RNA structure has been analyzed by biophysical method such as NMR (nuclear magnetic resonance), which has not been popular because the RNA with small size only is available for the structural analysis with NMR.1 So biochemical methods using structure specific enzymes and chemicals have widely been used for the analysis of RNA structure. [2][3][4][5][6][7][8]19 Enzymes and chemical which have mainly been used for probing RNA structure in solution, are doublestrand-specific RNase V1, single-strand-specific nuclease S1, RNase T1 which has the specificity for a guanine in single strand region, and kethoxal (3-ethoxy-1,1-dihydroxy-2-butanone), which modify the N1 and N2 of guanine in the single strand. Hydroxyl radical (•OH) has also been used for the high-order structure analysis of RNA. Exposed nucleotides are damaged by hydroxyl radical while nucleotides involved in tertiary contacts are protected from damage, making it a favorable approach for establishing exterior/ interior relations for RNA.9-15 Radicals are generated from Fe(II)-EDTA with hydrogen peroxide (H 2 O 2 ). Ascorbate (or DTT) is added to reduce Fe(III) to Fe(II). Hydrogen abstraction from the ribose 4' carbon leads to strand scission. In-line probing is also an RNA-structure probing method recently developed by Breaker group. [16][17][18] This method has been used to examine secondary structure of RNAs and whether RNAs undergo structural rearrangements under the different incubation conditions. In-line probing takes advantage of the fact that the spontaneous cleavage of RNA is dependent on the local structure at each internucleotide linkage. RNA degrades through a nucleophilic attack by the 2' oxygen on the adjacent phosphorus. Cleavage occurs efficiently when the attacking 2' oxygen, the phosphorus and the departing 5' oxygen of the phosphodiester linkage are in a linear configuration. Linkages in double strand region of a folded RNA show resistance to cleavage because it is difficult for the atoms to be held in an in-line configuration. However, if folding does not restrict its structure, linkages occasionally take on in-line geometry through random motion and therefore are subject to a spontaneous cleavage.RNA aptamers which are capable of interacting with the guanine-rich sequence, were selected from a random-sequence RNA library. In this work, the secondary structure of the RNA aptamer 11-48-2, one of the selected RNA aptamers (Fig. 1) was predicted with the CLC RNA workbench ver. 4.2 program accessed on the internet (www.clcbio.com/ index.php?id=1042) and examined with RNA structural probes such as RNase T1, RNase V1 and nuclease S1. Because prior to getting the information for the interaction between an RNA aptamer and a ligand RNA, the determination of the structure of selected RNA aptamers is important.The structure of RNA aptamer 11-48-2 including primer sequence was probed in binding buffer with RNase T1, RNase V1, and nuclease S1 (Fig. 2). G16, G23 and G45
