Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy
In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and inte...
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Frontiers Media S.A.
2021-09-01
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2021.725541/full |
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| author | Debolina Bandyopadhyay Debolina Bandyopadhyay Padmaja P. Mishra Padmaja P. Mishra |
| author_facet | Debolina Bandyopadhyay Debolina Bandyopadhyay Padmaja P. Mishra Padmaja P. Mishra |
| author_sort | Debolina Bandyopadhyay |
| collection | DOAJ |
| description | In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster’s resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif. |
| first_indexed | 2024-12-17T23:25:01Z |
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| last_indexed | 2024-12-17T23:25:01Z |
| publishDate | 2021-09-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-2aadcb09fa0d4b7ea9dc06c5a708ac102022-12-21T21:28:47ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2021-09-01810.3389/fmolb.2021.725541725541Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET MicrospectroscopyDebolina Bandyopadhyay0Debolina Bandyopadhyay1Padmaja P. Mishra2Padmaja P. Mishra3Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, IndiaHBNI, Mumbai, IndiaSingle-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, IndiaHBNI, Mumbai, IndiaIn addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster’s resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.https://www.frontiersin.org/articles/10.3389/fmolb.2021.725541/fullsm-FRET spectroscopyDNA secondary structureDNA hairpinG-quadruplexHolliday junctionsi-motif |
| spellingShingle | Debolina Bandyopadhyay Debolina Bandyopadhyay Padmaja P. Mishra Padmaja P. Mishra Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy Frontiers in Molecular Biosciences sm-FRET spectroscopy DNA secondary structure DNA hairpin G-quadruplex Holliday junctions i-motif |
| title | Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy |
| title_full | Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy |
| title_fullStr | Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy |
| title_full_unstemmed | Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy |
| title_short | Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy |
| title_sort | decoding the structural dynamics and conformational alternations of dna secondary structures by single molecule fret microspectroscopy |
| topic | sm-FRET spectroscopy DNA secondary structure DNA hairpin G-quadruplex Holliday junctions i-motif |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2021.725541/full |
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