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Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Interplay of Water molecules and Mg2+ ions in stability of RNA containing non-Watson-Crick base pairs

The segments of RNA, containing non-Watson-Crick base pairs, are stabilized by external factors like other part of RNA, proteins or metal ions. Eubacterial 5S RNA Loop-E [pdb: 354D] is made up of 11 Base-pairs, where 7 of those are Non-Watson-Crick type (fig: a). Non-Watson-crick base pairs of Loop-E creates specific identification site for ribosomal protein L25. Non-Watson-Crick base pairs in loop-E are stabilized by Mg2+ ions through water mediated interactions. The Mg2+ ions stabilize eubacterial loop-E in different ways than other small RNA oligomers (Serra and Westhop (2002)). Earlier study explained the dynamics of water molecules around Mg2+ ions and bases and showed the stability of base pairs of loop E even in absence of Mg2+ ions (Auffinger and Westhof (2003), Reblova and Sponer (2004)). The analysis on stabilization of RNA base pairs by water molecules working as H-bonding clamps (Chawla and Cavallo (2014)) showed the possibility of specific water molecule network around these non-WC base pairs. In current work we are trying to identify and analyze the gradual adaptation of water network and dynamics around non-Watson-Crick base pairs with respect to change in positions of deep grooved Mg 2+ ions (fig: b). The free energy profile of loop-E with respect to position of Mg 2+ ions and its effect on other part of RNA will also be discussed.

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Acknowledgement: Department of Biotechnology (DBT) for the BINC fellowship provided to SS.

References
    M. J. Serra, M. J., J. D., T. D., B. L., K. R. & Westhop, E. (2002). Effects of magnesium ions on the stabilization of RNA oligomers of defined structures. RNA 8, 307-323.

    P. Auffinger, P. A., L. B. & Westhof, E. (2003). The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. Chemistry & Biology 10, 551-561.

    K. Reblova, K.R., N. S., J. K., N. B. & Sponer, J. (2004). Long-Residency Hydration, Cation Binding, and Dynamics of Loop E/Helix IV rRNA-L25 Protein Complex. Biophysical Journal 87, 3397-3412.

    M. Chawla, M.C., S. A., R. O. & Cavallo, L. (2014). Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs, Nuc. Acids Res. 42, 714-726.


Sudhanshu Shanker
Pradipta Bandyopadhyay

School of Computational and integrative Sciences
Jawaharlal Nehru University
New Delhi, 110067, India

Mob: (+91) 9971965854