1
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Beck KM, Nielsen P. Double-Headed 2'-Deoxynucleotides That Hybridize to DNA and RNA Targets via Normal and Reverse Watson-Crick Base Pairs. J Org Chem 2022; 87:5113-5124. [PMID: 35363467 DOI: 10.1021/acs.joc.1c03063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Through the use of modified nucleotides, synthetic nucleic acids have found several fields of application within biotechnology and in the pharmaceutical industry. We have previously introduced nucleotides with an additional functional nucleobase linked to C2' of arabinonucleotides (BX). These double-headed nucleotides fit neatly into DNA·DNA duplexes, where they can replace the corresponding natural dinucleotides and thus condense the molecular information. Here, we introduce a 2'-deoxy version of the BX design with inversion of the C2' stereochemistry (dSBX) with the aim of obtaining improved RNA recognition. Specifically, dSBX analogues with cytosine or isocytosine attached to C2' of 2'-deoxyuridine (dSUC and dSUiC) were synthesized and evaluated in duplexes. Whereas the dSBX design did not outperform the BX design in terms of mimicking dinucleotides in nucleic acid duplexes, it was able to engage in reverse Watson-Crick pairing using its 2'-base. This was evident from the ability of the dSUC cytosine to form stable mis-matching base pairs with opposite cytosines identified as hemiprotonated C·C+ pairs. Furthermore, specific base-pairing with guanine was only observed for the isocytosine-bearing dSUiC monomer. Very stable duplexes were obtained with dSUC/iC monomers in each strand indicating that fully modified double-headed nucleic acid sequences could be based on the dSBX design.
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Affiliation(s)
- Kasper M Beck
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Poul Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
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2
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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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3
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Beck KM, Sharma PK, Hornum M, Risgaard NA, Nielsen P. Double-headed nucleic acids condense the molecular information of DNA to half the number of nucleotides. Chem Commun (Camb) 2021; 57:9128-9131. [PMID: 34498649 DOI: 10.1039/d1cc03539h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nucleotide monomers that hold two nucleobases each, i.e. double-headed nucleotides, have been shown to form two sets of functional Watson-Crick base pairs when incorporated into dsDNA, and they hereby behave as dinucleotides. To form the basis for fully modified double-headed nucleic acids (DhNA), we have prepared three new DhNA monomers and can now demonstrate that the molecular information of 10 Watson-Crick base pairs can be condensed to highly stable 5-mer DhNA duplexes.
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Affiliation(s)
- Kasper M Beck
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense DK-5230, Denmark.
| | - Pawan K Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra, 136119, India
| | - Mick Hornum
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense DK-5230, Denmark.
| | - Nikolaj A Risgaard
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense DK-5230, Denmark.
| | - Poul Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense DK-5230, Denmark.
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4
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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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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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6
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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Beck KM, Krogh MB, Hornum M, Ludford PT, Tor Y, Nielsen P. Double-headed nucleotides as xeno nucleic acids: information storage and polymerase recognition. Org Biomol Chem 2020; 18:7213-7223. [PMID: 32909574 PMCID: PMC7517788 DOI: 10.1039/d0ob01426e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Xeno nucleic acids (XNAs) are artificial genetic systems based on sugar-modified nucleotides. Herein, we investigate double-headed nucleotides as a new XNA. A new monomer, AT, is presented, and together with previous double-headed nucleotide monomers, new nucleic acid motifs consisting of up to five consecutive A·T base pairs have been obtained. Sections composed entirely of double-headed nucleotides are well-tolerated within a DNA duplex and can condense the genetic information. For instance, a 13-mer duplex is condensed to an 11-mer modified duplex containing four double-headed nucleotides while simultaneously improving duplex thermal stability with +14.0 °C. Also, the transfer of information from double-headed to natural nucleotides by DNA polymerases has been examined. The first double-headed nucleoside triphosphate was prepared but could not be recognized and incorporated by the tested DNA polymerases. On the other hand, it proved possible for Therminator DNA polymerase to transfer the information of a double-headed nucleotide in a template sequence to natural DNA under controlled conditions.
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Affiliation(s)
- Kasper M Beck
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
| | - Marie B Krogh
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
| | - Mick Hornum
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
| | - Paul T Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Poul Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
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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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