D2O: assignment of nonexchangeable protons and analysis of solution conformation. Biophys Chem 1981; 14:369-74. [PMID: 6279200 DOI: 10.1016/0301-4622(81)85040-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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48
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Stone MP, Borer PN. H-NMR of U-G-A and U-G-A-A in D2O: assignment of nonexchangeable protons and analysis of solution conformation. Biophys Chem 1981; 14:363-8. [PMID: 6279199 DOI: 10.1016/0301-4622(81)85039-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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49
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Crowther JB, Jones R, Hartwick RA. High-performance liquid chromatography of the oligonucleotides. J Chromatogr A 1981. [DOI: 10.1016/s0021-9673(00)88100-5] [Citation(s) in RCA: 10] [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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50
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Stone MP, Johnson DL, Borer PN. Unusual structures in single-stranded ribonucleic acid: proton nuclear magnetic resonance of AUCCA in deuterium oxide. Biochemistry 1981; 20:3604-10. [PMID: 6167285 DOI: 10.1021/bi00515a046] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Conformational features of the oligoribonucleic acid (oligo-RNA) A1-U2-C3-C4-A5 are explored by proton nuclear magnetic resonance (NMR). The sequence is a molecular cognate of a portion of the T psi C loop and stem regions of yeast tRNAPhe. The molecule forms at least two classes of flexible yet ordered structures. Class I states are similar in spectral properties to the component oligomers, AU, AUC, and AUCC, and are likely to be standard right-helical structures. Class II states are characterized by a 2'-endo pucker at A1 and unusually large shielding of several C3 and U2 protons. Most of these features are consistent with identifying the class II solution structures with the "arch" conformation for the T psi C region determined by X-ray crystallography of yeast tRNAPhe.
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