Azobenzene Photoisomerization-Induced Destabilization of B-DNA

Biswas, Mithun; Burghardt, Irène

doi:10.1016/j.bpj.2014.06.044

Cited by 34 publications

(45 citation statements)

References 43 publications

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“…It should also be noted that our previous results for an azobenzene in DNA with the LT linker and without any moiety in the opposite strand showed destabilization of DNA only at elevated temperature. 29 One of the main ingredients of our analysis has been the construction of a suitable local reference frame. The implementation of such a local frame not only is helpful for this particular analysis but also provides a general approach to deal with the structural changes of any nonresidual or foreign molecule covalently bound to the system.…”

Section: Resultsmentioning

confidence: 99%

“…41 The stacking interactions between any two bases can be mapped by monitoring either the center of mass distances or the buried surface area (BSA) between the bases and comparing them against mean values of these parameters obtained from reference simulations. 24,29 Here, we refer to the BSA, as in ref 29, but adopt a slightly modified approach to calculate the stacking stability. Let us consider the distribution of BSA between two bases calculated from a native RNA simulation where the bases remain visually stacked.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

“…Hence, we use here suitable measures of (de)-stabilization, notably stacking and hydrogen bonding. 24,25,29 Stacking interactions between adjacent bases and Watson− Crick hydrogen bonding between base pairs are the two main factors contributing to the stability of DNA and RNA duplexes. 46,47 Although the relative importance of these two types of interactions is still controversial, stacking interactions are thought to play a predominant role on the grounds of experimental investigations.…”

Section: Presence Of Opposite (Uracil) Basementioning

confidence: 99%

“…22,26 Finally, NMR spectroscopic analysis and computer modeling were performed in the context of understanding the superiority of 2′,6′-methyl-substituted azobenzene for the photoregulation of DNA and RNA. 22,28 Our recent modeling works in this field focused on the following two aspects: First, to develop a theoretical framework to capture the effect of the fast photoswitching dynamics on the slow conformational changes in DNA 29 and second, to analyze the destabilization of an RNA hairpin structure by covalently linked trans vs cis-azobenzenes. 24 In the second study, a detailed analysis of the effects of stacking and hydrogen bonding was given for the RNA hairpin structure.…”

Section: Introductionmentioning

confidence: 99%

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In Search of an Efficient Photoswitch for Functional RNA: Design Principles from a Microscopic Analysis of Azobenzene-linker-RNA Dynamics with Different Linkers

et al. 2015

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The design of optimal photoswitches to regulate nucleic acid functionality is a considerable challenge. Azobenzene switches that are covalently bound to the nucleic acid backbone are a paradigm example that has been studied using different types of linker species connecting the chromophore to the backbone. To support experimental efforts to construct optimal azobenzene-linker-RNA combinations, we introduce here a systematic approach for theoretical analysis, which provides criteria for the local embedding of the chromophore via a chosen linker. Using a local reference frame adapted to the chromophore, quantitative measures are provided for (i) the propensity of stacking in competition with a drift toward the minor or major groove, (ii) the tendency to disrupt the native hydrogen bond network, (iii) the structural flexibility of the chromophore-linker combination, and (iv) the correlations with the presence of a base in the opposite strand. Large differences in structural stability between the trans and cis forms of the azobenzene chromophore, according to these criteria, indicate good functionality and lead to significant differences in melting temperatures. In particular, a recently synthesized deoxyribose linker proves optimal within the set of azobenzene-linker-RNA combinations considered.

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Section: Resultsmentioning

confidence: 99%

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Section: Presence Of Opposite (Uracil) Basementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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In Search of an Efficient Photoswitch for Functional RNA: Design Principles from a Microscopic Analysis of Azobenzene-linker-RNA Dynamics with Different Linkers

et al. 2015

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“…86,87 Evidently, molecular dynamic simulations and T m experiments of duplexes have both indicated that the stabilizing effect is sufficient to offset the asymmetric distortion in DNA backbones resulted from the addition of azobenzene residues. 88,89 This makes it feasible to use azobenzene as a noninvasive molecular switch for controlling TMSD reactions in DNA seesaw circuits without sacricing sequence specicity.…”

Section: Leveraging Azobenzene-functionalized Oligonucleotides In Tmsmentioning

confidence: 99%

Renewable DNA seesaw logic circuits enabled by photoregulation of toehold-mediated strand displacement

et al. 2017

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An important achievement in the field of DNA-based computation has been the development of experimental protocols for evaluation of Boolean logic circuits. These protocols for DNA circuits generally take as inputs single-stranded DNA molecules that encode Boolean values, and via a series of DNA hybridization reactions then release ssDNA strands to indicate Boolean output values. However, most of these DNA circuit protocols are use-once only, and there remains the major challenge of designing DNA circuits to be renewable for use with multiple sets of inputs. Prior proposed schemes to make DNA gates renewable suffered from multiple problems, including waste accumulation, signal restoration, noise tolerance, and limited scalable complexity. In this work, we propose a scalable design and in silico verifications for photoregulated renewable DNA seesaw logic circuits, which after processing a given set of inputs, can be repeatedly reset to reliably process other distinct inputs. To achieve renewability, specific toeholds in the system are labeled with photoresponsive molecules such as azobenzene to modulate the effective rate constants of toehold-mediated strand displacement (TMSD) reactions. Our proposed design strategy of leveraging the collective effect of TMSD and azobenzene-mediated dehybridization may provide new perspectives on achieving synchronized and localized control of DNA hybridizations in complex and scalable reaction networks efficiently and economically. Various devices such as molecular walkers and motors could potentially be engineered reusable, be simulated and subsequently implemented using our simplified design strategy.

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How Photoisomerization Drives Peptide Folding and Unfolding: Insights from QM/MM and MM Dynamics Simulations

et al. 2016

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Photoswitchable azobenzene cross-linkers can control the folding and unfolding of peptides by photoisomerization and can thus regulate peptide affinities and enzyme activities.U sing quantum mechanics/molecular mechanics (QM/MM) methods and classical MM force fields,w er eport the first molecular dynamics simulations of the photoinduced folding and unfolding processes in the azobenzene crosslinked FK-11 peptide.Wefind that the interactions between the peptide and the azobenzene cross-linker are crucial for controlling the evolution of the secondary structure of the peptide and responsible for accelerating the folding and unfolding events.T hey also modify the photoisomerization mechanism of the azobenzene cross-linker compared with the situation in vacuo or in solution.Anefficient light-sensitive peptide can be constructed by cross-linking aphotoswitchable small cross-linker molecule to the peptide backbone;photoinduced structural changes of the cross-linker can trigger reversible changes in peptide conformations.T his kind of photoresponse can provide an avenue for probing and manipulating complex living systems.[1] Thep hotoinduced conformational dynamics of peptides with built-in azobenzenes has been exploited to probe functional changes of proteins,t omanipulate enzyme activities,a nd to control cell signaling.[2] However,adetailed mechanistic understanding of these processes at the atomistic level is still lacking.Experimentally,t ime-resolved infrared spectroscopy was employed to monitor the conformational dynamics of crosslinked peptides;itwas found that both folding and unfolding processes show complex spectral kinetics and strongly depend on the photoexcitation wavelength and on temperature. [3] Computationally,a zobenzene-linked peptides were explored by classical molecular dynamics (MD) simulations.[4] However,i nt hese studies,t he initial nonadiabatic photoisomerization was not considered or was only simulated using as imple model potential, and the effects of the photoisomerization on the subsequent conformational dynamics of peptides were not investigated;m oreover,o nly the photoinduced folding dynamics was simulated in those studies. [4] Theu nfolding dynamics of cross-linked peptides has rarely been explored experimentally because peptide unfolding processes are generally endothermic and difficult to study. [4f] Asalient dynamical feature of these cross-linked peptides is that their folding and unfolding processes are significantly accelerated compared with peptides without cross-linkers. [3a] This speedup must originate from the interaction between the cross-linker and the peptide.Athorough understanding of this interplay is crucial to rationalize the folding and unfolding dynamics of cross-linked peptides,t os elect appropriate cross-linkers,t ooptimize cross-linking positions,a nd eventually to control these photoinduced conformational changes. It is difficult to obtain detailed information on these interactions solely from experiment, and it is thus desirable to perform th...

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Azobenzene Photoisomerization-Induced Destabilization of B-DNA

Cited by 34 publications

References 43 publications

In Search of an Efficient Photoswitch for Functional RNA: Design Principles from a Microscopic Analysis of Azobenzene-linker-RNA Dynamics with Different Linkers

In Search of an Efficient Photoswitch for Functional RNA: Design Principles from a Microscopic Analysis of Azobenzene-linker-RNA Dynamics with Different Linkers

Renewable DNA seesaw logic circuits enabled by photoregulation of toehold-mediated strand displacement

How Photoisomerization Drives Peptide Folding and Unfolding: Insights from QM/MM and MM Dynamics Simulations

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