Revealing the DNA Unwinding Activity and Mechanism of Fork Reversal by RecG While Exposed to Variants of Stalled Replication-fork at Single-Molecular Resolution.

RecG, belonging to the category of Superfamily-2 plays a vital role in rescuing different kinds of stalled fork. The elemental mechanism of the helicase activity of RecG with several non-homologous stalled fork structures resembling intermediates formed during the process of DNA repair has been investigated in the present study to capture the dynamic stages of genetic rearrangement. The functional characterization has been exemplified through quantifying the response of the substrate in terms of their molecular heterogeneity and dynamical response by employing single-molecule fluorescence methods.

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 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.

Vital insights into prokaryotic genome compaction by nucleoid-associated protein (NAP) and illustration of DNA flexure angles at single-molecule resolution.

Integration Host Factor (IHF) is a heterodimeric site-specific nucleoid-associated protein (NAP), well known for its DNA bending ability. Although the IHF induced bending states of DNA have been captured by both X-ray Crystallography and Atomic Force Microscopy (AFM), the range of flexibility and degree of heterogeneity in terms of quantitative analysis of the nucleoprotein complex has largely remained unexplored. Binding of IHF leads to introduction of two kinks in the dsDNA that allowed us to come up with a quadrilateral model.

Real-Time Monitoring of the Multistate Conformational Dynamics of Polypurine Reverse Hoogsteen Hairpin To Capture Their Triplex-Affinity for Gene Silencing by smFRET Microspectroscopy.

Single-molecule Förster resonance energy transfer microspectroscopic methods are employed for real-time monitoring and to gain deeper insights into the formation of the polypurine reverse Hoogsteen hairpin (PPRH) and its triplex-forming activity. The heterogeneity in the behavior of individual PPRHs has been documented, and it is seen that the degree of anharmonic plasticity of the antiparallel hairpin is stabilized by the formation of reverse Hoogsteen (RH) bonds. While being involved in the hairpin formation, they flip reversibly between the open and closed conformations, irrespective of the concentration of ions present in their microenvironment.