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Thermodynamic examination of the ion effect and cellular crowding on nucleic acids (LB210)
Author(s) -
Comfort Hallie,
Grover Neena
Publication year - 2014
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.28.1_supplement.lb210
Subject(s) - rna , nucleic acid , chemistry , pyrophosphate , biophysics , folding (dsp implementation) , polyethylene glycol , peg ratio , biochemistry , thiamine pyrophosphate , enzyme , cofactor , biology , finance , gene , electrical engineering , economics , engineering
Ions play essential roles in forming functional RNA structures and can act as nucleophiles in RNA catalytic reactions. Under physiological conditions, folding of RNA requires potassium and magnesium ions. Nearly 30% of the cellular volume is occupied by ions and macromolecules. Cellular crowding affects the stability of nucleic acids by changing the availability of ions and water (excluded volume effect). To mimic cellular conditions, polyethylene glycol (PEG) is used as a “crowder.” RNA folding experiments on Group I introns show formation of more compact RNA structures at lower concentrations of magnesium ions in the presence of PEG. In this study, we are using the pyrophosphate sensor helix of the thiamine pyrophosphate (TPP)‐ binding riboswitch to examine the ion and crowding effects on small RNA. The stability of multiple bulge and helix constructs was studied using thermal denaturation experiments in varying ion and PEG conditions. Different cations, anions, and PEG concentrations influence small DNA and RNA stability. Comparative thermodynamic data from these experiments will be presented. Grant Funding Source : This work was supported by NSF grant, MCB‐0950582 to NG.