Abstract
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.
Highlights
Nucleic acids are known to have a considerable regulatory or functional role at different stages of the majority of the cellular processes
We have focused on documenting the possible intricate details of the dynamic conformers of four different secondary structures of DNA, viz., the DNA hairpin, Holliday junction, G-quadruplex, and i-motifs collocated by employing single-molecule Forster’s resonance energy transfer (sm-FRET) as the preeminent tool
We have presented a summary of the conformational dynamics of the important DNA secondary structures extracted at the molecular level by sm-FRET
Summary
Nucleic acids are known to have a considerable regulatory or functional role at different stages of the majority of the cellular processes. The catalytic branch migration process through the ring of helicases has been precisely explored using sm-FRET studies, and it has been observed that instead of facilitating the melting of DNA base pairs by pulling the DNA through the central core, the helicase freezes the junction dynamics by arresting it at open-X conformation. Upon the binding of telomerase with the substrate irrespective of the process of catalytic activity, a partial unfolding of the G-quartet structure occurs through hybridization of the RNA unit of the telomerase with the telomeric DNA and that has been witnessed via a singlestep drop in the FRET efficiency state when the labeled telomeric DNA is exposed to a high concentration of template RNA. After complete unwinding, there occurs release of BLM from the single-stranded DNA (ssDNA) and immediate refolding of the ssDNA into GQ (Wu et al, 2015)
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