1
|
Nishizawa S, Tu G, Ogata D, Miyauchi K, Ohkubo A. Development of antiparallel-type triplex-forming oligonucleotides containing quinoline derivatives capable of recognizing a T–A base pair in a DNA duplex. Bioorg Med Chem 2022; 71:116934. [DOI: 10.1016/j.bmc.2022.116934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/02/2022]
|
2
|
Ohkubo A, Ohnishi T, Nishizawa S, Nishimura Y, Hisamatsu S. The ability of a triplex-forming oligonucleotide to recognize T-A and C-G base pairs in a DNA duplex is enhanced by incorporating N-acetyl-2,7-diaminoquinoline. Bioorg Med Chem 2020; 28:115350. [PMID: 32115336 DOI: 10.1016/j.bmc.2020.115350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/16/2020] [Accepted: 01/21/2020] [Indexed: 12/21/2022]
Abstract
A triplex-forming oligonucleotide (TFO) can recognize the homopurine-homopyrimidine sequence in DNA duplexes and inhibit the transcription of targeted mRNAs. Recently, we reported that N-acetyl-2,7-diamino-1,8-naphthyridine (DANac), incorporated into a TFO, has high binding ability and base recognition selectivity for the pyrimidine bases in the purine-rich chain of the DNA duplex at pH 7.4. However, it was found in this study that the difference in the Tm values between the pyrimidine bases and purine bases decreased by more than 4 °C at pH 6.0-7.0. To improve the low base recognition selectivity of the TFO, we designed a new artificial base, DAQac, with a quinoline skeleton. The Tm values of the triplexes containing DAQac:T-A or DAQac:C-G were more than 13 °C higher than those of the triplexes containing DAQac:A-T or DAQac:G-C at pH 7.4. We also observed that under more acidic conditions (pH 6.0-7.0), the base recognition selectivity of DAQac in a triplex was higher than that of DANac, although the binding ability of DAQac in a triplex was similar to that of DANac. Additionally, we found that DAQac, incorporated into the TFO, could accurately recognize the MeC-G base pair in the hairpin DNA, similar to the C-G base pair.
Collapse
Affiliation(s)
- Akihiro Ohkubo
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
| | - Tatsuya Ohnishi
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Shuhei Nishizawa
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Yuri Nishimura
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Shugo Hisamatsu
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| |
Collapse
|
3
|
Nakamura S, Kawabata H, Fujimoto K. Double duplex invasion of DNA induced by ultrafast photo-cross-linking using 3-cyanovinylcarbazole for antigene methods. Chem Commun (Camb) 2017. [DOI: 10.1039/c7cc01746d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
New photoresponsive antigene probes containingCNVK andCNU have a high double-duplex invasion capability upon photoirradiation because of the inhibition of photo-cross-linking between the probes.
Collapse
Affiliation(s)
- Shigetaka Nakamura
- Department of Advanced Science and Technology
- Japan Advanced Institute Science and Technology
- Nomi
- Japan
| | - Hayato Kawabata
- Department of Advanced Science and Technology
- Japan Advanced Institute Science and Technology
- Nomi
- Japan
| | - Kenzo Fujimoto
- Department of Advanced Science and Technology
- Japan Advanced Institute Science and Technology
- Nomi
- Japan
| |
Collapse
|
4
|
Hu Y, Lin F, Wu T, Wang Y, Zhou XS, Shao Y. Fluorescently Sensing of DNA Triplex Assembly Using an Isoquinoline Alkaloid as Selector, Stabilizer, Inducer, and Switch-On Emitter. Chem Asian J 2016; 11:2041-8. [DOI: 10.1002/asia.201600459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Yuehua Hu
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Fan Lin
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Tao Wu
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Ying Wang
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Xiao-Shun Zhou
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Yong Shao
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| |
Collapse
|
5
|
Goldsmith G, Rathinavelan T, Yathindra N. Selective Preference of Parallel DNA Triplexes Is Due to the Disruption of Hoogsteen Hydrogen Bonds Caused by the Severe Nonisostericity between the G*GC and T*AT Triplets. PLoS One 2016; 11:e0152102. [PMID: 27010368 PMCID: PMC4807104 DOI: 10.1371/journal.pone.0152102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/08/2016] [Indexed: 12/14/2022] Open
Abstract
Implications of DNA, RNA and RNA.DNA hybrid triplexes in diverse biological functions, diseases and therapeutic applications call for a thorough understanding of their structure-function relationships. Despite exhaustive studies mechanistic rationale for the discriminatory preference of parallel DNA triplexes with G*GC & T*AT triplets still remains elusive. Here, we show that the highest nonisostericity between the G*GC & T*AT triplets imposes extensive stereochemical rearrangements contributing to context dependent triplex destabilisation through selective disruption of Hoogsteen scheme of hydrogen bonds. MD simulations of nineteen DNA triplexes with an assortment of sequence milieu reveal for the first time fresh insights into the nature and extent of destabilization from a single (non-overlapping), double (overlapping) and multiple pairs of nonisosteric base triplets (NIBTs). It is found that a solitary pair of NIBTs, feasible either at a G*GC/T*AT or T*AT/G*GC triplex junction, does not impinge significantly on triplex stability. But two overlapping pairs of NIBTs resulting from either a T*AT or a G*GC interruption disrupt Hoogsteen pair to a noncanonical mismatch destabilizing the triplex by ~10 to 14 kcal/mol, implying that their frequent incidence in multiples, especially, in short sequences could even hinder triplex formation. The results provide (i) an unambiguous and generalised mechanistic rationale for the discriminatory trait of parallel triplexes, including those studied experimentally (ii) clarity for the prevalence of antiparallel triplexes and (iii) comprehensive perspectives on the sequence dependent influence of nonisosteric base triplets useful in the rational design of TFO's against potential triplex target sites.
Collapse
Affiliation(s)
- Gunaseelan Goldsmith
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, India
- Manipal University, Manipal, India
| | | | - Narayanarao Yathindra
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, India
| |
Collapse
|
6
|
Wang Y, Hu Y, Wu T, Zhou X, Shao Y. Triggered Excited-State Intramolecular Proton Transfer Fluorescence for Selective Triplex DNA Recognition. Anal Chem 2015; 87:11620-4. [DOI: 10.1021/acs.analchem.5b02851] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ying Wang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Yuehua Hu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Tao Wu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Xiaoshun Zhou
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Yong Shao
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| |
Collapse
|
7
|
Ohkubo A, Yamada K, Ito Y, Yoshimura K, Miyauchi K, Kanamori T, Masaki Y, Seio K, Yuasa H, Sekine M. Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs. Nucleic Acids Res 2015; 43:5675-86. [PMID: 26013815 PMCID: PMC4499124 DOI: 10.1093/nar/gkv496] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/03/2015] [Indexed: 11/28/2022] Open
Abstract
A triplex-forming oligonucleotide (TFO) could be a useful molecular tool for gene therapy and specific gene modification. However, unmodified TFOs have two serious drawbacks: low binding affinities and high sequence-dependencies. In this paper, we propose a new strategy that uses a new set of modified nucleobases for four-base recognition of TFOs, and thereby overcome these two drawbacks. TFOs containing a 2’-deoxy-4N-(2-guanidoethyl)-5-methylcytidine (dgC) residue for a C-G base pair have higher binding and base recognition abilities than those containing 2’-OMe-4N-(2-guanidoethyl)-5-methylcytidine (2’-OMegC), 2’-OMe-4N-(2-guanidoethyl)-5-methyl-2-thiocytidine (2’-OMegCs), dgC and 4S-(2-guanidoethyl)-4-thiothymidine (gsT). Further, we observed that N-acetyl-2,7-diamino-1,8-naphtyridine (DANac) has a higher binding and base recognition abilities for a T-A base pair compared with that of dG and the other DNA derivatives. On the basis of this knowledge, we successfully synthesized a fully modified TFO containing DANac, dgC, 2’-OMe-2-thiothymidine (2’-OMesT) and 2’-OMe-8-thioxoadenosine (2’-OMesA) with high binding and base recognition abilities. To the best of our knowledge, this is the first report in which a fully modified TFO accurately recognizes a complementary DNA duplex having a mixed sequence under neutral conditions.
Collapse
Affiliation(s)
- Akihiro Ohkubo
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Kenji Yamada
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Yu Ito
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Kiichi Yoshimura
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Koichiro Miyauchi
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Hideya Yuasa
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| |
Collapse
|