Development of Single-Molecule Electrical Identification Method for Cyclic Adenosine Monophosphate Signaling Pathway
Cyclic adenosine monophosphate (cAMP) is an important research target because it activates protein kinases, and its signaling pathway regulates the passage of ions and molecules inside a cell. To detect the chemical reactions related to the cAMP intracellular signaling pathway, cAMP, adenosine triph...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-03-01
|
| Series: | Nanomaterials |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2079-4991/11/3/784 |
| _version_ | 1797540799437602816 |
|---|---|
| author | Yuki Komoto Takahito Ohshiro Masateru Taniguchi |
| author_facet | Yuki Komoto Takahito Ohshiro Masateru Taniguchi |
| author_sort | Yuki Komoto |
| collection | DOAJ |
| description | Cyclic adenosine monophosphate (cAMP) is an important research target because it activates protein kinases, and its signaling pathway regulates the passage of ions and molecules inside a cell. To detect the chemical reactions related to the cAMP intracellular signaling pathway, cAMP, adenosine triphosphate (ATP), adenosine monophosphate (AMP), and adenosine diphosphate (ADP) should be selectively detected. This study utilized single-molecule quantum measurements of these adenosine family molecules to detect their individual electrical conductance using nanogap devices. As a result, cAMP was electrically detected at the single molecular level, and its signal was successfully discriminated from those of ATP, AMP, and ADP using the developed machine learning method. The discrimination accuracies of a single cAMP signal from AMP, ADP, and ATP were found to be 0.82, 0.70, and 0.72, respectively. These values indicated a 99.9% accuracy when detecting more than ten signals. Based on an analysis of the feature values used for the machine learning analysis, it is suggested that this discrimination was due to the structural difference between the ribose of the phosphate site of cAMP and those of ATP, ADP, and AMP. This method will be of assistance in detecting and understanding the intercellular signaling pathways for small molecular second messengers. |
| first_indexed | 2024-03-10T13:06:07Z |
| format | Article |
| id | doaj.art-b8b3c569ee0b4ef79173f52696f70de8 |
| institution | Directory Open Access Journal |
| issn | 2079-4991 |
| language | English |
| last_indexed | 2024-03-10T13:06:07Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Nanomaterials |
| spelling | doaj.art-b8b3c569ee0b4ef79173f52696f70de82023-11-21T11:08:19ZengMDPI AGNanomaterials2079-49912021-03-0111378410.3390/nano11030784Development of Single-Molecule Electrical Identification Method for Cyclic Adenosine Monophosphate Signaling PathwayYuki Komoto0Takahito Ohshiro1Masateru Taniguchi2Institute of Science and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, JapanInstitute of Science and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, JapanInstitute of Science and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, JapanCyclic adenosine monophosphate (cAMP) is an important research target because it activates protein kinases, and its signaling pathway regulates the passage of ions and molecules inside a cell. To detect the chemical reactions related to the cAMP intracellular signaling pathway, cAMP, adenosine triphosphate (ATP), adenosine monophosphate (AMP), and adenosine diphosphate (ADP) should be selectively detected. This study utilized single-molecule quantum measurements of these adenosine family molecules to detect their individual electrical conductance using nanogap devices. As a result, cAMP was electrically detected at the single molecular level, and its signal was successfully discriminated from those of ATP, AMP, and ADP using the developed machine learning method. The discrimination accuracies of a single cAMP signal from AMP, ADP, and ATP were found to be 0.82, 0.70, and 0.72, respectively. These values indicated a 99.9% accuracy when detecting more than ten signals. Based on an analysis of the feature values used for the machine learning analysis, it is suggested that this discrimination was due to the structural difference between the ribose of the phosphate site of cAMP and those of ATP, ADP, and AMP. This method will be of assistance in detecting and understanding the intercellular signaling pathways for small molecular second messengers.https://www.mdpi.com/2079-4991/11/3/784DNAcyclic AMPsingle-molecule detectionnanogapsecond messenger |
| spellingShingle | Yuki Komoto Takahito Ohshiro Masateru Taniguchi Development of Single-Molecule Electrical Identification Method for Cyclic Adenosine Monophosphate Signaling Pathway Nanomaterials DNA cyclic AMP single-molecule detection nanogap second messenger |
| title | Development of Single-Molecule Electrical Identification Method for Cyclic Adenosine Monophosphate Signaling Pathway |
| title_full | Development of Single-Molecule Electrical Identification Method for Cyclic Adenosine Monophosphate Signaling Pathway |
| title_fullStr | Development of Single-Molecule Electrical Identification Method for Cyclic Adenosine Monophosphate Signaling Pathway |
| title_full_unstemmed | Development of Single-Molecule Electrical Identification Method for Cyclic Adenosine Monophosphate Signaling Pathway |
| title_short | Development of Single-Molecule Electrical Identification Method for Cyclic Adenosine Monophosphate Signaling Pathway |
| title_sort | development of single molecule electrical identification method for cyclic adenosine monophosphate signaling pathway |
| topic | DNA cyclic AMP single-molecule detection nanogap second messenger |
| url | https://www.mdpi.com/2079-4991/11/3/784 |
| work_keys_str_mv | AT yukikomoto developmentofsinglemoleculeelectricalidentificationmethodforcyclicadenosinemonophosphatesignalingpathway AT takahitoohshiro developmentofsinglemoleculeelectricalidentificationmethodforcyclicadenosinemonophosphatesignalingpathway AT masaterutaniguchi developmentofsinglemoleculeelectricalidentificationmethodforcyclicadenosinemonophosphatesignalingpathway |