1
|
Basu S, Roy SK, Barcenas G, Li L, Yurke B, Knowlton WB, Lee J. Enhanced Photo-Cross-Linking of Thymines in DNA Holliday Junction-Templated Squaraine Dimers. Biochemistry 2023; 62:3234-3244. [PMID: 37906841 DOI: 10.1021/acs.biochem.3c00471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Programmable self-assembly of dyes using DNA templates to promote exciton delocalization in dye aggregates is gaining considerable interest. New methods to improve the rigidity of the DNA scaffold and thus the stability of the molecular dye aggregates to encourage exciton delocalization are desired. In these dye-DNA constructs, one potential way to increase the stability of the aggregates is to create an additional covalent bond via photo-cross-linking reactions between thymines in the DNA scaffold. Specifically, we report an approach to increase the yield of photo-cross-linking reaction between thymines in the core of a DNA Holliday junction while limiting the damage from UV irradiation to DNA. We investigated the effect of the distance between thymines on the photo-cross-linking reaction yields by using linkers with different lengths to tether the dyes to the DNA templates. By comprehensively evaluating the photo-cross-linking reaction yields of dye-DNA aggregates using linkers with different lengths, we conclude that interstrand thymines tend to photo-cross-link more efficiently with short linkers. A higher cross-linking yield was achieved due to the shorter intermolecular distance between thymines influenced by strong dye-dye interactions. Our method establishes the possibility of improving the stability of DNA-scaffolded dye aggregates, thereby expanding their use in exciton-based applications such as light harvesting, nanoscale computing, quantum computing, and optoelectronics.
Collapse
Affiliation(s)
- Shibani Basu
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Simon K Roy
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - German Barcenas
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| |
Collapse
|
2
|
|
3
|
Yamayoshi A, Matsuyama Y, Kushida M, Kobori A, Murakami A. Novel photodynamic effect of a psoralen-conjugated oligonucleotide for the discrimination of the methylation of cytosine in DNA. Photochem Photobiol 2014; 90:716-22. [PMID: 24372306 DOI: 10.1111/php.12232] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/17/2013] [Indexed: 12/11/2022]
Abstract
DNA methylation and demethylation significantly affect the deactivation and activation processes of gene expression significantly. In particular, C-5-methylation of cytosine in the CpG islands is important for the epigenetic modification in genes, which plays a key role in regulating gene expression. The determination of the location and frequency of DNA methylation is important for the elucidation of the mechanisms of cell differentiation and carcinogenesis. Here we designed a psoralen-conjugated oligonucleotide (PS-oligo) for the discrimination of 5-methylcytosine (5-mC) in DNA. The cross-linking behavior of psoralen derivatives with pyrimidine bases, such as thymine, uracil and cytosine has been well discussed, but there are no reports which have examined whether cross-linking efficiency of psoralen with cytosine would be changed with or without C-5 methylation. We found that the cross-linking efficiency of PS-oligo with target-DNA containing 5-mC was greatly increased compared to the case of target-DNA without 5-mC, approximately seven-fold higher. Here we report a new aspect of the photocross-linking behavior of psoralen with 5-mC that is applicable to a simple, sequence-specific and quantitative analysis for the discrimination of 5-mC in DNA, which can be applicable to study the epigenetic behavior of gene expressions.
Collapse
Affiliation(s)
- Asako Yamayoshi
- Department of Biomolecular Engineering, Kyoto Institute of Technology, Matsugasaki, Sakuo-ku, Kyoto, Japan
| | | | | | | | | |
Collapse
|
4
|
Fujimo K, Konishi-Hiratsuka K, Sakamoto T. Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand. Int J Mol Sci 2013; 14:5765-74. [PMID: 23481638 PMCID: PMC3634424 DOI: 10.3390/ijms14035765] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/12/2013] [Accepted: 02/26/2013] [Indexed: 02/02/2023] Open
Abstract
Selective photocrosslinking reaction between 3-cyanovinylcarbazole nucleoside (CNVK) and 5-methylcytosine (mC), which is known as epigenetic modification in genomic DNA, was developed. The reaction was completely finished within 5 s of 366 nm irradiation, and the rate of this photocrosslinking reaction was ca. 30-fold higher than that in the case of unmodified normal cytosine. There were no significant differences in the thermodynamic parameters and the kinetics of hybrid formation of oligonucleotide (ODN) containing CNVK and its complementary ODN containing C or mC at the photocrosslinking site, and suggesting that the quick and selective photoreaction has potential for the selective detection of mC in the DNA strand via the photocrosslinking reaction.
Collapse
Affiliation(s)
- Kenzo Fujimo
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan; E-Mails: (K.K.-H.); (T.S.)
- Research Center for Bio-Architecture, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
- Author to whom correspondence should be addressed; E-Mail: ; Tel./Fax: +81-761-51-1671
| | - Kaoru Konishi-Hiratsuka
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan; E-Mails: (K.K.-H.); (T.S.)
| | - Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan; E-Mails: (K.K.-H.); (T.S.)
| |
Collapse
|