Decreased water activity in nanoconfinement contributes to the folding of G-quadruplex and i-motif structures

Sagun Jonchhe; Shankar Pandey; Tomoko Emura; Kumi Hidaka; Mohammad Akter Hossain; Prakash Shrestha; Hiroshi Sugiyama; Masayuki Endo; Hanbin Mao

doi:10.1073/pnas.1805939115

Decreased water activity in nanoconfinement contributes to the folding of G-quadruplex and i-motif structures

Sagun Jonchhe, Shankar Pandey, Tomoko Emura, Kumi Hidaka, Mohammad Akter Hossain, Prakash Shrestha, Hiroshi Sugiyama, Masayuki Endo, Hanbin Mao

Chemistry

Research output: Contribution to journal › Article › peer-review

43 Scopus citations

Abstract

Due to the small size of a nanoconfinement, the property of water contained inside is rather challenging to probe. Herein, we measured the amount of water molecules released during the folding of individual G-quadruplex and i-motif structures, from which water activities are estimated in the DNA nanocages prepared by 5 × 5 to 7 × 7 helix bundles (cross-sections, 9 × 9 to 15 × 15 nm). We found water activities decrease with reducing cage size. In the 9 × 9-nm cage, water activity was reduced beyond the reach of regular cosolutes such as polyethylene glycol (PEG). With this set of nanocages, we were able to retrieve the change in water molecules throughout the folding trajectory of G-quadruplex or i-motif. We found that water molecules absorbed from the unfolded to the transition states are much fewer than those lost from the transition to the folded states. The overall loss of water therefore drives the folding of G-quadruplex or i-motif in nanocages with reduced water activities.

Original language	English
Pages (from-to)	9539-9544
Number of pages	6
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	115
Issue number	38
DOIs	https://doi.org/10.1073/pnas.1805939115
State	Published - Sep 18 2018

Bibliographical note

Publisher Copyright:
© 2018 National Academy of Sciences. All rights reserved.

Funding

This project was supported by the Japan Society for the Promotion of Science (JSPS) and the National Science Foundation (NSF) under the JSPS–NSF International Collaborations in Chemistry [CHE-1415883 (to H.S. and H.M.)]. H.M. also acknowledges support from the NSF (CHE-1609514). M.E. acknowledges supports from JSPS KAKENHI (Grant-in-Aid for Scientific Research) (Grants 24104002, 15H03837, and 16K14033). ACKNOWLEDGMENTS. This project was supported by the Japan Society for the Promotion of Science (JSPS) and the National Science Foundation (NSF) under the JSPS–NSF International Collaborations in Chemistry [CHE-1415883 (to H.S. and H.M.)]. H.M. also acknowledges support from the NSF (CHE-1609514). M.E. acknowledges supports from JSPS KAKENHI (Grant-in-Aid for Scientific Research) (Grants 24104002, 15H03837, and 16K14033).

Funders	Funder number
National Science Foundation Arctic Social Science Program	CHE-1609514, CHE-1415883
National Science Foundation Arctic Social Science Program
Centre International de Recherche aux Frontières de la Chimie
Japan Society for the Promotion of Science	24104002, 16K14033, 18KK0139, 15H03837
Japan Society for the Promotion of Science
National Science Foundation Arctic Social Science Program

Keywords

DNA origami nanocage
G-quadruplex
I-motif
Nanoconfinement
Water activity

ASJC Scopus subject areas

General

Access to Document

10.1073/pnas.1805939115

Cite this

Jonchhe, S., Pandey, S., Emura, T., Hidaka, K., Hossain, M. A., Shrestha, P., Sugiyama, H., Endo, M., & Mao, H. (2018). Decreased water activity in nanoconfinement contributes to the folding of G-quadruplex and i-motif structures. Proceedings of the National Academy of Sciences of the United States of America, 115(38), 9539-9544. https://doi.org/10.1073/pnas.1805939115

@article{5fb8a29a0c2b46279a6adfd8ff59bdee,

title = "Decreased water activity in nanoconfinement contributes to the folding of G-quadruplex and i-motif structures",

abstract = "Due to the small size of a nanoconfinement, the property of water contained inside is rather challenging to probe. Herein, we measured the amount of water molecules released during the folding of individual G-quadruplex and i-motif structures, from which water activities are estimated in the DNA nanocages prepared by 5 × 5 to 7 × 7 helix bundles (cross-sections, 9 × 9 to 15 × 15 nm). We found water activities decrease with reducing cage size. In the 9 × 9-nm cage, water activity was reduced beyond the reach of regular cosolutes such as polyethylene glycol (PEG). With this set of nanocages, we were able to retrieve the change in water molecules throughout the folding trajectory of G-quadruplex or i-motif. We found that water molecules absorbed from the unfolded to the transition states are much fewer than those lost from the transition to the folded states. The overall loss of water therefore drives the folding of G-quadruplex or i-motif in nanocages with reduced water activities.",

keywords = "DNA origami nanocage, G-quadruplex, I-motif, Nanoconfinement, Water activity",

author = "Sagun Jonchhe and Shankar Pandey and Tomoko Emura and Kumi Hidaka and Hossain, \{Mohammad Akter\} and Prakash Shrestha and Hiroshi Sugiyama and Masayuki Endo and Hanbin Mao",

year = "2018",

month = sep,

day = "18",

doi = "10.1073/pnas.1805939115",

language = "English",

volume = "115",

pages = "9539--9544",

number = "38",

}

Jonchhe, S, Pandey, S, Emura, T, Hidaka, K, Hossain, MA, Shrestha, P, Sugiyama, H, Endo, M & Mao, H 2018, 'Decreased water activity in nanoconfinement contributes to the folding of G-quadruplex and i-motif structures', Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 38, pp. 9539-9544. https://doi.org/10.1073/pnas.1805939115

TY - JOUR

T1 - Decreased water activity in nanoconfinement contributes to the folding of G-quadruplex and i-motif structures

AU - Jonchhe, Sagun

AU - Pandey, Shankar

AU - Emura, Tomoko

AU - Hidaka, Kumi

AU - Hossain, Mohammad Akter

AU - Shrestha, Prakash

AU - Sugiyama, Hiroshi

AU - Endo, Masayuki

AU - Mao, Hanbin

PY - 2018/9/18

Y1 - 2018/9/18

N2 - Due to the small size of a nanoconfinement, the property of water contained inside is rather challenging to probe. Herein, we measured the amount of water molecules released during the folding of individual G-quadruplex and i-motif structures, from which water activities are estimated in the DNA nanocages prepared by 5 × 5 to 7 × 7 helix bundles (cross-sections, 9 × 9 to 15 × 15 nm). We found water activities decrease with reducing cage size. In the 9 × 9-nm cage, water activity was reduced beyond the reach of regular cosolutes such as polyethylene glycol (PEG). With this set of nanocages, we were able to retrieve the change in water molecules throughout the folding trajectory of G-quadruplex or i-motif. We found that water molecules absorbed from the unfolded to the transition states are much fewer than those lost from the transition to the folded states. The overall loss of water therefore drives the folding of G-quadruplex or i-motif in nanocages with reduced water activities.

AB - Due to the small size of a nanoconfinement, the property of water contained inside is rather challenging to probe. Herein, we measured the amount of water molecules released during the folding of individual G-quadruplex and i-motif structures, from which water activities are estimated in the DNA nanocages prepared by 5 × 5 to 7 × 7 helix bundles (cross-sections, 9 × 9 to 15 × 15 nm). We found water activities decrease with reducing cage size. In the 9 × 9-nm cage, water activity was reduced beyond the reach of regular cosolutes such as polyethylene glycol (PEG). With this set of nanocages, we were able to retrieve the change in water molecules throughout the folding trajectory of G-quadruplex or i-motif. We found that water molecules absorbed from the unfolded to the transition states are much fewer than those lost from the transition to the folded states. The overall loss of water therefore drives the folding of G-quadruplex or i-motif in nanocages with reduced water activities.

KW - DNA origami nanocage

KW - G-quadruplex

KW - I-motif

KW - Nanoconfinement

KW - Water activity

UR - https://www.scopus.com/pages/publications/85053551928

UR - https://www.scopus.com/inward/citedby.url?scp=85053551928&partnerID=8YFLogxK

U2 - 10.1073/pnas.1805939115

DO - 10.1073/pnas.1805939115

M3 - Article

C2 - 30181280

AN - SCOPUS:85053551928

SN - 0027-8424

VL - 115

SP - 9539

EP - 9544

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 38

ER -

Decreased water activity in nanoconfinement contributes to the folding of G-quadruplex and i-motif structures

Abstract

Bibliographical note

Funding

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this