Hexapeptides That Inhibit Processing of Branched DNA Structures Induce a Dynamic Ensemble of Holliday Junction Conformations

Cannon, Brian; Kachroo, Aashiq H.; Jarmoskaite, Inga; Jayaram, Makkuni; Russell, Rick

doi:10.1074/jbc.m115.663930

Cited by 6 publications

(9 citation statements)

References 49 publications

(80 reference statements)

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“…FRET histograms were generated from multiple fields of view and were best fit by a single-peak, Gaussian distribution using Levenberg–Marquardt optimization. The heat maps were generated from the standard deviations and mean FRET values calculated from each trace for hundreds of individual molecules as previously described …”

Section: Methodsmentioning

confidence: 99%

Differential Effects of Strand Asymmetry on the Energetics and Structural Flexibility of DNA Internal Loops

Tran

Cannon

2017

Biochemistry

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Internal loops within structured nucleic acids disrupt local base stacking and destabilize neighboring helical domains; however, these structural motifs also expand the conformational and functional capabilities of structured nucleic acids. Variations in the size, distribution of loop nucleotides on opposing strands (strand asymmetry), and sequence alter their biophysical properties. Here, the thermodynamics and structural flexibility of oligo-T-rich DNA internal loops were systematically investigated in terms of loop size and strand asymmetry. From optical melting experiments, a thermodynamic prediction model is proposed for the energetic penalty of internal loops that accounts for diminishing enthalpic and increasing entropic contributions due to loop size and strand asymmetry for bulges, asymmetric loops, and symmetric loops. These single-stranded domains become less sequence-dependent and more polymeric as the loop size increases. Single-molecule fluorescence resonance energy transfer studies reveal a gradual transition in conformation and structural flexibility from an elongated domain to an increasingly flexible bend that results from increasing strand asymmetry. The findings provide a framework for understanding the thermodynamic and conformational effects of internal loops for the rational design of functional DNA nanostructures.

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Section: Methodsmentioning

confidence: 99%

Differential Effects of Strand Asymmetry on the Energetics and Structural Flexibility of DNA Internal Loops

Tran

Cannon

2017

Biochemistry

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“…Mg 2+ stabilizes DNA 3WJ conformers but can permit structural rearrangements that switch the helical stacking partners. Interestingly, the observed interconversion rates for J11 are comparable to the transition rates observed in 4WJs that involve the exchange of stacking partners under similar Mg 2+ concentrations [39,42,52]. The presence of the bulge domain likely increases the flexibility at the junction, and these unpaired nucleotides participate in stacking interactions within the core that specify the preferred stacked conformers.…”

Section: J11 Exhibits Dynamic Transitions Between A/b and A/c Conformersmentioning

confidence: 53%

“…Experimental observations suggest that 3WJs predominantly favor a single conformer, although structural and electrophoretic studies of bulged 3WJs have proposed that some 3WJ sequences may fold into both conformers [29,36,37]. This folding behavior of DNA 3WJs would seemingly contrast with the behavior of DNA four-way junctions (4WJs), which can be mobile and readily undergo structural transitions between different coaxial stacking arrangements of its four helical domains [38][39][40][41][42].…”

Section: Introductionmentioning

confidence: 99%

Detection of Mg2+-dependent, coaxial stacking rearrangements in a bulged three-way DNA junction by single-molecule FRET

Leveille

Tran

Dingillo

et al. 2019

Biophysical Chemistry

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Three-way helical junctions (3WJs) arise in genetic processing, and they have architectural and functional roles in structured nucleic acids. An internal bulge at the junction core allows the helical domains to become oriented into two possible, coaxially stacked conformers. Here, the helical stacking arrangements for a series of bulged, DNA 3WJs were examined using ensemble fluorescence resonance energy transfer (FRET) and single-molecule FRET (smFRET) approaches. The 3WJs varied according to the GC content and sequence of the junction core as well as the pyrimidine content of the internal bulge. Mg 2+ titration experiments by ensemble FRET show that both stacking conformations have similar Mg 2+ requirements for folding. Strikingly, smFRET experiments reveal that a specific junction sequence can populate both conformers and that this junction undergoes continual interconversion between the two stacked conformers. These findings will support the development of folding principles for the rational design of functional DNA nanostructures.

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“…Also, the FRET states due to peptide binding depict the acquirement of a range of configurations, viz., the two forms of stacked-X and square planar states, and hence, it has been hypothesized that peak barriers between the states reduce due to the presence of peptides. However, even in hexapeptide bound conditions, the conformational diversity in the GC-based junction reduced with a greater preference toward the iso II state (Cannon et al, 2015). The time resolution of the sm-FRET method has successfully extracted the sequential intermediate dynamical state of the HJs bound to junction-resolving enzymes.…”

Section: Holliday Junctionmentioning

confidence: 99%

Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy

Bandyopadhyay

Mishra

2021

Front. Mol. Biosci.

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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.

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Hexapeptides That Inhibit Processing of Branched DNA Structures Induce a Dynamic Ensemble of Holliday Junction Conformations

Cited by 6 publications

References 49 publications

Differential Effects of Strand Asymmetry on the Energetics and Structural Flexibility of DNA Internal Loops

Differential Effects of Strand Asymmetry on the Energetics and Structural Flexibility of DNA Internal Loops

Detection of Mg2+-dependent, coaxial stacking rearrangements in a bulged three-way DNA junction by single-molecule FRET

Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy

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