Remarkable similarity of force induced dsRNA conformational changes to stretched dsDNA and their detection using electrical measurements

Aggarwal, Ankur; Bag, Saientan; Maiti, Prabal K.

doi:10.1039/c8cp03574a

Cited by 18 publications

(59 citation statements)

References 61 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Accordingly, charge transport in RNA can significantly differ from that in DNA and is worth thorough investigation. However, while multiple theoretical and experimental studies addressed charge transport in DNA [16][17][18][19], such studies for RNA [14,20,21] are rare. Very recently, it was shown that charge transport along the DNA molecule plays an important role in regulation of the replication process [18] and DNA repair [19], and disruption of DNA conductivity may cause severe diseases [22].…”

Section: Of 10mentioning

confidence: 99%

Walking around Ribosomal Small Subunit: A Possible “Tourist Map” for Electron Holes

Sosorev

2021

Molecules

View full text Add to dashboard Cite

Despite several decades of research, the physics underlying translation—protein synthesis at the ribosome—remains poorly studied. For instance, the mechanism coordinating various events occurring in distant parts of the ribosome is unknown. Very recently, we suggested that this allosteric mechanism could be based on the transport of electric charges (electron holes) along RNA molecules and localization of these charges in the functionally important areas; this assumption was justified using tRNA as an example. In this study, we turn to the ribosome and show computationally that holes can also efficiently migrate within the whole ribosomal small subunit (SSU). The potential sites of charge localization in SSU are revealed, and it is shown that most of them are located in the functionally important areas of the ribosome—intersubunit bridges, Fe4S4 cluster, and the pivot linking the SSU head to its body. As a result, we suppose that hole localization within the SSU can affect intersubunit rotation (ratcheting) and SSU head swiveling, in agreement with the scenario of electronic coordination of ribosome operation. We anticipate that our findings will improve the understanding of the translation process and advance molecular biology and medicine.

show abstract

Section: Of 10mentioning

confidence: 99%

Walking around Ribosomal Small Subunit: A Possible “Tourist Map” for Electron Holes

Sosorev

2021

Molecules

View full text Add to dashboard Cite

show abstract

“…dsDNA exhibits different force-extension regimes with Hookean behavior at low forces and a drastic elongation of its length at a force of 65 pN [1,6]. This is followed by an overstretching behavior where dsDNA transforms to a completely new structural phase-broadly described as a thermodynamically melted form (with broken Watson-Crick base-pairs) or a structurally intact base-pair stacking alignment in a ladder-like fashion (the so-called S-DNA) [6,[51][52][53].…”

Section: Structural Transitions In Dsdna Under Forcementioning

confidence: 99%

“…dsDNA has been studied in various conditions, such as unzipping, shearing, stretching, and under a torque, to mimic different biological scenarios [1]. These have provided increased insights to various interesting aspects of DNA such as emergence of S-DNA upon overstretching [5,10,51,52], modifications of DNA structural and mechanical properties under different environments such as drug intercalators [15 ], salts [17 ,46 ] and ionic liquids [26 ]. These information are the key inputs for DNA nanotechnological applications, enabling researchers to design various DNA nanostructures like DNA nanotubes [32,33 ] and DNA nanorobots for drug delivery [65], as well as in DNA nanoelectronics [51,52].…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

What do we know about DNA mechanics so far?

Aggarwal

Naskar

Sahoo

et al. 2020

Current Opinion in Structural Biology

Self Cite

View full text Add to dashboard Cite

The DNA molecule, apart from carrying the genetic information, plays a crucial role in a variety of biological processes and finds applications in drug design, nanotechnology and nanoelectronics. The molecule undergoes significant structural transitions under the influence of forces due to physiological and non-physiological environments. Here, we summarize the insights gained from simulations and single-molecule experiments on the structural transitions and mechanics of DNA under force, as well as its elastic properties, in various environmental conditions, and discuss appealing future directions.

show abstract

“…tRNA and ribosomal RNA (rRNA) [15]. While multiple theoretical and experimental studies addressed charge transport in DNA [16][17][18][19], such studies for RNA [14,20,21] are rare. Very recently, it was shown that charge transport along the DNA molecule plays important role in regulation of the replication process [18] and DNA repair [19], and disruption of DNA conductivity may cause severe diseases [22].…”

Section: Introductionmentioning

confidence: 99%

Walking Around Ribosomal Small Subunit: A Possible “Tourist Map” for an Electron Hole

Sosorev¹

2021

Preprint

View full text Add to dashboard Cite

Despite several decades of research, the physics underlying translation – protein synthesis at the ribosome – remains poorly studied. For instance, the mechanism coordinating various events occurring in distant parts of the ribosome is unknown. Very recently, we have suggested that this allosteric mechanism could be based on the transport of electric charges (electron holes) along RNA molecules and localization of these charges in the functionally important areas; this assumption was justified using tRNA as an example. In this study, we turn to the ribosome and show computationally that holes can also efficiently migrate within the whole ribosomal small subunit (SSU). The potential sites of charge localization in SSU are revealed, and it is shown that most of them are located in the functionally important areas of the ribosome – intersubunit bridges, Fe4S4 cluster and the pivot linking the SSU head to the body. As a result, we suppose that hole localization within the SSU can affect intersubunit rotation (ratcheting) and SSU head swiveling, in agreement with the scenario of electronic coordination of ribosome operation. We anticipate that our findings will improve the understanding of the translation process and advance the molecular biology and medicine.

show abstract

Remarkable similarity of force induced dsRNA conformational changes to stretched dsDNA and their detection using electrical measurements

Abstract: We show the emergence of S-RNA under stretching in analogy to S-DNA and propose a method for its detection using electrical measurement.

Cited by 18 publications

References 61 publications

Walking around Ribosomal Small Subunit: A Possible “Tourist Map” for Electron Holes

Walking around Ribosomal Small Subunit: A Possible “Tourist Map” for Electron Holes

What do we know about DNA mechanics so far?

Walking Around Ribosomal Small Subunit: A Possible “Tourist Map” for an Electron Hole

Contact Info

Product

Resources

About