Atomic structures of RNA nanotubes and their comparison with DNA nanotubes

Supriyo Naskar, Himanshu Joshi, Banani Chakraborty, Nadrian C. Seeman, Prabal K. Maiti

Research output: Contribution to journalArticle

Abstract

We present a computational framework to model RNA based nanostructures and study their microscopic structures. We model hexagonal nanotubes made of 6 dsRNA (RNTs) connected by double crossover (DX) at different positions. Using several hundred nano-second (ns) long all-atom molecular dynamics simulations, we study the atomic structure, conformational change and elastic properties of RNTs in the presence of explicit water and ions. Based on several structural quantities such as root mean square deviation (RMSD) and root mean square fluctuation (RMSF), we find that the RNTs are almost as stable as DNA nanotubes (DNTs). Although the central portion of the RNTs maintain its cylindrical shape, both the terminal regions open up to give rise to a gating like behavior which can play a crucial role in drug delivery. From the bending angle distribution, we observe that the RNTs are more flexible than DNTs. The calculated persistence length of the RNTs is in the micron range which is an order of magnitude higher than that of a single dsRNA. The stretch modulus of the RNTs from the contour length distribution is in the range of 4-7 nN depending on the sequence. The calculated persistence length and stretch modulus are in the same range of values as in the case of DNTs. To understand the structural properties of RNTs at the individual base-pair level we have also calculated all the helicoidal parameters and analyzed the relative flexibility and rigidity of RNTs having a different sequence. These findings emphasized the fascinating properties of RNTs which will expedite further theoretical and experimental studies in this field.

Original languageEnglish (US)
Pages (from-to)14863-14878
Number of pages16
JournalNanoscale
Volume11
Issue number31
DOIs
StatePublished - Aug 21 2019

Fingerprint

RNA
Nanotubes
DNA
Drug delivery
Rigidity
Molecular dynamics
Structural properties
Nanostructures
Ions
Atoms
Water
Computer simulation

ASJC Scopus subject areas

  • Materials Science(all)

Cite this

Naskar, S., Joshi, H., Chakraborty, B., Seeman, N. C., & Maiti, P. K. (2019). Atomic structures of RNA nanotubes and their comparison with DNA nanotubes. Nanoscale, 11(31), 14863-14878. https://doi.org/10.1039/c9nr00786e

Atomic structures of RNA nanotubes and their comparison with DNA nanotubes. / Naskar, Supriyo; Joshi, Himanshu; Chakraborty, Banani; Seeman, Nadrian C.; Maiti, Prabal K.

In: Nanoscale, Vol. 11, No. 31, 21.08.2019, p. 14863-14878.

Research output: Contribution to journalArticle

Naskar, S, Joshi, H, Chakraborty, B, Seeman, NC & Maiti, PK 2019, 'Atomic structures of RNA nanotubes and their comparison with DNA nanotubes', Nanoscale, vol. 11, no. 31, pp. 14863-14878. https://doi.org/10.1039/c9nr00786e
Naskar, Supriyo ; Joshi, Himanshu ; Chakraborty, Banani ; Seeman, Nadrian C. ; Maiti, Prabal K. / Atomic structures of RNA nanotubes and their comparison with DNA nanotubes. In: Nanoscale. 2019 ; Vol. 11, No. 31. pp. 14863-14878.
@article{67737387140242309c3704d10cc721de,
title = "Atomic structures of RNA nanotubes and their comparison with DNA nanotubes",
abstract = "We present a computational framework to model RNA based nanostructures and study their microscopic structures. We model hexagonal nanotubes made of 6 dsRNA (RNTs) connected by double crossover (DX) at different positions. Using several hundred nano-second (ns) long all-atom molecular dynamics simulations, we study the atomic structure, conformational change and elastic properties of RNTs in the presence of explicit water and ions. Based on several structural quantities such as root mean square deviation (RMSD) and root mean square fluctuation (RMSF), we find that the RNTs are almost as stable as DNA nanotubes (DNTs). Although the central portion of the RNTs maintain its cylindrical shape, both the terminal regions open up to give rise to a gating like behavior which can play a crucial role in drug delivery. From the bending angle distribution, we observe that the RNTs are more flexible than DNTs. The calculated persistence length of the RNTs is in the micron range which is an order of magnitude higher than that of a single dsRNA. The stretch modulus of the RNTs from the contour length distribution is in the range of 4-7 nN depending on the sequence. The calculated persistence length and stretch modulus are in the same range of values as in the case of DNTs. To understand the structural properties of RNTs at the individual base-pair level we have also calculated all the helicoidal parameters and analyzed the relative flexibility and rigidity of RNTs having a different sequence. These findings emphasized the fascinating properties of RNTs which will expedite further theoretical and experimental studies in this field.",
author = "Supriyo Naskar and Himanshu Joshi and Banani Chakraborty and Seeman, {Nadrian C.} and Maiti, {Prabal K.}",
year = "2019",
month = "8",
day = "21",
doi = "10.1039/c9nr00786e",
language = "English (US)",
volume = "11",
pages = "14863--14878",
journal = "Nanoscale",
issn = "2040-3364",
publisher = "Royal Society of Chemistry",
number = "31",

}

TY - JOUR

T1 - Atomic structures of RNA nanotubes and their comparison with DNA nanotubes

AU - Naskar, Supriyo

AU - Joshi, Himanshu

AU - Chakraborty, Banani

AU - Seeman, Nadrian C.

AU - Maiti, Prabal K.

PY - 2019/8/21

Y1 - 2019/8/21

N2 - We present a computational framework to model RNA based nanostructures and study their microscopic structures. We model hexagonal nanotubes made of 6 dsRNA (RNTs) connected by double crossover (DX) at different positions. Using several hundred nano-second (ns) long all-atom molecular dynamics simulations, we study the atomic structure, conformational change and elastic properties of RNTs in the presence of explicit water and ions. Based on several structural quantities such as root mean square deviation (RMSD) and root mean square fluctuation (RMSF), we find that the RNTs are almost as stable as DNA nanotubes (DNTs). Although the central portion of the RNTs maintain its cylindrical shape, both the terminal regions open up to give rise to a gating like behavior which can play a crucial role in drug delivery. From the bending angle distribution, we observe that the RNTs are more flexible than DNTs. The calculated persistence length of the RNTs is in the micron range which is an order of magnitude higher than that of a single dsRNA. The stretch modulus of the RNTs from the contour length distribution is in the range of 4-7 nN depending on the sequence. The calculated persistence length and stretch modulus are in the same range of values as in the case of DNTs. To understand the structural properties of RNTs at the individual base-pair level we have also calculated all the helicoidal parameters and analyzed the relative flexibility and rigidity of RNTs having a different sequence. These findings emphasized the fascinating properties of RNTs which will expedite further theoretical and experimental studies in this field.

AB - We present a computational framework to model RNA based nanostructures and study their microscopic structures. We model hexagonal nanotubes made of 6 dsRNA (RNTs) connected by double crossover (DX) at different positions. Using several hundred nano-second (ns) long all-atom molecular dynamics simulations, we study the atomic structure, conformational change and elastic properties of RNTs in the presence of explicit water and ions. Based on several structural quantities such as root mean square deviation (RMSD) and root mean square fluctuation (RMSF), we find that the RNTs are almost as stable as DNA nanotubes (DNTs). Although the central portion of the RNTs maintain its cylindrical shape, both the terminal regions open up to give rise to a gating like behavior which can play a crucial role in drug delivery. From the bending angle distribution, we observe that the RNTs are more flexible than DNTs. The calculated persistence length of the RNTs is in the micron range which is an order of magnitude higher than that of a single dsRNA. The stretch modulus of the RNTs from the contour length distribution is in the range of 4-7 nN depending on the sequence. The calculated persistence length and stretch modulus are in the same range of values as in the case of DNTs. To understand the structural properties of RNTs at the individual base-pair level we have also calculated all the helicoidal parameters and analyzed the relative flexibility and rigidity of RNTs having a different sequence. These findings emphasized the fascinating properties of RNTs which will expedite further theoretical and experimental studies in this field.

UR - http://www.scopus.com/inward/record.url?scp=85070821319&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85070821319&partnerID=8YFLogxK

U2 - 10.1039/c9nr00786e

DO - 10.1039/c9nr00786e

M3 - Article

C2 - 31355845

AN - SCOPUS:85070821319

VL - 11

SP - 14863

EP - 14878

JO - Nanoscale

JF - Nanoscale

SN - 2040-3364

IS - 31

ER -