This work was supported by grants from the National Institute of Health RO1-GM085130 and National Science Foundation MCB0929394. We thank Dr. Marion Schmidt for her hospitality and for allowing us to film in her laboratory.

1. Preparation of Footprinting Reagents
<ol>
	<li>Prepare a 10x reaction buffer containing 100 mM sodium cacodylate, 1 mM EDTA, and 1 M KCl. Adjust the pH to 7.4. Filter the buffer using a 0.2 &mu;M acetate filter device (Nalgene). Remark: do not pipet RNA directly into 10x buffer.</li>
	<li>Prepare the titration reaction mix for each reaction as indicated in Table 1. The volume of the titration mix (1x buffer and Mg(II) at the desired concentration) should be 90 &mu;l, before adding 10&mu;l of RNA in 1x buffer.</li>
	...

<ol>
	<li>Tullius, T. D., Dombroski, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hydroxyl+radical+"footprinting":+high-resolution+information+about+DNA-protein+contacts+and+application+to+lambda+repressor+and+Cro+protein.">Hydroxyl radical "footprinting": high-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein.</a> Proc. Natl. Acad. Sci. U.S.A. 83, 5469-5473 (1986).</li><li>Celander, D. W., Cech, T. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Iron(II)-ethylenediaminetetraacetic+acid+catalyzed+cleavage+of+RNA+and+DNA+oligonucleotides:+similar+reactivity+toward+single-+and+double-stranded+forms.">Iron(II)-ethylenediaminetetraacetic acid catalyzed cleavage of RNA and DNA oligonucleotides: similar reactivity toward single- and double-stranded forms.</a> Biochemistry. 29, 1355-1361 (1990).</li><li>Celander, D. W., Cech, T. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visualizing+the+higher+order+folding+of+a+catalytic+RNA+molecule.">Visualizing the higher order folding of a catalytic RNA molecule.</a> Science. 251, 401-407 (1991).</li><li>Sclavi, B., Sullivan, M., Chance, M. R., Brenowitz, M., Woodson, S. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+folding+at+millisecond+intervals+by+synchrotron+hydroxyl+radical+footprinting.">RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting.</a> Science. 279, 1940-1943 (1998).</li><li>Tullius, T. D., Dombroski, B. A., Churchill, M., Kam, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hydroxyl+radical+footprinting:+a+high-resolution+method+for+mapping+protein-DNA+contacts.">Hydroxyl radical footprinting: a high-resolution method for mapping protein-DNA contacts.</a> Methods. Enzym. 155, 537-558 (1987).</li><li>Milligan, J. F., Groebe, D. R., Witherell, G. W., Uhlenbeck, O. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Oligoribonucleotide+synthesis+using+T7+RNA+polymerase+and+synthetic+DNA+templates.">Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates.</a> Nucleic. Acids. Res. 15, 8783-8798 (1987).</li><li>Schlatterer, J. C., Brenowitz, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Complementing+global+measures+of+RNA+folding+with+local+reports+of+backbone+solvent+accessibility+by+time+resolved+hydroxyl+radical+footprinting.">Complementing global measures of RNA folding with local reports of backbone solvent accessibility by time resolved hydroxyl radical footprinting.</a> Methods. 49, 142-147 (2009).</li><li>Sambrook, J., Russell, D. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Molecular Cloning: A Laboratory Manual. , (2001).</li><li>Zaug, A. J., Grosshans, C. A., Cech, T. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sequence-specific+endoribonuclease+activity+of+the+Tetrahymena+ribozyme:+enhanced+cleavage+of+certain+oligonucleotide+substrates+that+form+mismatched+ribozyme-substrate+complexes.">Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes.</a> Biochemistry. 27, 8924-8931 (1988).</li><li>Knapp, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enzymatic+approaches+to+probing+of+RNA+secondary+and+tertiary+structure.">Enzymatic approaches to probing of RNA secondary and tertiary structure.</a> Methods. Enzym. 180, 192-212 (1989).</li><li>Slatko, B. E., Albright, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Denaturing+gel+electrophoresis+for+sequencing.">Denaturing gel electrophoresis for sequencing.</a> Curr. Protoc. Mol. Biol. Chapter 7, Unit 7.6-Unit 7.6 (2001).</li><li>Das, R., Laederach, A., Pearlman, S. M., Herschlag, D., Altman, R. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SAFA:+semi-automated+footprinting+analysis+software+for+high-throughput+quantification+of+nucleic+acid+footprinting+experiments.">SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments.</a> RNA. 11, 344-354 (2005).</li><li>Simmons, K., Martin, J. S., Shcherbakova, I., Laederach, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+quantification+and+analysis+of+kinetic+*OH+radical+footprinting+data+using+SAFA.">Rapid quantification and analysis of kinetic *OH radical footprinting data using SAFA.</a> Methods. Enzym. 468, 47-66 (2009).</li><li>Uchida, T., He, Q., Ralston, C. Y., Brenowitz, M., Chance, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Linkage+of+monovalent+and+divalent+ion+binding+in+the+folding+of+the+P4-P6+domain+of+the+Tetrahymena+ribozyme.">Linkage of monovalent and divalent ion binding in the folding of the P4-P6 domain of the Tetrahymena ribozyme.</a> Biochemistry. 41, 5799-5806 (2002).</li><li>Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R., Doudna, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Crystal+structure+of+a+group+I+ribozyme+domain:+principles+of+RNA+packing.">Crystal structure of a group I ribozyme domain: principles of RNA packing.</a> Science. 273, 1678-1685 (1996).</li><li>Petri, V., Brenowitz, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+nucleic+acids+footprinting:+thermodynamic+and+kinetic+approaches.">Quantitative nucleic acids footprinting: thermodynamic and kinetic approaches.</a> Curr. Opin. Biotechnol. 8, 36-44 (1997).</li><li>Takamoto, K., Das, R., He, Q., Doniach, S., Brenowitz, M., Herschlag, D., Chance, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Principles+of+RNA+compaction:+insights+from+the+equilibrium+folding+pathway+of+the+P4-P6+RNA+domain+in+monovalent+cations.">Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations.</a> J. Mol. Biol. 343, 1195-1206 (2004).</li><li>Brenowitz, M., Senear, D. F., Shea, M. A., Ackers, G. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+DNase+footprint+titration:+a+method+for+studying+protein-DNA+interactions.">Quantitative DNase footprint titration: a method for studying protein-DNA interactions.</a> Methods. Enzym. 130, 132-181 (1986).</li><li>Shcherbakova, I., Mitra, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hydroxyl-radical+footprinting+to+probe+equilibrium+changes+in+RNA+tertiary+structure.">Hydroxyl-radical footprinting to probe equilibrium changes in RNA tertiary structure.</a> Methods. Enzym. 468, 31-46 (2009).</li><li>Howlett, G. J., Minton, A. P., Rivas, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analytical+ultracentrifugation+for+the+study+of+protein+association+and+assembly.">Analytical ultracentrifugation for the study of protein association and assembly.</a> Curr. Opinion. Chem. Biol. 10, 430-436 (2006).</li><li>McGinnis, J. L., Duncan, C. D., Weeks, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+SHAPE+and+hydroxyl+radical+analysis+of+RNA+structure+and+ribonucleoprotein+assembly.">High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assembly.</a> Methods. Enzym. 468, 67-89 (2009).</li><li>Jonikas, M. A., Radmer, R. J., Laederach, A., Das, R., Pearlman, S., Herschlag, D., Altman, R. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coarse-grained+modeling+of+large+RNA+molecules+with+knowledge-based+potentials+and+structural+filters.">Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters.</a> RNA. 15, 189-199 (2009).</li></ol>

Hydroxyl radical footprinting is a valuable tool to assess the solvent accessible surface area of nucleic acids. Qualitative and quantitative formation of tertiary structure14 can be followed as a function of parameters such as ion type and concentration, pH, temperature, binding proteins or folding co-factors. The compelling combination of a straight forward and inexpensive protocol and the resulting solvent accessibility and folding information on a single-nucleotide level makes this method very attractive. ...

<table border="1">
	<tbody>
		<tr>
			<th>Name</th>
			<th>Company</th>
			<th>Cat#</th>
		</tr>
		<tr>
			<td>Sodium Cacodylate
			(Caution! Toxic)	 	
			</td>
			<td>Sigma</td>
			<td>C4945-25g</td>
		</tr>
		<tr>
			<td>EDTA (0.5 M)</td>
			<td>Ambion</td>
			<td>AM9260G</td>
		</tr>
		<tr>
			<td>DEPC treated water</td>
			<td>Ambion</td>
			<td>AM9915G</td>
		</tr>
		<tr>
			<td>Sodium Acetate (3 M)</td>
			<td>Ambion</td>
			<td>AM9740</td>
		</tr>
		<tr>
			<td>MgCl2 (1 M)</td>
			<td>Ambion</td>
			<td>AM9530G</td>
		</tr>
		<tr>
			<td>Urea</td>
			<td>Ambion</td>
			<td>AM9902</td>
		</tr>
		<tr>
			<td>Sodium Citrate</td>
			<td>Sigma</td>
			<td>W302600</td>
		</tr>
		<tr>
			<td>tRNA</td>
			<td>Sigma</td>
			<td>R-7876</td>
		</tr>
		<tr>
			<td>Sodium-L-ascorbate</td>
			<td>Sigma</td>
			<td>A7631-25g</td>
		</tr>
		<tr>
			<td>Fe(NH4)2(SO4)2 . 6 H2O</td>
			<td>Sigma</td>
			<td>F1543-500g</td>
		</tr>
		<tr>
			<td>RNase T1</td>
			<td>Fermentas</td>
			<td>EN0541</td>
		</tr>
		<tr>
			<td>Hydrogen Peroxide (30%)</td>
			<td>Sigma</td>
			<td>349887</td>
		</tr>
	</tbody>
</table>

monitoring equilibrium changes in rna structure by 'peroxidative' and 'oxidative' hydroxyl radical footprinting

RNA molecules play an essential role in biology. In addition to transmitting genetic information, RNA can fold into unique tertiary structures fulfilling a specific biologic role as regulator, binder or catalyst. Information about tertiary contact formation is essential to understand the function of RNA molecules. Hydroxyl radicals (&bull;OH) are unique probes of the structure of nucleic acids due to their high reactivity and small size.1 When used as a footprinting probe, hydroxyl radicals map the solvent accessible surface of the phosphodiester backbone of DNA1 and RNA2 with as fine as single nucleotide resolution. Hydroxyl radical footprinting can be used to identify the nucleotides within an intermolecular contact surface, e.g. in DNA-protein1 and RNA-protein complexes. Equilibrium3 and kinetic4 transitions can be determined by conducting hydroxyl radical footprinting as a function of a solution variable or time, respectively. A key feature of footprinting is that limited exposure to the probe (e.g., 'single-hit kinetics') results in the uniform sampling of each nucleotide of the polymer.5
In this video article, we use the P4-P6 domain of the Tetrahymena ribozyme to illustrate RNA sample preparation and the determination of a Mg(II)-mediated folding isotherms. We describe the use of the well known hydroxyl radical footprinting protocol that requires H2O2 (we call this the 'peroxidative' protocol) and a valuable, but not widely known, alternative that uses naturally dissolved O2 (we call this the 'oxidative' protocol). An overview of the data reduction, transformation and analysis procedures is presented.

Watch this Scientific Journal Video about Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting at JoVE.com

Monitoring Equilibrium Changes in RNA Structure by &#039;Peroxidative&#039; and &#039;Oxidative&#039; Hydroxyl Radical Footprinting

This protocol describes how to quantify the Mg(II)-dependent formation of RNA tertiary structure by two methods of hydroxyl radical footprinting.

Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting

RNA molecules play an essential role in biology. In addition to transmitting genetic information, RNA can fold into unique tertiary structures fulfilling ...

monitoring-equilibrium-changes-rna-structure-peroxidative-oxidative

Research

JoVE Journal

Biology

14.2K ビュー.  Hunter College. このプロトコルは、Mg（II）依存性ヒドロキシルラジカルフットプリンティングの2つの方法でRNA三次構造の形成を定量化する方法について説明します。