Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional Structures
Topological variants of single-strand DNA (ssDNA) structures, referred to as “functional DNA,” have been detected in regulatory regions of many genes and are thought to affect gene expression. Two fluorescent analog...
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| Format: | Article |
| Language: | English |
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Wiley
2011-01-01
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| Series: | Journal of Nucleic Acids |
| Online Access: | http://dx.doi.org/10.4061/2011/986820 |
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| _version_ | 1832560432873734144 |
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| author | Yogini P. Bhavsar Samantha M. Reilly Randy M. Wadkins |
| author_facet | Yogini P. Bhavsar Samantha M. Reilly Randy M. Wadkins |
| author_sort | Yogini P. Bhavsar |
| collection | DOAJ |
| description | Topological variants of single-strand DNA
(ssDNA) structures, referred to as
“functional DNA,” have been detected
in regulatory regions of many genes and are
thought to affect gene expression. Two fluorescent
analogs of deoxycytidine, Pyrrolo-dC (PdC) and
1,3-diaza-2-oxophenoxazine (tC∘), can be incorporated into DNA.
Here, we describe spectroscopic studies of both
analogs to determine fluorescent properties
that report on structural transitions from
double-strand DNA (dsDNA) to ssDNA, a common
pathway in the transition to functional DNA
structures. We obtained fluorescence-detected
circular dichroism (FDCD) spectra,
steady-state fluorescence spectra, and
fluorescence lifetimes of the fluorophores in
DNA. Our results show that PdC is
advantageous in fluorescence lifetime studies
because of a distinct ~2 ns change between paired
and unpaired bases. However, tC∘ is a better probe for FDCD
experiments that report on the helical
structure of DNA surrounding the fluorophore.
Both fluorophores provide complementary data
to measure DNA structural transitions. |
| format | Article |
| id | doaj-art-1aca5d73bc8e469595facfbc5d011dbd |
| institution | Kabale University |
| issn | 2090-021X |
| language | English |
| publishDate | 2011-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Nucleic Acids |
| spelling | doaj-art-1aca5d73bc8e469595facfbc5d011dbd2025-02-03T01:27:35ZengWileyJournal of Nucleic Acids2090-021X2011-01-01201110.4061/2011/986820986820Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional StructuresYogini P. Bhavsar0Samantha M. Reilly1Randy M. Wadkins2Department of Chemistry and Biochemistry, The University of Mississippi, Coulter Hall, Room 409, MS 38677, USADepartment of Chemistry and Biochemistry, The University of Mississippi, Coulter Hall, Room 409, MS 38677, USADepartment of Chemistry and Biochemistry, The University of Mississippi, Coulter Hall, Room 409, MS 38677, USATopological variants of single-strand DNA (ssDNA) structures, referred to as “functional DNA,” have been detected in regulatory regions of many genes and are thought to affect gene expression. Two fluorescent analogs of deoxycytidine, Pyrrolo-dC (PdC) and 1,3-diaza-2-oxophenoxazine (tC∘), can be incorporated into DNA. Here, we describe spectroscopic studies of both analogs to determine fluorescent properties that report on structural transitions from double-strand DNA (dsDNA) to ssDNA, a common pathway in the transition to functional DNA structures. We obtained fluorescence-detected circular dichroism (FDCD) spectra, steady-state fluorescence spectra, and fluorescence lifetimes of the fluorophores in DNA. Our results show that PdC is advantageous in fluorescence lifetime studies because of a distinct ~2 ns change between paired and unpaired bases. However, tC∘ is a better probe for FDCD experiments that report on the helical structure of DNA surrounding the fluorophore. Both fluorophores provide complementary data to measure DNA structural transitions.http://dx.doi.org/10.4061/2011/986820 |
| spellingShingle | Yogini P. Bhavsar Samantha M. Reilly Randy M. Wadkins Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional Structures Journal of Nucleic Acids |
| title | Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional Structures |
| title_full | Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional Structures |
| title_fullStr | Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional Structures |
| title_full_unstemmed | Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional Structures |
| title_short | Evaluation of Fluorescent Analogs of Deoxycytidine for Monitoring DNA Transitions from Duplex to Functional Structures |
| title_sort | evaluation of fluorescent analogs of deoxycytidine for monitoring dna transitions from duplex to functional structures |
| url | http://dx.doi.org/10.4061/2011/986820 |
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