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Title: Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules

Abstract

Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs.

Authors:
; ; ORCiD logo; ; ORCiD logo
Publication Date:
Research Org.:
Brookhaven National Lab. (BNL), Upton, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); Univ. of Arkansas; Arkansas Department of Higher Education; National Science Foundation (NSF)
OSTI Identifier:
1631488
Alternate Identifier(s):
OSTI ID: 1661640
Report Number(s):
BNL-219827-2020-JAAM
Journal ID: ISSN 1424-8220; SENSC9; PII: s20113112
Grant/Contract Number:  
38596; SC0012704; ABI-0189; ABI-0226; ABI-0277; ABI-0326; 003049-00001A; 1826642
Resource Type:
Published Article
Journal Name:
Sensors
Additional Journal Information:
Journal Name: Sensors Journal Volume: 20 Journal Issue: 11; Journal ID: ISSN 1424-8220
Publisher:
MDPI AG
Country of Publication:
Switzerland
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; nucleic acids; interactions; elasticity; bending; molecular spring

Citation Formats

Freeland, Jack, Zhang, Lihua, Wang, Shih-Ting, Ruiz, Mason, and Wang, Yong. Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules. Switzerland: N. p., 2020. Web. doi:10.3390/s20113112.
Freeland, Jack, Zhang, Lihua, Wang, Shih-Ting, Ruiz, Mason, & Wang, Yong. Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules. Switzerland. doi:https://doi.org/10.3390/s20113112
Freeland, Jack, Zhang, Lihua, Wang, Shih-Ting, Ruiz, Mason, and Wang, Yong. Sun . "Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules". Switzerland. doi:https://doi.org/10.3390/s20113112.
@article{osti_1631488,
title = {Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules},
author = {Freeland, Jack and Zhang, Lihua and Wang, Shih-Ting and Ruiz, Mason and Wang, Yong},
abstractNote = {Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs.},
doi = {10.3390/s20113112},
journal = {Sensors},
number = 11,
volume = 20,
place = {Switzerland},
year = {2020},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: https://doi.org/10.3390/s20113112

Figures / Tables:

Figure 1 Figure 1: Illustration of sensing amplifiers based on bent DNA bows. (a) Construction of DNA bows from synthesized single-stranded DNA. The 5′- and 3′- ends of the DNA strands are indicated, along with arrows from 5′ to 3′. The nick in the bent DNA bow is highlighted by the greenmore » triangle. (b) Linear unbent DNA as negative controls. CF: fully double-stranded DNA; CM: partially double stranded DNA in the middle; CR: partially double-stranded DNA in the right. (c) Relaxation of bending elastic energy in DNA bows by forming dimers, timers, and higher-order oligomers. The 5′- and 3′ ends of the DNA strands, the direction from 5′ to 3′, and the location of the nicks are highlighted similarly to panel a. (d) Sketch of the procedure for detecting DNA interactions with ions and molecules, visualized by gel electrophoresis as an example. R stands for the bands corresponding to the relaxed species (dimers, trimers, etc.). B indicates the band for the bent DNA bows. S represents the band for the unhybridized single-stranded DNA.« less

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