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Effects of Small Molecules on Nuclei...

Adams, Miranda Sue.

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Effects of Small Molecules on Nucleic Acid Stability and Improvements to RNA Structure Prediction.

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	Effects of Small Molecules on Nucleic Acid Stability and Improvements to RNA Structure Prediction./
作者:	Adams, Miranda Sue.
出版者:	Ann Arbor : ProQuest Dissertations & Theses, : 2020,
面頁冊數:	147 p.
附註:	Source: Dissertations Abstracts International, Volume: 81-12, Section: B.
Contained By:	Dissertations Abstracts International81-12B.
標題:	Biochemistry. -
電子資源:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=27959331
ISBN:	9798645483364

Effects of Small Molecules on Nucleic Acid Stability and Improvements to RNA Structure Prediction.
Adams, Miranda Sue.

Effects of Small Molecules on Nucleic Acid Stability and Improvements to RNA Structure Prediction. - Ann Arbor : ProQuest Dissertations & Theses, 2020 - 147 p.

Source: Dissertations Abstracts International, Volume: 81-12, Section: B.

Thesis (Ph.D.)--Saint Louis University, 2020.

This item must not be sold to any third party vendors.

Nucleic acids possess a strong relationship between structure and function, so it is essential to improve understanding of nucleic acid structure and interactions with small molecules in order to better understand nucleic acid function and potential contacts with therapeutic agents.To improve RNA 2D structure prediction methods, 20% polyethylene glycol (PEG) 200, was introduced as a crowding agent, and optical melting experiments were conducted to determine the effect of a small crowding agent on RNA duplex stability. RNA duplexes are, on average, 1.02 kcal/mol less stable in the presence of 20% PEG 200 compared to predictions for RNA with no crowding agent. The data collected here was used to derive nearest neighbor parameters accounting for 20% PEG 200. These can be used to improve RNA secondary structure prediction in vivo. A promising method to predict RNA 3D structure is to identify and characterize sequence-structure patterns among RNA 3D structures of a particular 2D structure motif. To this end, a Python-based pipeline was developed to identify and characterize RNA sequence-structure patterns using RNA tetraloops as a test case. Six tetraloop sequence families were identified by the protocol, three of the families were previously identified by the literature, and the remaining three are new sequence families. The protocol can be used on other RNA secondary structure motifs and is a potential tool to aid RNA 3D structure predictions. NMR is a powerful technique used to derive 3D structures of RNA in solution. In this work, NMR was used to identify the structural features of the GGUA tetraloop. While the GGUA tetraloop is sequentially similar to the well-characterized GNRA tetraloop fold, the data gathered from a variety of NMR experiments indicate that the GGUA tetraloop is not adopting the signature GNRA fold.Finally, the interaction between DNA and a variety of naphthalimide derivatives was characterized to assess binding strength and potential correlations to cytotoxicity. Mitonafide, a 3-nitro substituted naphthalimide derivative, was the most stabilizing combination according to the thermodynamic data. The thermodynamic data agreed with preliminary cell assay studies, suggesting a potential correlation between DNA-intercalator thermodynamics and cytotoxicity.

ISBN: 9798645483364Subjects--Topical Terms:

518028
Biochemistry.
Subjects--Index Terms:

DNA

Effects of Small Molecules on Nucleic Acid Stability and Improvements to RNA Structure Prediction.
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520 $a Nucleic acids possess a strong relationship between structure and function, so it is essential to improve understanding of nucleic acid structure and interactions with small molecules in order to better understand nucleic acid function and potential contacts with therapeutic agents.To improve RNA 2D structure prediction methods, 20% polyethylene glycol (PEG) 200, was introduced as a crowding agent, and optical melting experiments were conducted to determine the effect of a small crowding agent on RNA duplex stability. RNA duplexes are, on average, 1.02 kcal/mol less stable in the presence of 20% PEG 200 compared to predictions for RNA with no crowding agent. The data collected here was used to derive nearest neighbor parameters accounting for 20% PEG 200. These can be used to improve RNA secondary structure prediction in vivo. A promising method to predict RNA 3D structure is to identify and characterize sequence-structure patterns among RNA 3D structures of a particular 2D structure motif. To this end, a Python-based pipeline was developed to identify and characterize RNA sequence-structure patterns using RNA tetraloops as a test case. Six tetraloop sequence families were identified by the protocol, three of the families were previously identified by the literature, and the remaining three are new sequence families. The protocol can be used on other RNA secondary structure motifs and is a potential tool to aid RNA 3D structure predictions. NMR is a powerful technique used to derive 3D structures of RNA in solution. In this work, NMR was used to identify the structural features of the GGUA tetraloop. While the GGUA tetraloop is sequentially similar to the well-characterized GNRA tetraloop fold, the data gathered from a variety of NMR experiments indicate that the GGUA tetraloop is not adopting the signature GNRA fold.Finally, the interaction between DNA and a variety of naphthalimide derivatives was characterized to assess binding strength and potential correlations to cytotoxicity. Mitonafide, a 3-nitro substituted naphthalimide derivative, was the most stabilizing combination according to the thermodynamic data. The thermodynamic data agreed with preliminary cell assay studies, suggesting a potential correlation between DNA-intercalator thermodynamics and cytotoxicity.
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