Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2009 Dec 16;131(49):17759-61.
doi: 10.1021/ja905795v.

Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases

U Deva Priyakumar  1 , Changbong Hyeon, D Thirumalai, Alexander D Mackerell Jr
Affiliations

Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases

U Deva Priyakumar et al. J Am Chem Soc. .

Abstract

Urea titration of RNA by urea is an effective approach to investigate the forces stabilizing this biologically important molecule. We used all atom molecular dynamics simulations using two urea force fields and two RNA constructs to elucidate in atomic detail the destabilization mechanism of folded RNA in aqueous urea solutions. Urea denatures RNA by forming multiple hydrogen bonds with the RNA bases and has little influence on the phosphodiester backbone. Most significantly we discovered that urea engages in stacking interactions with the bases. We also estimate, for the first time, the m-value for RNA, which is a measure of the strength of urea-RNA interactions. Our work provides a conceptual understanding of the mechanism by which urea enhances RNA folding rates.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Effect of urea on the P5GA hairpin. A. Secondary structure map of P5GA. B. Probability distribution of the N1–N3, N1–N1 and N1–O2 inter-atomic distances of the GC(AU), GA and GU base pairs, respectively, in the stem. The dotted line is the integrated probability over the distances.
Figure 2
Figure 2
Probability distributions of the dihedral angles along phosphodiester backbone of the RNA hairpin at [C]=0, 6, 8 M.
Figure 3
Figure 3
A. RDFs of OU around the RNA nitrogen atoms at 6M and 8M urea. The water RDFs are scaled by 5 and 10 for the urea oxygen plots. Results are shown for the RNA backbone atoms (phosphodiester and sugar oxygen) and RNA bases. B. Structure with multiple hydrogen bonds between urea and RNA base and phosphate group. The panels on the right show the structure of urea-base stacking and the corresponding RDFs between the urea carbon and C4, C5, C2 (A and G) and C5, C6 (C and U) atoms. The contributions from individual atom are in SI Fig.13.
Figure 4
Figure 4
Urea-induced structural transitions. A. The structure of RNA duplex (left). Inverse N1–N3 distances of the four base pairs (color-code, blue, green, red and black are used consistently) as a function of time at [C] = 0M (top) and [C[ = 6M (bottom); B. Fraction of bound fB and change in free energy ΔG as a function of urea concentrations. The fit is made for m-value analysis; C. RDFs of urea oxygen and water oxygen with respect to H1 atom of the G base when the duplex is bound or denatured at [C]=6 M.
See this image and copyright information in PMC

References

    1. Fersht A. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. W. H. Freeman Company; 1998.
    2. Tanford C. J. Am. Chem. Soc. 1964;86:2050–2059.
    3. Makhatadze GI, Privalov PL. J. Mol. Biol. 1992;226:491–505. - PubMed
    4. Myers JK, Pace CN, Scholtz JM. Protein Sci. 1995;4:2138–2148. - PMC - PubMed
    1. Pan J, Thirumalai D, Woodson SA. J. Mol. Biol. 1997;273:7–13. - PubMed
    2. Rook MS, Treiber DK, Williamson JR. Proc. Natl. Acad. Sci. 1998;281:609–620. - PubMed
    3. Shelton VM, Sosnick TR, Pan T. Biochemistry. 1999;38:16831–16839. - PubMed
    4. Sclavi B, Woodson SA, Sullivan M, Chance MR, Brenowitz M. J. Mol. Biol. 1997;266:144–159. - PubMed
    1. Robinson DR, Jencks WP. J. Am. Chem. Soc. 1965;87:2462–2469. - PubMed
    2. Wallqvist A, Covell DG, Thirumalai D. J. Am. Chem. Soc. 1998;120:427–428.
    3. Vanzi F, Madan B, Sharp K. J. Am. Chem. Soc. 1998;120:10748–10753.
    4. Tobi D, Elber R, Thirumalai D. Biopolymers. 2003;68:359–369. - PubMed
    5. Soper AK, Castner EW, Luzar A. Biophys. Chem. 2003;105:649–666. - PubMed
    6. Bennion BJ, Daggett V. Proc. Natl. Acad. Sci. 2003;100:5142–5147. - PMC - PubMed
    7. O'Brien EP, Dima RI, Brooks B, Thirumalai D. J. Am. Chem. Soc. 2007;129:7346–7353. - PubMed
    8. Hua L, Zhou R, Thirumalai D, Berne BJ. Proc. Natl. Acad. Sci. 2008;105:16928–16933. - PMC - PubMed
    9. England JR, Pande VS, Haran G. J. Chem. Soc. 2008;130:11854–11855. - PMC - PubMed
    1. Mason PE, Neilson GW, Enderby JE, Saboungi M-L, Dempsey CE, MacKerell AD, Brady JW. J. Am. Chem. Soc. 2004;126(11):462–11470. - PubMed
    1. Rudisser S, Tinoco I., Jr. J. Mol. Biol. 2000;295:1211–1223. - PubMed

Publication types