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Qiao JQ, Liang C, Zhu ZY, Cao ZM, Zheng WJ, Lian HZ. Monolithic alkylsilane column: A promising separation medium for oligonucleotides by ion-pair reversed-phase liquid chromatography. J Chromatogr A 2018; 1569:168-177. [PMID: 30077461 DOI: 10.1016/j.chroma.2018.07.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/19/2018] [Accepted: 07/24/2018] [Indexed: 02/06/2023]
Abstract
In this paper, a monolithic octadecylsilane column and particle-packed octadecylsilane columns were used to investigate the retention behaviors of oligonucleotides by ion-pair reversed-phase liquid chromatography (IP-RPLC). Results showed that, with same base composition, hairpin oligonucleotides always had weaker retention than corresponding random coil oligonucleotides on the monolithic column, but not on the particle-packed columns. In addition, the linear correlation between the retention factor k of oligonucleotides and the reciprocal of temperature (1/T), especially for hairpins, was relatively weaker on the particle-packed columns, as compared to the correlation on the monolithic column. The correlation between k and 1/T became weaker with decreasing particle size of the particle-packed columns. Moreover, results revealed that the overall retention order on the particle-packed column with small particles (3 μm) differed greatly from that on the monolithic column. In contrast, the retention order on the 10 μm particle-packed column was very close to that on the monolithic column. From the above, we inferred that oligonucleotides could keep their primary conformations unchanged when passing through the monolithic column, attributed to the special pore structures of the monolith. However, the conformations of oligonucleotides were suppressed or even destroyed when oligonucleotides passed through the particle-packed columns. This because the narrow and tortuous channels created by the stacked stationary phase particles could lead to more complex and unequable retention behaviors. Therefore, the monolithic column exhibited better retention regularity for oligonucleotides of secondary structure especially for hairpins than the particle-packed columns. It is noteworthy that the monolith-based IP-RPLC opens an intriguing prospect in accurately elucidating the retention behaviors of oligonucleotides.
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Affiliation(s)
- Jun-Qin Qiao
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Chao Liang
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Zhen-Yu Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Zhao-Ming Cao
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Wei-Juan Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Hong-Zhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China.
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Yao J, Dai Q, Liu Z, Zhou L, Xu J. Circular RNAs in Organ Fibrosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1087:259-273. [DOI: 10.1007/978-981-13-1426-1_21] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Amiri AR, Macgregor RB. The effect of hydrostatic pressure on the thermal stability of DNA hairpins. Biophys Chem 2011; 156:88-95. [DOI: 10.1016/j.bpc.2011.02.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Revised: 02/02/2011] [Accepted: 02/08/2011] [Indexed: 11/29/2022]
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Kwok T, Heinrich J, Jung-Shiu J, Meier MG, Mathur S, Moelling K. Reduction of gene expression by a hairpin-loop structured oligodeoxynucleotide: alternative to siRNA and antisense. Biochim Biophys Acta Gen Subj 2009; 1790:1170-8. [PMID: 19505533 DOI: 10.1016/j.bbagen.2009.05.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 04/29/2009] [Accepted: 05/22/2009] [Indexed: 10/20/2022]
Abstract
BACKGROUND We previously described the inhibition of HIV-1 replication by a 54-mer hairpin-loop structured oligodeoxynucleotide (ODN) A, which binds the polypurine tract (PPT) on HIV-1 RNA. ODN A was shown to lead to reduced viral RNA in virions or early during infection. METHODS AND RESULTS Here we demonstrated that ODN A was able to cause hydrolysis of viral RNA not only by retroviral RT-associated RNase H but also cellular RNase H1 and RNase H2 in vitro. Furthermore, ODN A reduced gene expression in a dose-dependent manner in a cell-based reporter assay where a PPT sequence was inserted in the 5' untranslated region of the reporter gene. The efficacy of ODN A was higher than that of its siRNA and antisense counterparts. By knocking down cellular RNases H, we showed that RNase H1 contributed to the gene silencing by ODN A but the possibility of a partial contribution of RNase H-independent mechanisms could not be ruled out. GENERAL SIGNIFICANCE Our findings highlight the potential application of hairpin-loop structured ODNs for reduction of gene expression in mammalian cells and underscore the possibility of using ODN A to trigger the hydrolysis of HIV RNA in infected cells by cellular RNases H.
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Affiliation(s)
- Terry Kwok
- Institute of Medical Virology, University of Zurich, Gloriastrasse 30, CH 8006 Zurich, Switzerland
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Wang Y, Ng MTT, Zhou T, Li X, Tan CH, Li T. C3-Spacer-containing circular oligonucleotides as inhibitors of human topoisomerase I. Bioorg Med Chem Lett 2008; 18:3597-602. [PMID: 18490159 DOI: 10.1016/j.bmcl.2008.04.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2008] [Revised: 04/25/2008] [Accepted: 04/30/2008] [Indexed: 11/18/2022]
Abstract
Some dumbbell-shaped circular oligonucleotides containing internal C3-spacers and Topo I-binding sites were designed and synthesized which displayed high inhibitory efficiency on the activity of human Topo I as well as resisted the degradation by some DNA repair enzymes.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, 3 Science Drive 3, National University of Singapore, Singapore 117543, Singapore
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Li X, Tao Ng MT, Wang Y, Liu X, Li T. Dumbbell-shaped circular oligonucleotides as inhibitors of human topoisomerase I. Bioorg Med Chem Lett 2007; 17:4967-71. [PMID: 17591440 DOI: 10.1016/j.bmcl.2007.06.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 06/04/2007] [Accepted: 06/07/2007] [Indexed: 10/23/2022]
Abstract
A dumbbell-shaped circular oligonucleotide containing topoisomerase I-binding sites and two mismatched base pairs in its sequence has been designed and synthesized. Our further studies demonstrate that this particularly designed oligonucleotide displays an IC(50) value of 9 nM in its inhibition on the activity of human topoisomerase I, a magnitude smaller than that of camptothecin, an anticancer drug currently in clinical use.
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Affiliation(s)
- Xinming Li
- Department of Chemistry, 3 Science Drive 3, National University of Singapore, Singapore, Singapore
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Chin TM, Chang CM, Huang HW, Lo LL. Bimolecular triplex formation between 5'-d-(AG)nT4(CT)n and 5'-d-(TC)n as functions of helix length and buffer. J Biomol Struct Dyn 2005; 22:35-43. [PMID: 15214803 DOI: 10.1080/07391102.2004.10506978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
It was observed that a group of unusually stable DNA hairpins (Hn: 5'-d-(AG)nT4(CT)n, n = 2-4) were directed to homopyrimidine sequences (Pn: 5'-d-(TC)n) by py x pu x py-type triplex formation, resulting in high binding affinity and specificity. The spectroscopic results (UV and CD) showed that the short bimolecular triplex Hn:Pn could be formed in acidic conditions (pH 4.5-6.0) as helix length n > 2, and further extending to neutral pH as n = 4. This hairpin strategy for recognition of a pyrimidine strand has a substantial binding advantage over either the conventional linear analog or simple Watson-Crick complement. Triplex stability of Hn with Pn is not only pH-dependent, as expected for triplexes involving C+. GC triads, but also sensitive to the buffer. The triplex H4:P4 was formed in the phosphate buffers of pH 6.0-7.0 but already dissociated above pH 6.5 in the buffer of cacodylate, MOPSO or PIPES. By contrast, the nature of a buffer had no major influence on stability of a hairpin duplex. Here we provide a simple triplex system, and the data presented here may be useful in defining the experimental conditions necessary to stabilize triplex DNA.
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Affiliation(s)
- T-M Chin
- Institute of Applied Chemistry, Chinese Culture University, Taipei 111, Taiwan.
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Tok JBH, Wong W, Baboolal N. Binding of aminoglycoside antibiotics with modified A-site 16S rRNA construct containing non-nucleotide linkers. Bioorg Med Chem Lett 2002; 12:365-70. [PMID: 11814798 DOI: 10.1016/s0960-894x(01)00760-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The design and synthesis of synthetically modified cyclic A-site 16S rRNA construct is reported. The binding characteristics of several members of the aminoglycoside antibiotics with this novel class of synthetically modified A-site 16S rRNA constructs were subsequently investigated.
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Affiliation(s)
- Jeffrey B-H Tok
- Department of Chemistry & Natural Sciences, York College and Graduate Center of the City University of New York, 94-20 Guy R. Brewer Blvd., Jamaica, NY 11451, USA.
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Affiliation(s)
- V V. Demidov
- Center for Advanced Biotechnology, Boston University, 36 Cummington St., Fl. 2nd, 02215, Tel.: +1-617-353-8490; fax: +1-617-353-8501, Boston, MA, USA
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Kuhn H, Frank-Kamenetskii MD, Demidov VV. High-purity preparation of a large DNA dumbbell. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2001; 11:149-53. [PMID: 11446590 DOI: 10.1089/108729001300338672] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We report on the efficient biochemical synthesis of a large DNA dumbbell starting from a pair of short DNA hairpins with long single-stranded tails of arbitrary sequence. The DNA dumbbell is obtained by enzymatic ligation yielding a 94-bp duplex stem closed at both termini by single-stranded loops of 5 nt. Following ligation, all unligated precursors and monoligated by-products were multiply biotinylated via nick-translation or primer-extension or both. Thus, they could readily be removed from the DNA dumbbell preparation by a mild biomagnetic separation procedure. The closed conformation of the purified DNA dumbbell was verified by its altered gel mobility as compared with unligated or monoligated samples and by an exonuclease assay. Considering the promising therapeutic potential of DNA dumbbells, the developed biosynthetic approach could be used for high-purity preparation of longer, covalently closed DNA decoys.
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Affiliation(s)
- H Kuhn
- Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, MA 02215, USA
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