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Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting.

Publication ,  Journal Article
Rangadurai, A; Shi, H; Xu, Y; Liu, B; Abou Assi, H; Boom, JD; Zhou, H; Kimsey, IJ; Al-Hashimi, HM
Published in: Proc Natl Acad Sci U S A
June 14, 2022

Thermodynamic preferences to form non-native conformations are crucial for understanding how nucleic acids fold and function. However, they are difficult to measure experimentally because this requires accurately determining the population of minor low-abundance (<10%) conformations in a sea of other conformations. Here, we show that melting experiments enable facile measurements of thermodynamic preferences to adopt nonnative conformations in DNA and RNA. The key to this "delta-melt" approach is to use chemical modifications to render specific minor non-native conformations the major state. The validity and robustness of delta-melt is established for four different non-native conformations under various physiological conditions and sequence contexts through independent measurements of thermodynamic preferences using NMR. Delta-melt is faster relative to NMR, simple, and cost-effective and enables thermodynamic preferences to be measured for exceptionally low-populated conformations. Using delta-melt, we obtained rare insights into conformational cooperativity, obtaining evidence for significant cooperativity (1.0 to 2.5 kcal/mol) when simultaneously forming two adjacent Hoogsteen base pairs. We also measured the thermodynamic preferences to form G-C+ and A-T Hoogsteen and A-T base open states for nearly all 16 trinucleotide sequence contexts and found distinct sequence-specific variations on the order of 2 to 3 kcal/mol. This rich landscape of sequence-specific non-native minor conformations in the DNA double helix may help shape the sequence specificity of DNA biochemistry. Thus, melting experiments can now be used to access thermodynamic information regarding regions of the free energy landscape of biomolecules beyond the native folded and unfolded conformations.

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Published In

Proc Natl Acad Sci U S A

DOI

EISSN

1091-6490

Publication Date

June 14, 2022

Volume

119

Issue

24

Start / End Page

e2112496119

Location

United States

Related Subject Headings

  • Ultraviolet Rays
  • Thermodynamics
  • RNA
  • Nucleic Acid Conformation
  • Freezing
  • DNA
  • Base Sequence
 

Citation

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Rangadurai, A., Shi, H., Xu, Y., Liu, B., Abou Assi, H., Boom, J. D., … Al-Hashimi, H. M. (2022). Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting. Proc Natl Acad Sci U S A, 119(24), e2112496119. https://doi.org/10.1073/pnas.2112496119
Rangadurai, Atul, Honglue Shi, Yu Xu, Bei Liu, Hala Abou Assi, John D. Boom, Huiqing Zhou, Isaac J. Kimsey, and Hashim M. Al-Hashimi. “Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting.Proc Natl Acad Sci U S A 119, no. 24 (June 14, 2022): e2112496119. https://doi.org/10.1073/pnas.2112496119.
Rangadurai A, Shi H, Xu Y, Liu B, Abou Assi H, Boom JD, et al. Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting. Proc Natl Acad Sci U S A. 2022 Jun 14;119(24):e2112496119.
Rangadurai, Atul, et al. “Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting.Proc Natl Acad Sci U S A, vol. 119, no. 24, June 2022, p. e2112496119. Pubmed, doi:10.1073/pnas.2112496119.
Rangadurai A, Shi H, Xu Y, Liu B, Abou Assi H, Boom JD, Zhou H, Kimsey IJ, Al-Hashimi HM. Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting. Proc Natl Acad Sci U S A. 2022 Jun 14;119(24):e2112496119.
Journal cover image

Published In

Proc Natl Acad Sci U S A

DOI

EISSN

1091-6490

Publication Date

June 14, 2022

Volume

119

Issue

24

Start / End Page

e2112496119

Location

United States

Related Subject Headings

  • Ultraviolet Rays
  • Thermodynamics
  • RNA
  • Nucleic Acid Conformation
  • Freezing
  • DNA
  • Base Sequence