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Golyshev VM, Pyshnyi DV, Lomzov AA. Effects of Phosphoryl Guanidine Modification of Phosphate Residues on the Structure and Hybridization of Oligodeoxyribonucleotides. J Phys Chem B 2021; 125:2841-2855. [PMID: 33724825 DOI: 10.1021/acs.jpcb.0c10214] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phosphoryl guanidine oligonucleotides (PGOs) are promising tools for biological research and development of biosensors and therapeutics. We performed structural and hybridization analyses of octa-, deca-, and dodecamers with all phosphate residues modified by 1,3-dimethylimidazolidine-2-imine moieties. Similarity of the B-form double helix between native and modified duplexes was noted. In PGO duplexes, we detected a decrease in the proportion of C2'-endo and an increased proportion of C1'-exo sugar conformations of the modified chain. Applicability of the two-state model to denaturation transition of all studied duplexes was proved for the first time. Sequence-dependent effects of this modification on hybridization properties were observed. The thermal stability of PGO complexes is almost native at 100 mM NaCl and slightly increases with decreasing ionic strength. An increase in water activity and dramatic changes in interaction with cations and in solvation of PGOs and their duplexes were noted, resulting in slight elevation of the melting temperature after an ionic-strength decrease from 1 M NaCl down to deionized water. Decreased binding of sodium ions and decreased water solvation were documented for PGOs and their duplexes. In contrast to DNA, the PGO duplex formation leads to a release of several cations. The water shell is significantly more disordered near PGOs and their complexes. Nevertheless, changes in solvation during the formation of native and PGO complexes are similar and indicate that it is possible to develop models for predictive calculations of the thermodynamic properties of phosphoryl guanidine oligomers. Our results may help devise an approach for the rational design of PGOs as novel improved molecular probes and tools for many modern methods involving oligonucleotides.
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Affiliation(s)
- Victor M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
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Blanchard H, Bum-Erdene K, Hugo MW. Inhibitors of Galectins and Implications for Structure-Based Design of Galectin-Specific Therapeutics. Aust J Chem 2014. [DOI: 10.1071/ch14362] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Galectins are a family of galactoside-specific lectins that are involved in a myriad of metabolic and disease processes. Due to roles in cancer and inflammatory and heart diseases, galectins are attractive targets for drug development. Over the last two decades, various strategies have been used to inhibit galectins, including polysaccharide-based therapeutics, multivalent display of saccharides, peptides, peptidomimetics, and saccharide-modifications. Primarily due to galectin carbohydrate binding sites having high sequence identities, the design and development of selective inhibitors targeting particular galectins, thereby addressing specific disease states, is challenging. Furthermore, the use of different inhibition assays by research groups has hindered systematic assessment of the relative selectivity and affinity of inhibitors. This review summarises the status of current inhibitors, strategies, and novel scaffolds that exploit subtle differences in galectin structures that, in conjunction with increasing available data on multiple galectins, is enabling the feasible design of effective and specific inhibitors of galectins.
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Ye M, Guillaume J, Liu Y, Sha R, Wang R, Seeman NC, Canary JW. Site-specific inter-strand cross-links of DNA duplexes. Chem Sci 2013; 4:1319-1329. [PMID: 23894693 PMCID: PMC3719409 DOI: 10.1039/c2sc21775a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We report the development of technology that allows inter-strand coupling across various positions within one turn of DNA. Four 2'-modified nucleotides were synthesized as protected phosphoramidites and incorporated into DNA oligonucleotides. The modified nucleotides contain either 5-atom or 16-atom linker components, with either amine or carboxylic acid functional groups at their termini, forming 10 or 32 atom (11 or 33 bond) linkages. Chemical coupling of the amine and carboxylate groups in designed strands resulted in the formation of an amide bond. Coupling efficiency as a function of trajectory distance between the individual linker components was examined. For those nucleotides capable of forming inter-strand cross-links (ICLs), coupling yields were found to depend on temperature, distance, and linker length, enabling several approaches that can control regioselective linkage. In the most favorable cases, the coupling yields are quantitative. Spectroscopic measurements of strands that were chemically cross-linked indicate that the global structure of the DNA duplex does not appear to be distorted from the B form after coupling. Thermal denaturing profiles of those strands were shifted to somewhat higher temperatures than those of their respective control duplexes. Thus, the robust amide ICLs formed by this approach are site-specific, do not destabilize the rest of the duplex, and only minimally perturb the secondary structure.
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Affiliation(s)
- Miao Ye
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Johan Guillaume
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Yu Liu
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Risheng Wang
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - James W. Canary
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
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Liu Y, Wang R, Ding L, Sha R, Seeman NC, Canary JW. Templated synthesis of nylon nucleic acids and characterization by nuclease digestion. Chem Sci 2012; 3:1930-1937. [PMID: 23125913 PMCID: PMC3486707 DOI: 10.1039/c2sc20129a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nylon nucleic acids containing oligouridine nucleotides with pendent polyamide linkers and flanked by unmodified heteronucleotide sequences were prepared by DNA templated synthesis. Templation was more efficient than the single-stranded synthesis: Coupling step yields were as high as 99.2%, with up to 7 amide linkages formed in the synthesis of a molecule containing 8 modified nucleotides. Controlled digestion by calf spleen phosphodiesterase enabled the mapping of modified nucleotides in the sequences. A combination of complete degradation of nylon nucleic acids by snake venom phosphodiesterase and dephosphorylation of the resulting nucleotide fragments by bacterial alkaline phosphatase, followed by LCMS analysis, clarified the linear structure of the oligo-amide linkages. The templated synthesis strategy afforded nylon nucleic acids in the target structure and was compatible with the presence heteronucleotides. The complete digestion procedure produced a new species of DNA analogues, nylon ribonucleosides, which display nucleosides attached via a 2'-alkylthio linkage to each diamine and dicarboxylate repeat unit of the original nylon nucleic acids. The binding affinity of a nylon ribonucleoside octamer to the complementary DNA was evaluated by thermal denaturing experiments. The octamer was found to form stable duplexes with an inverse dependence on salt concentration, in contrast to the salt-dependent DNA control.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Risheng Wang
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Liang Ding
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Roujie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - James W. Canary
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
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Prestinari C, Richert C. Intrastrand locks increase duplex stability and base pairing selectivity. Chem Commun (Camb) 2011; 47:10824-6. [PMID: 21863176 DOI: 10.1039/c1cc14008f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Oligodeoxynucleotide probes with disulfide locks between neighboring nucleobases show increases in melting point for duplexes with RNA target strands of up to 7.6 °C. The weakly pairing TT dimers are replaced with locked 2'-deoxy-5-(thioalkynyl)uridine residues via automated synthesis.
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Affiliation(s)
- Cora Prestinari
- Institute for Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70565 Stuttgart, Germany
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Bell NM, Micklefield J. Chemical modification of oligonucleotides for therapeutic, bioanalytical and other applications. Chembiochem 2010; 10:2691-703. [PMID: 19739190 DOI: 10.1002/cbic.200900341] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Neil M Bell
- School of Chemistry, The University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, UK
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Tercero N, Wang K, Gong P, Levicky R. Morpholino monolayers: preparation and label-free DNA analysis by surface hybridization. J Am Chem Soc 2009; 131:4953-61. [PMID: 19296583 PMCID: PMC2730437 DOI: 10.1021/ja810051q] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Surface hybridization, a reaction in which nucleic acid molecules in solution react with nucleic acid partners immobilized on a surface, is widely practiced in life science research. In these applications the immobilized partner, or "probe", is typically single-stranded DNA. Because DNA is strongly charged, high salt conditions are required to enable binding between analyte nucleic acids ("targets") in solution and the DNA probes. High salt, however, compromises prospects for label-free monitoring or control of the hybridization reaction through surface electric fields; it also stabilizes secondary structure in target species that can interfere with probe-target recognition. In this work, initial steps toward addressing these challenges are taken by introducing morpholinos, a class of uncharged DNA analogues, for surface-hybridization applications. Monolayers of morpholino probes on gold supports can be fabricated with methods similar to those employed with DNA and are shown to hybridize efficiently and sequence-specifically with target strands. Hybridization-induced changes in the interfacial charge organization are analyzed with electrochemical methods and compared for morpholino and DNA probe monolayers. Molecular mechanisms connecting surface hybridization state to the interfacial capacitance are identified and interpreted through comparison to numerical Poisson-Boltzmann calculations. Interestingly, positive as well as negative capacitive responses (contrast inversion) to hybridization are possible, depending on surface populations of mobile ions as controlled by the applied potential. Quantitative comparison of surface capacitance with target coverage (targets/area) reveals a nearly linear relationship and demonstrates sensitivities (limits of quantification) in the picogram per square millimeter range.
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Affiliation(s)
- Napoleon Tercero
- Dept. of Chemical & Biological Engineering, Polytechnic Institute of New York University, Brooklyn, NY 11201
- Dept. of Chemical Engineering, Columbia University, New York, NY 10027
| | - Kang Wang
- Dept. of Chemical & Biological Engineering, Polytechnic Institute of New York University, Brooklyn, NY 11201
| | - Ping Gong
- Dept. of Chemical Engineering, Columbia University, New York, NY 10027
| | - Rastislav Levicky
- Dept. of Chemical & Biological Engineering, Polytechnic Institute of New York University, Brooklyn, NY 11201
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Zabost E, Nowicka AM, Donten M, Stojek Z. Substantial difference between temperature dependencies of dsDNA predenaturation process obtained by voltammetry and spectroscopy. Phys Chem Chem Phys 2009; 11:8933-8. [DOI: 10.1039/b906752c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Liu Y, Kuzuya A, Sha R, Guillaume J, Wang R, Canary JW, Seeman NC. Coupling across a DNA helical turn yields a hybrid DNA/organic catenane doubly tailed with functional termini. J Am Chem Soc 2008; 130:10882-3. [PMID: 18661989 PMCID: PMC2712227 DOI: 10.1021/ja8041096] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe the synthesis of a hybrid DNA/organic macrocycle that is prepared by formation of an amide linkage across one full turn of DNA. Formation of a catenane proved that the linkage crossed a turn rather than running along the phosphodiester backbone contour. The product, a doubly tailed catenane, contains 5'- and 3'-termini that can be functionalized further or used to incorporate the catenane structure into other DNA assemblies.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, New York University, New York, New York 10003, USA
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