1
|
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.
Collapse
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
| |
Collapse
|
2
|
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
| |
Collapse
|
3
|
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
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
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.
Collapse
Affiliation(s)
- Mick Hornum
- Nucleic Acid Center, Department of Physics, Chemistry & Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
| | | | | | | | | | | |
Collapse
|
6
|
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.
Collapse
|
7
|
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.
Collapse
|
8
|
Hornum M, Djukina A, Sassnau AK, Nielsen P. Synthesis of new C-5-triazolyl-functionalized thymidine analogs and their ability to engage in aromatic stacking in DNA : DNA and DNA : RNA duplexes. Org Biomol Chem 2016; 14:4436-47. [DOI: 10.1039/c6ob00609d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Stacking interactions of substituted triazoles in the major groove were studied, and with a polar uracil, increased duplex stabilities were found.
Collapse
Affiliation(s)
- Mick Hornum
- Nucleic Acid Center
- Department of Physics
- Chemistry & Pharmacy
- University of Southern Denmark
- DK-5230 Odense
| | - Alevtina Djukina
- Nucleic Acid Center
- Department of Physics
- Chemistry & Pharmacy
- University of Southern Denmark
- DK-5230 Odense
| | - Ann-Katrin Sassnau
- Nucleic Acid Center
- Department of Physics
- Chemistry & Pharmacy
- University of Southern Denmark
- DK-5230 Odense
| | - Poul Nielsen
- Nucleic Acid Center
- Department of Physics
- Chemistry & Pharmacy
- University of Southern Denmark
- DK-5230 Odense
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|