Decoding the energy pathway by which a DNA unravels is the holy grail of biologists and physicists alike. The underlying physics is an intriguing competition of entropy ordering and disordering in the bound and unbound base-pairs of the intermediate bubbles. We re-examine this in a controlled denaturation study with picoliter solutions of DNA molecules confined in a resonating microfluidic cantilever. To our surprise, a unique entropy fluctuation interplay of the denaturation bubbles is revealed, apparent in a two-stage transition profile. The dynamic dissipation at resonance , which we record, faithfully captures the base-pair binding-unbinding energy landscape, revealing the singular entropy fluctuation characteristic. We attribute the characteristic to the onset of an energy fluctuation scale observable only at the small volume scales employed. The fluctuations apparently favor entropy ordering over disordering at biologically relevant T< 42C in a non-equilibrium transition pathway. The observed ordering energetics suggests the probability of an intermediate collapsed-bubble conformation releasing energy, sufficient to unbind the bubble ends. An alternate energy pathway thus surfaces complementing molecular zipper and bubble state cooperativity transitions. Fluctuation theorem supports our argument, which we further validate from DNA solutions across varying oligomer lengths, base pair moieties, and concentrations. This new information of fluctuation driven ordering energetics can contribute to new insights on DNA transcription, the integral basis of life. The nanomechanical dynamic dissipation paradigm of investigating picoliter bio-samples as introduced offers a new method for investigating other interesting challenges such as folding of proteins and cell proliferation, which also evolve through similar energetics of non-equilibrium processes .
A double-stranded DNA unravels thermally through intermediate denatured bubble segments. Intrinsically, fluctuations ensue at the bubble boundaries from non-equilibrium (NE) energy exchanges with the environment. However, such details gets obscured by large population kinetics at the macroscale, associating equilibrium pathway to the unravelling landscape. In this work, we capture evidence of fluctuation energetics with picoliter samples in a microfluidic cantilever. We exploit nanomechanical resonance to measure the NE energy exchanges through dissipation, revealing a crucial pre-melting transition at T~ 42C . This signifies that unravelling possibly proceeds via intermediate collapsed-bubble conformations releasing energy, sufficient to unbind bubble ends, assisting further unbinding. Fluctuation theorem explains the observations opening further avenues to investigate fluctuation kinetics in other biological phenomena that also proceed through similar NE energetics .
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Decoding the energy pathway by which a DNA unravels is the holy grail of biologists and physicists alike. The underlying physics is an intriguing competition of entropy ordering and disordering in the bound and unbound base-pairs of the intermediate bubbles. We re-examine this in a controlled denaturation study with picoliter solutions of DNA molecules confined in a resonating
A double-stranded DNA unravels thermally through intermediate denatured bubble segments. Intrinsically, fluctuations ensue at the bubble boundaries from non-equilibrium (NE) energy exchanges with the environment. However, such details gets obscured by large population kinetics at the macroscale, associating equilibrium pathway to the unravelling landscape. In this work, we capture evidence of fluctuation energetics with picoliter samples in a
R
To our surprise, a unique entropy fluctuation interplay of the denaturation bubbles is revealed, apparent in a two-stage transition profile. The dynamic dissipation at resonance , which we record, faithfully captures the base-pair binding-unbinding energy landscape, revealing the singular entropy fluctuation characteristic. We attribute the characteristic to the onset of an energy fluctuation scale observable only at the small volume scales employed. The fluctuations apparently favor entropy ordering over disordering at biologically relevant T<
We exploit nanomechanical resonance to measure the NE energy exchanges through dissipation, revealing a crucial pre-melting transition at T~
R
in a non-equilibrium transition pathway. The observed ordering energetics suggests the probability of an
. This signifies that unravelling possibly proceeds via
R
conformation
conformations
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the bubble ends. An alternate energy pathway thus surfaces complementing molecular zipper and bubble state cooperativity transitions. Fluctuation theorem supports our argument, which we further validate from DNA solutions across varying oligomer lengths, base pair moieties, and concentrations. This new information of fluctuation driven ordering energetics can contribute to new insights on DNA transcription, the integral basis of life. The nanomechanical dynamic dissipation paradigm of investigating picoliter bio-samples as introduced offers a new method for investigating other interesting challenges such as folding of proteins and cell proliferation, which also evolve through similar energetics of non-equilibrium processes
bubble ends, assisting further unbinding. Fluctuation theorem explains the observations opening further avenues to investigate fluctuation kinetics in other biological phenomena that also proceed through similar NE energetics