1
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Sawamoto H, Sasaki T, Takegawa-Araki T, Utsugi M, Furukawa H, Hirakawa Y, Yamairi F, Kurita T, Murahashi K, Yamada K, Ohta T, Kumagai S, Takemiya A, Obika S, Kotera J. Synthesis and properties of a novel modified nucleic acid, 2'-N-methanesulfonyl-2'-amino-locked nucleic acid. Bioorg Med Chem Lett 2023; 88:129289. [PMID: 37068560 DOI: 10.1016/j.bmcl.2023.129289] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
2'-Amino-locked nucleic acid has a functionalizable nitrogen atom at the 2'-position of its furanose ring that can provide desired properties to a nucleic acid as a scaffold. In this study, we synthesized a novel nucleic acid, 2'-N-methanesulfonyl-2'-amino-locked nucleic acid (ALNA[Ms]) and conducted comparative studies on the physical and pharmacological properties of the ALNA[Ms] and on conventional nucleic acids, such as 2'-methylamino-LNA (ALNA[Me]), which is a classical 2'-amino-LNA derivative, and also on 2',4'-BNA/LNA (LNA). ALNA[Ms] oligomers exhibited binding affinities for the complementary RNA strand that are similar to those of conventional nucleic acids. Four types of ALNA[Ms] nucleosides exhibited no genotoxicity in bacterial reverse mutation assays. The knockdown abilities of Malat1 RNA using the Matat1 antisense oligonucleotide (ASO) containing ALNA[Ms] were higher than those of ALNA[Me] and were closer to those of LNA. Furthermore, the ASO containing ALNA[Ms] showed different tissue tropism from that containing LNA. ALNA[Ms] exhibited biological activities that were distinct from conventional constrained nucleic acids, suggesting the possibility that ALNA[Ms] can serve as novel modified nucleic acids in oligonucleotide therapeutics.
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Affiliation(s)
- Hiroaki Sawamoto
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan.
| | - Takashi Sasaki
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan.
| | - Tomo Takegawa-Araki
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Masayuki Utsugi
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Hiroyuki Furukawa
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Yoko Hirakawa
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Fumiko Yamairi
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Takashi Kurita
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Karin Murahashi
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Katsuya Yamada
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Tetsuya Ohta
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Shinji Kumagai
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Akihiro Takemiya
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jun Kotera
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
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2
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2'-N-Alkylaminocarbonyl-2'-amino-LNA: Synthesis, duplex stability, nuclease resistance, and in vitro anti-microRNA activity. Bioorg Med Chem 2023; 78:117148. [PMID: 36580743 DOI: 10.1016/j.bmc.2022.117148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
2'-Amino-LNA has the potential to acquire various functions through chemical modification at the 2'-nitrogen atom. This study focused on 2'-N-alkylaminocarbonyl 2'-amino-LNA, which is a derivative of 2'-amino-LNA. We evaluated its practical usefulness as a chemical modification of anti-miRNA oligonucleotide. The synthesis of phosphoramidites of 2'-N-alkylaminocarbonyl substituted 2'-amino-LNA bearing thymine and 5-methylcytosine proceeded in good yields. Incorporating the 2'-N-alkylaminocarbonyl-2'-amino-LNA monomers into oligonucleotides improved the duplex stability for complementary RNA strands and robust nuclease resistance. Moreover, 2'-N-alkylaminocarbonyl-2'-amino-LNA is a promising scaffold that significantly increases the potency of anti-miRNA oligonucleotides.
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3
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Takegawa-Araki T, Yasukawa K, Iwazaki N, Maruyama H, Furukawa H, Sawamoto H, Obika S. Parallel synthesis of oligonucleotides containing N-acyl amino-LNA and their therapeutic effects as anti-microRNAs. Org Biomol Chem 2022; 20:9351-9361. [PMID: 36383101 DOI: 10.1039/d2ob01809h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
2'-Amino-locked nucleic acid (ALNA), maintains excellent duplex stability, and the nitrogen at the 2'-position is an attractive scaffold for functionalization. Herein, a facile and efficient method for the synthesis of various 2'-N-acyl amino-LNA derivatives by direct acylation of the 2'-amino moiety contained in the synthesized oligonucleotides and its fundamental properties are described. The introduction of the acylated amino-LNA enhances the potency of the molecules as therapeutic anti-microRNA oligonucleotides.
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Affiliation(s)
- Tomo Takegawa-Araki
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Kai Yasukawa
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Norihiko Iwazaki
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hideto Maruyama
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hiroyuki Furukawa
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hiroaki Sawamoto
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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4
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Beck KM, Pham RL, Nanim RA, Laustsen A, Nielsen P. Double‐Headed Nucleotides with Increased Base‐Pairing Affinity and Specificity. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kasper M. Beck
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Robert L. Pham
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Rita A. Nanim
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Anders Laustsen
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Poul Nielsen
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
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5
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Debreczeni N, Bege M, Herczeg M, Bereczki I, Batta G, Herczegh P, Borbás A. Tightly linked morpholino-nucleoside chimeras: new, compact cationic oligonucleotide analogues. Org Biomol Chem 2021; 19:8711-8721. [PMID: 34586122 DOI: 10.1039/d1ob01174j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The polyanionic phosphodiester backbone of nucleic acids contributes to high nuclease sensitivity and low cellular uptake and is therefore a major obstacle to the biological application of native oligonucleotides. Backbone modifications, particularly charge alterations is a proven strategy to provide artificial oligonucleotides with improved properties. Here, we describe the synthesis of a new type of oligonucleotide analogues consisting of a morpholino and a ribo- or deoxyribonucleoside in which the 5'-amino group of the nucleoside unit provides the nitrogen of the morpholine ring. The synthetic protocol is compatible with trityl and dimethoxytrityl protecting groups and azido functionality, and was extended to the synthesis of higher oligomers. The chimeras are positively charged in aqueous medium, due to the N-alkylated tertiary amine structure of the morpholino unit.
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Affiliation(s)
- Nóra Debreczeni
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- Doctoral School of Chemistry, University of Debrecen, Hungary
- Institute of Healthcare Industry, University of Debrecen, H-4032, Debrecen, Nagyerdei körút 98, Hungary
| | - Miklós Bege
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- Institute of Healthcare Industry, University of Debrecen, H-4032, Debrecen, Nagyerdei körút 98, Hungary
- MTA-DE Molecular Recognition and Interaction Research Group, UD, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Mihály Herczeg
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- Research Group for Oligosaccharide Chemistry of HAS, UD, H-4032, Debrecen, Egyetem tér 1, Hungary
| | - Ilona Bereczki
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- National Virology Laboratory, Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary
| | - Gyula Batta
- Department of Organic Chemistry, University of Debrecen, H-4032, Debrecen, Hungary
| | - Pál Herczegh
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- National Virology Laboratory, Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary
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6
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Verma V, Maity J, Maikhuri VK, Sharma R, Ganguly HK, Prasad AK. Double-headed nucleosides: Synthesis and applications. Beilstein J Org Chem 2021; 17:1392-1439. [PMID: 34194579 PMCID: PMC8204177 DOI: 10.3762/bjoc.17.98] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022] Open
Abstract
Double-headed nucleoside monomers have immense applications for studying secondary nucleic acid structures. They are also well-known as antimicrobial agents. This review article accounts for the synthetic methodologies and the biological applications of double-headed nucleosides.
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Affiliation(s)
- Vineet Verma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Jyotirmoy Maity
- Department of Chemistry, St. Stephen’s College, University of Delhi, Delhi-110 007, India
| | - Vipin K Maikhuri
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Ritika Sharma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Himal K Ganguly
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata-700 054, India
| | - Ashok K Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
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7
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Beck KM, Ruder L, Nicolai TS, Pham RL, Risgaard NA, Hornum M, Nielsen P. Double‐Headed Nucleotides with Non‐Native Nucleobases: Synthesis and Duplex Studies. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Kasper M. Beck
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Linette Ruder
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Tine S. Nicolai
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Robert L. Pham
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Nikolaj A. Risgaard
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Mick Hornum
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Poul Nielsen
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
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8
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Gupta MK, Madhanagopal BR, Ganesh KN. Peptide Nucleic Acid with Double Face: Homothymine–Homocytosine Bimodal Cα-PNA (bm-Cα-PNA) Forms a Double Duplex of the bm-PNA2:DNA Triplex. J Org Chem 2020; 86:414-428. [DOI: 10.1021/acs.joc.0c02158] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Manoj Kumar Gupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| | - Bharath Raj Madhanagopal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| | - Krishna N. Ganesh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
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9
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García-Raso A, Terrón A, Balle B, López-Zafra A, Frontera A, Barceló-Oliver M, Fiol JJ. Crystal structures of N6-modified-amino acid nucleobase analogs( iii): adenine–valeric acid, adenine–hexanoic acid and adenine–gabapentine. NEW J CHEM 2020. [DOI: 10.1039/d0nj02538k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
H-bonding networks, anion–π and π–π interactions in the crystal structures of N6-modified-amino acid adenine analogs are investigated by means of DFT calculations and X-ray crystallography analysis.
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Affiliation(s)
- Angel García-Raso
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma
- Spain
| | - Angel Terrón
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma
- Spain
| | - Bartomeu Balle
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma
- Spain
| | - Adela López-Zafra
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma
- Spain
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma
- Spain
| | | | - Juan J. Fiol
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma
- Spain
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10
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Hornum M, Stendevad J, Sharma PK, Kumar P, Nielsen RB, Petersen M, Nielsen P. Base-Pairing Properties of Double-Headed Nucleotides. Chemistry 2019; 25:7387-7395. [PMID: 30942502 DOI: 10.1002/chem.201901077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Indexed: 12/28/2022]
Abstract
Nucleotides that contain two nucleobases (double-headed nucleotides) have the potential to condense the information of two separate nucleotides into one. This presupposes that both bases must successfully pair with a cognate strand. Here, double-headed nucleotides that feature cytosine, guanine, thymine, adenine, hypoxanthine, and diaminopurine linked to the C2'-position of an arabinose scaffold were developed and examined in full detail. These monomeric units were efficiently prepared by convergent synthesis and incorporated into DNA oligonucleotides by means of the automated phosphoramidite method. Their pairing efficiency was assessed by UV-based melting-temperature analysis in several contexts and extensive molecular dynamics studies. Altogether, the results show that these double-headed nucleotides have a well-defined structure and invariably behave as functional dinucleotide mimics in DNA duplexes.
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Affiliation(s)
- Mick Hornum
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Julie Stendevad
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Pawan K Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra, Haryana, 136119, India
| | - Pawan Kumar
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Rasmus B Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Michael Petersen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Poul Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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11
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Pons R, Ibáñez C, Buades AB, Franconetti A, Garcia‐Raso A, Fiol JJ, Terrón A, Molins E, Frontera A. Synthesis, X‐ray characterization and density functional theory studies of N
6
‐benzyl‐N
6
‐methyladenine–M(II) complexes (M = Zn, Cd): The prominent role of π–π, C–H···π and anion–π interactions. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.4906] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Roser Pons
- Departament de QuímicaUniversitat de les Illes Balears Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares) Spain
| | - Cristina Ibáñez
- Departament de QuímicaUniversitat de les Illes Balears Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares) Spain
| | - Ana B. Buades
- Departament de QuímicaUniversitat de les Illes Balears Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares) Spain
| | - Antonio Franconetti
- Departament de QuímicaUniversitat de les Illes Balears Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares) Spain
| | - Angel Garcia‐Raso
- Departament de QuímicaUniversitat de les Illes Balears Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares) Spain
| | - Juan J. Fiol
- Departament de QuímicaUniversitat de les Illes Balears Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares) Spain
| | - Angel Terrón
- Departament de QuímicaUniversitat de les Illes Balears Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares) Spain
| | - Elies Molins
- Institut de Ciència de Materials de Barcelona (ICMAB‐CSIC), Campus Universitat Autònoma de Barcelona 08193 Cerdanyola Spain
| | - Antonio Frontera
- Departament de QuímicaUniversitat de les Illes Balears Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares) Spain
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12
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Beck K, Reslow-Jacobsen C, Hornum M, Henriksen C, Nielsen P. A double-headed nucleotide with two cytosines: DNA with condensed information and improved duplex stability. Bioorg Med Chem Lett 2019; 29:740-743. [PMID: 30655212 DOI: 10.1016/j.bmcl.2019.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/02/2019] [Indexed: 10/27/2022]
Abstract
Double-headed nucleotide monomers are capable of condensing the genetic information of DNA. Herein, a double-headed nucleotide with two cytosine bases (CC) is constructed. The additional cytosine is connected through a methylene linker to the 2'-position of arabinocytidine. The nucleotide is incorporated into oligonucleotides and its effect on duplex stability is studied. For single incorporations, a thermal stabilization of 4.0 °C is found as compared to the unmodified duplex and it is shown that both nucleobases of CC participate in Watson-Crick base pairing. In combination with the previously published UT monomer, it is also shown that multiple incorporations are tolerated. For instance, a 16-mer sequence is targeted by a 13-mer oligonucleotide by using one CC and two UT monomers without compromising the overall duplex stability. Finally, the potential of double-headed nucleotides in triplex-forming oligonucleotides is studied, however, with the conclusion that the present design is not well-suited for this function.
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Affiliation(s)
- Kasper Beck
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Charlotte Reslow-Jacobsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Mick Hornum
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Christian Henriksen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Poul Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark.
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13
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García-Raso A, Terrón A, López-Zafra A, García-Viada A, Barta A, Frontera A, Lorenzo J, Rodríguez-Calado S, Vázquez-López EM, Fiol JJ. Crystal structures of N6-modified-amino acid related nucleobase analogs (II): hybrid adenine-β-alanine and adenine-GABA molecules. NEW J CHEM 2019. [DOI: 10.1039/c9nj02279a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
H-Bonding networks and anion–π interactions in the crystal structures of N6-modified-amino acid adenine analogs are investigated using X-ray crystallography and DFT calculations.
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Affiliation(s)
- Angel García-Raso
- Departament de Química
- Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Angel Terrón
- Departament de Química
- Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Adela López-Zafra
- Departament de Química
- Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | | | - Agostina Barta
- Departament de Química
- Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Julia Lorenzo
- Instituto de Biotecnología y Biomedicina
- Departamento de Bioquímica y Biologia Molecular
- Universidad Autónoma de Barcelona
- Barcelona
- Spain
| | - Sergi Rodríguez-Calado
- Instituto de Biotecnología y Biomedicina
- Departamento de Bioquímica y Biologia Molecular
- Universidad Autónoma de Barcelona
- Barcelona
- Spain
| | - Ezequiel M. Vázquez-López
- Instituto de Investigación Sanitaria Galicia Sur/Universidade de Vigo
- Departamento de Química Inorgánica
- Facultade de Química
- Edificio Ciencias Experimentais
- E-36310 Vigo
| | - Juan J. Fiol
- Departament de Química
- Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
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14
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Hari Y, Osawa T, Yamashita S, Nakanishi A, Ito Y. Synthesis and Hybridization Properties of Oligonucleotides Including 2’-N-Alkoxycarbonyl-2’-amino-LNA Derivatives. HETEROCYCLES 2019. [DOI: 10.3987/com-18-s(f)46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Hornum M, Sharma PK, Reslow-Jacobsen C, Kumar P, Petersen M, Nielsen P. Condensing the information in DNA with double-headed nucleotides. Chem Commun (Camb) 2018; 53:9717-9720. [PMID: 28820207 DOI: 10.1039/c7cc05047j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A normal duplex holds as many Watson-Crick base pairs as the number of nucleotides in its constituent strands. Here we establish that single nucleotides can be designed to functionally imitate dinucleotides without compromising binding affinity. This effectively allows sequence information to be more compact and concentrated to fewer phosphates.
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Affiliation(s)
- Mick Hornum
- Nucleic Acid Center, Department of Physics, Chemistry & Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
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16
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García-Raso A, Terrón A, Bauzá A, Frontera A, Molina JJ, Vázquez-López EM, Fiol JJ. Crystal structures of N6-modified-aminoacid/peptide nucleobase analogs: hybrid adenine–glycine and adenine–glycylglycine molecules. NEW J CHEM 2018. [DOI: 10.1039/c8nj02147c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anion–π interactions in crystal structures of N6-modified-aminoacid and dipeptide adenine analogs are investigated using X-ray crystallography and DFT calculations.
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Affiliation(s)
- Angel García-Raso
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma (Baleares)
- Spain
| | - Angel Terrón
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma (Baleares)
- Spain
| | - Antonio Bauzá
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma (Baleares)
- Spain
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma (Baleares)
- Spain
| | - Jhon J. Molina
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma (Baleares)
- Spain
| | - Ezequiel M. Vázquez-López
- Instituto de Investigación Sanitaria Galicia Sur/Universidade de Vigo
- Departamento de Química Inorgánica
- Facultade de Química
- Edificio Ciencias Experimentais
- E-36310 Vigo
| | - Juan J. Fiol
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma (Baleares)
- Spain
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17
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Oligodeoxynucleotides containing 2'-amino-LNA nucleotides as constrained morpholino phosphoramidate and phosphorodiamidate monomers. Bioorg Med Chem Lett 2017; 27:3173-3176. [PMID: 28552336 DOI: 10.1016/j.bmcl.2017.05.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 11/23/2022]
Abstract
Incorporation in a 2'→5' direction of a phosphorodiamidite 2'-amino-LNA-T nucleotide as the morpholino phosphoramidate and N,N-dimethylamino phosphorodiamidate monomers into six oligonucleotides is reported. Thermal denaturation studies showed that the novel 2'-amino-LNA-based morpholino monomers exert a destabilizing effects on duplexes formed with complementary DNA and RNA.
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18
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Flexible double-headed cytosine-linked 2'-deoxycytidine nucleotides. Synthesis, polymerase incorporation to DNA and interaction with DNA methyltransferases. Bioorg Med Chem 2016; 24:1268-76. [PMID: 26899597 DOI: 10.1016/j.bmc.2016.01.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/25/2016] [Accepted: 01/29/2016] [Indexed: 12/31/2022]
Abstract
New types of double-headed 2'-deoxycytidine 5'-O-triphosphates (dC(XC)TPs) bearing another cytosine or 5-fluorocytosine linked through a flexible propargyl, homopropargyl or pent-1-ynyl linker to position 5 were prepared by the aqueous Sonogashira cross-coupling reactions of 5-iodo-dCTP with the corresponding (fluoro)cytosine-alkynes. The modified dC(XC)TPs were good substrates for DNA polymerases and were used for enzymatic synthesis of cytosine-functionalized DNA by primer extension or PCR. The cytosine- or fluorocytosine-linked DNA probes did not significantly inhibit DNA methyltransferases and did not cross-link to these proteins.
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19
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Sharma PK, Kumar P, Nielsen P. Double-Headed Nucleotides: Building Blocks for New Nucleic Acid Architectures. Aust J Chem 2016. [DOI: 10.1071/ch16021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Double-headed nucleotides are nucleotides with two nucleobases. These have been investigated recently with the purpose of using the recognition potential of the additional nucleobases in various nucleic acid constructs. Presented here is a review of the double-headed nucleotide monomers investigated so far and their effects in nucleic acid duplexes and other secondary structures.
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20
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Kumar P, Sharma PK, Hansen J, Jedinak L, Reslow-Jacobsen C, Hornum M, Nielsen P. Three new double-headed nucleotides with additional nucleobases connected to C-5 of pyrimidines; synthesis, duplex and triplex studies. Bioorg Med Chem 2015; 24:742-9. [PMID: 26778611 DOI: 10.1016/j.bmc.2015.12.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 10/22/2022]
Abstract
In the search for double-coding DNA-systems, three new pyrimidine nucleosides, each coded with an additional nucleobase anchored to the major groove face, are synthesized. Two of these building blocks carry a thymine at the 5-position of 2'-deoxyuridine through a methylene linker and a triazolomethylene linker, respectively. The third building block carries an adenine at the 6-position of pyrrolo-2'-deoxycytidine through a methylene linker. These double-headed nucleosides are introduced into oligonucleotides and their effects on the thermal stabilities of duplexes are studied. All studied double-headed nucleotide monomers reduce the thermal stability of the modified duplexes, which is partially compensated by using consecutive incorporations of the modified monomers or by flanking the new double-headed analogs with members of our former series containing propyne linkers. Also their potential in triplex-forming oligonucleotides is studied for two of the new double-headed nucleotides as well as the series of analogs with propyne linkers. The most stable triplexes are obtained with single incorporations of additional pyrimidine nucleobases connected via the propyne linker.
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Affiliation(s)
- Pawan Kumar
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Pawan K Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra 136 119, India
| | - Jonas Hansen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Lukas Jedinak
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Charlotte Reslow-Jacobsen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Mick Hornum
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Poul Nielsen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark.
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21
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Dalager M, Andersen NK, Kumar P, Nielsen P, Sharma PK. Double-headed nucleotides introducing thymine nucleobases in the major groove of nucleic acid duplexes. Org Biomol Chem 2015; 13:7040-9. [PMID: 26053231 DOI: 10.1039/c5ob00872g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Four different double-headed nucleosides each combining two thymine nucleobases with different linkers were synthesised. The 5-position of 2'-deoxyuridine was connected to the N1-position of a thymine through either m- or p-disubstituted phenyl or phenylacetylene linkers by the use of Suzuki or Sonogashira couplings. When introduced into oligonucleotides, the thermal stability of dsDNA and DNA : RNA duplexes were determined and structural information was obtained from CD- and fluorescence spectroscopy. Also the recognition of abasic sites was studied. In general, the more stable duplexes were obtained with m- rather than p-substitution and with phenylacetylene rather than phenyl linkers.
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Affiliation(s)
- Michael Dalager
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark.
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22
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Kumar P, Sharma PK, Nielsen P. Double-headed nucleotides with arabino configuration: synthesis and hybridization properties. J Org Chem 2014; 79:11534-40. [PMID: 25375974 DOI: 10.1021/jo502189h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The formation of new nucleic acid motifs by using double-headed nucleotides is reported. Modified phosphoramidites carrying additional thymine or adenine attached to the 2'-position of arabinouridine through a methylene linker are conveniently prepared and incorporated into oligonucleotides to obtain the modified nucleotide monomers (a)U(T) and (a)U(A), respectively. The extension of a DNA double helix by one or two additional A:T base pairs is achieved by placing these modified monomers in the opposite strands in a so-called (+1)-zipper arrangement. Hence, 12 basepairs can be presented in an 11-mer or even a 10-mer duplex. The modified nucleotide monomers also behave as dinucleotides when base-paired with two complementary nucleotides from the opposite strand. A new nucleic acid motif is introduced when two (a)U(A) monomers recognize each other in the center of a duplex.
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Affiliation(s)
- Pawan Kumar
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , 5230 Odense M, Denmark
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23
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Kumar P, Sorinas AF, Nielsen LJ, Slot M, Skytte K, Nielsen AS, Jensen MD, Sharma PK, Vester B, Petersen M, Nielsen P. Double-coding nucleic acids: introduction of a nucleobase sequence in the major groove of the DNA duplex using double-headed nucleotides. J Org Chem 2014; 79:8020-30. [PMID: 25089572 DOI: 10.1021/jo501151w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A series of double-headed nucleosides were synthesized using the Sonogashira cross-coupling reaction. In the reactions, additional nucleobases (thymine, cytosine, adenine, or guanine) were attached to the 5-position of 2'-deoxyuridine or 2'-deoxycytidine through a propyne linker. The modified nucleosides were incorporated into oligonucleotides, and these were combined in different duplexes that were analyzed by thermal denaturation studies. All of the monomers were well tolerated in the DNA duplexes and induced only small changes in the thermal stability. Consecutive incorporations of the monomers led to increases in duplex stability owing to increased stacking interactions. The modified nucleotide monomers maintained the Watson-Crick base pair fidelity. Stable duplexes were observed with heavily modified oligonucleotides featuring 14 consecutive incorporations of different double-headed nucleotide monomers. Thus, modified duplexes with an array of nucleobases on the exterior of the duplex were designed. Molecular dynamics simulations demonstrated that the additional nucleobases could expose their Watson-Crick and/or Hoogsteen faces for recognition in the major groove. This presentation of nucleobases may find applications in providing molecular information without unwinding the duplex.
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Affiliation(s)
- Pawan Kumar
- Department of Physics, Chemistry and Pharmacy and ‡Department of Biochemistry and Molecular Biology, Nucleic Acid Center, University of Southern Denmark , 5230 Odense M, Denmark
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24
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Kumar P, Madsen CS, Nielsen P. Synthesis of 2′-O-(thymin-1-yl)methyluridine and its incorporation into secondary nucleic acid structures. Bioorg Med Chem Lett 2014; 23:6847-50. [PMID: 24432386 DOI: 10.1016/j.bmcl.2013.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A double-headed nucleoside wherein an additional thymine is attached to the 2'-O-position of uridine via a methylene linker is prepared and incorporated into oligonucleotides. With single incorporations of the modified nucleotide monomer, these oligonucleotides form duplexes with the complementary DNA sequences which are thermally less stable as compared to the unmodified duplexes. However, stabilization of bulged duplexes or three way junctions is observed. A cross-strand interaction between two additional thymines is also seen in a DNA-duplex, when specifically introduced in a so-called (+1)-zipper motif, however, much weaker than obtained with the corresponding analogue with the methylene linker directly attached to the 2'-C-position. This demonstrates that the ability to act as a compressed dinucleotide is unique for the latter and due to its perfect preorganization of the additional base in the duplex core.
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25
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26
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Kumar P, Sharma PK, Madsen CS, Petersen M, Nielsen P. The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone. Chembiochem 2013; 14:1072-4. [PMID: 23712945 DOI: 10.1002/cbic.201300086] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Indexed: 11/10/2022]
Abstract
Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand.
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Affiliation(s)
- Pawan Kumar
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
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27
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Madsen CS, Nielsen LJ, Pedersen NS, Lauritsen A, Nielsen P. Double-headed nucleotides in DNA-zipper structures; base–base interactions and UV-induced cross-coupling in the minor groove. RSC Adv 2013. [DOI: 10.1039/c3ra40857d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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28
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Lundin KE, Højland T, Hansen BR, Persson R, Bramsen JB, Kjems J, Koch T, Wengel J, Smith CIE. Biological activity and biotechnological aspects of locked nucleic acids. ADVANCES IN GENETICS 2013; 82:47-107. [PMID: 23721720 DOI: 10.1016/b978-0-12-407676-1.00002-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Locked nucleic acid (LNA) is one of the most promising new nucleic acid analogues that has been produced under the past two decades. In this chapter, we have tried to cover many of the different areas, where this molecule has been used to improve the function of synthetic oligonucleotides (ONs). The use of LNA in antisense ONs, including gapmers, splice-switching ONs, and siLNA, as well as antigene ONs, is reviewed. Pharmacokinetics as well as pharmacodynamics of LNA ONs and a description of selected compounds in, or close to, clinical testing are described. In addition, new LNA modifications and the adaptation of enzymes for LNA incorporation are reviewed. Such enzymes may become important for the development of stabilized LNA-containing aptamers.
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Affiliation(s)
- Karin E Lundin
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Novum, Huddinge, Stockholm, Sweden.
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29
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Madsen AS, Jørgensen AS, Jensen TB, Wengel J. Large scale synthesis of 2'-amino-LNA thymine and 5-methylcytosine nucleosides. J Org Chem 2012; 77:10718-28. [PMID: 23145501 DOI: 10.1021/jo302036h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thymine intermediate 17 has been synthesized on a multigram scale (50 g, 70 mmol) from starting sugar 1 in 15 steps in an overall yield of 73%, with only 5 purification steps. The key thymine intermediate 18 was obtained from 17 in a single step in 96% yield, whereas the key 5-methylcytosine intermediate 20 was obtained from 17 in 2 steps in 58% yield. This highly efficient large scale route necessitates only 2 and 3 novel steps to obtain N2'-functionalized thymine and 5-methylcytosine amino-LNA phosphoramidites from these key intermediates, respectively.
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Affiliation(s)
- Andreas Stahl Madsen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
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30
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Kumar P, Shaikh KI, Jørgensen AS, Kumar S, Nielsen P. Three pyrene-modified nucleotides: synthesis and effects in secondary nucleic acid structures. J Org Chem 2012; 77:9562-73. [PMID: 23039223 DOI: 10.1021/jo301571s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Synthesis of three pyrene-modified nucleosides was accomplished using the CuAAC reaction. Hereby, pyrene is attached either to the 5'-position of thymidine or to the 2'-position of 2'-deoxyuridine through triazolemethylene linkers, or to the 2'-position of 2'-deoxyuridine through a more rigid triazole linker. The three nucleosides were incorporated into oligonucleotides, and these were combined in different duplexes and other secondary structures, which were analyzed by thermal stability and fluorescence studies. The three monomers were found to have different impacts on the nucleic acid complexes. Hence, pyrene attached to the 5'-position shows a tendency for intercalation into the duplex as indicated by a general decrease in fluorescence intensity followed by an increase in duplex thermal stability. Pyrene attached to the 2'-position through a rigid triazole linker also shows a tendency for intercalation but with decrease in duplex stability, whereas the pyrene attached to the 2'-position through a triazolemethylene linker is primarily situated in the minor groove as indicated by an increase in fluorescence but here in most cases leading to increase in duplex stability. All three pyrene nucleotides lead to thermal stabilization of bulged duplexes and three-way junctions. In some cases when two pyrenes were introduced into the core of these complexes, the formation or disappearance of a fluorescence excimer band can be used to indicate the hybridization process. Hereby these oligonucleotides can act as specific recognition probes.
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Affiliation(s)
- Pawan Kumar
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
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31
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Madsen CS, Witzke S, Kumar P, Negi K, Sharma PK, Petersen M, Nielsen P. Additional base-pair formation in DNA duplexes by a double-headed nucleotide. Chemistry 2012; 18:7434-42. [PMID: 22532443 DOI: 10.1002/chem.201103467] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 03/13/2012] [Indexed: 11/08/2022]
Abstract
We have designed and synthesised a double-headed nucleotide that presents two nucleobases in the interior of a dsDNA duplex. This nucleotide recognises and forms Watson-Crick base pairs with two complementary adenosines in a Watson-Crick framework. Furthermore, with judicious positioning in complementary strands, the nucleotide recognises itself through the formation of a T:T base pair. Thus, two novel nucleic acid motifs can be defined by using our double-headed nucleotide. Both motifs were characterised by UV melting experiments, CD and NMR spectroscopy and molecular dynamics simulations. Both motifs leave the thermostability of the native dsDNA duplex largely unaltered. Molecular dynamics calculations showed that the double-headed nucleotides are accommodated in the dsDNA by entirely local perturbations and that the modified duplexes retain an overall B-type geometry with the dsDNA unwound by around 25 or 60°, respectively, in each of the modified motifs. Both motifs can be accommodated twice in a dsDNA duplex without incurring any loss of stability and extrapolating from this observation and the results of modelling, it is conceivable that both can be multiplied several times within a dsDNA duplex. These new motifs extend the DNA recognition repertoire and may form the basis for a complete series of double-headed nucleotides based on all 16 base combinations of the four natural nucleobases. In addition, both motifs can be used in the design of nanoscale DNA structures in which a specific duplex twist is required.
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Affiliation(s)
- Charlotte S Madsen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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32
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Enzymatic polymerisation involving 2'-amino-LNA nucleotides. Bioorg Med Chem Lett 2012; 22:3522-6. [PMID: 22503454 DOI: 10.1016/j.bmcl.2012.03.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 03/19/2012] [Accepted: 03/21/2012] [Indexed: 11/21/2022]
Abstract
The triphosphate of the thymine derivative of 2'-amino-LNA (2'-amino-LNA-TTP) was synthesised and found to be a good substrate for Phusion® HF DNA polymerase, allowing enzymatic synthesis of modified DNA encoded by an unmodified template. To complement this, 2'-amino-LNA-T phosphoramidites were incorporated into DNA oligonucleotides which were used as templates for enzymatic synthesis of unmodified DNA using either KOD, KOD XL or Phusion polymerases. 2'-Amino-LNA-T in the template and 2'-amino-LNA-TTP as a substrate both decreased reaction rate and yield compared to unmodified DNA, especially for sequences with multiple 2'-amino-LNA-T nucleotides.
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33
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Nicolaou KC, Ellery SP, Rivas F, Saye K, Rogers E, Workinger TJ, Schallenberger M, Tawatao R, Montero A, Hessell A, Romesberg F, Carson D, Burton D. Synthesis and biological evaluation of 2',4'- and 3',4'-bridged nucleoside analogues. Bioorg Med Chem 2011; 19:5648-69. [PMID: 21840722 PMCID: PMC3348725 DOI: 10.1016/j.bmc.2011.07.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/12/2011] [Accepted: 07/13/2011] [Indexed: 10/18/2022]
Abstract
Most nucleosides in solution typically exist in equilibrium between two major sugar pucker forms, N-type and S-type, but bridged nucleosides can be locked into one of these conformations depending on their specific structure. While many groups have researched these bridged nucleosides for the purpose of determining their binding affinity for antisense applications, we opted to look into the potential for biological activity within these conformationally-locked structures. A small library of 2',4'- and 3',4'-bridged nucleoside analogues was synthesized, including a novel 3',4'-carbocyclic bridged system. The synthesized compounds were tested for antibacterial, antitumor, and antiviral activities, leading to the identification of nucleosides possessing such biological activities. To the best of our knowledge, these biologically active compounds represent the first example of 2',4'-bridged nucleosides to demonstrate such properties. The most potent compound, nucleoside 33, exhibited significant antiviral activity against pseudoviruses SF162 (IC(50)=7.0 μM) and HxB2 (IC(50)=2.4 μM). These findings render bridged nucleosides as credible leads for drug discovery in the anti-HIV area of research.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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34
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Jørgensen AS, Shaikh KI, Enderlin G, Ivarsen E, Kumar S, Nielsen P. The synthesis of double-headed nucleosides by the CuAAC reaction and their effect in secondary nucleic acid structures. Org Biomol Chem 2011; 9:1381-8. [DOI: 10.1039/c0ob00438c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Johannsen MW, Crispino L, Wamberg MC, Kalra N, Wengel J. Amino acids attached to 2'-amino-LNA: synthesis and excellent duplex stability. Org Biomol Chem 2010; 9:243-52. [PMID: 21049102 DOI: 10.1039/c0ob00532k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of 2'-amino-LNA (the 2'-amino derivative of locked nucleic acid) has opened up a number of exciting possibilities with respect to modified nucleic acids. While maintaining the excellent duplex stability inferred by LNA-type oligonucleotides, the nitrogen in the 2'-position of 2'-amino-LNA monomers provides an excellent handle for functionalisation. Herein, the synthesis of amino acid functionalised 2'-amino-LNA derivatives is described. Following ON synthesis, a glycyl unit attached to the N2'-position of 2'-amino-LNA monomers was further acylated with a variety of amino acids. On binding to DNA/RNA complements, the modified ONs induce a marked increase in thermal stability, which is particularly apparent in a buffer system with a low salt concentration. The increase in thermal stability is thought to be caused, at least in part, by decreased electrostatic repulsion between the negatively charged phosphate backbones when positively charged amino acid residues are appended. Upon incorporation of more than one 2'-amino-LNA modification, the effects are found to be nearly additive. For comparison, 2'-amino-LNA derivatives modified with uncharged groups have been synthesised and their effect on duplex thermal stability likewise investigated.
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Affiliation(s)
- Marie W Johannsen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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36
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Shaikh KI, Madsen CS, Nielsen LJ, Jørgensen AS, Nielsen H, Petersen M, Nielsen P. Synthesis and Molecular Modelling of Double-Functionalised Nucleosides with Aromatic Moieties in the 5′-(S)-Position and Minor Groove Interactions in DNA Zipper Structures. Chemistry 2010; 16:12904-19. [DOI: 10.1002/chem.201001253] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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