Structural features of the L-argininamide-binding DNA aptamer studied with ESI-FTMS.
The 24-mer DNA aptamer of Harada and Frankel (Harada, K.; Frankel, A. D. EMBO J. 1995, 14, 5798-5811) that binds L-argininamide (L-Arm) was studied by electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). This DNA folds into a stem and loop such that the loop is able to engulf L-Arm. As controls, two derivatives of the same base composition, one with the same stem but a scrambled loop and the other with no ability to form a secondary structure, were studied. The two DNAs that could fold into stem-loop structures showed a more negatively charged distribution of ions than the linear control. This tendency was preserved in the presence of ligand; complexes expected to have more secondary structure had ions with more negative charges. Distinct species corresponding to no, one, and two bound L-Arm molecules were observed for each DNA. The fractional peak intensities were fit to a straightforward binding model and binding constants were obtained. Thus, ESI-FTMS can provide both qualitative and quantitative data regarding the structure of DNA and its interactions with noncovalent ligands.
Guo
Xinhua
X
Green Chemistry and Process Laboratory, Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, P R China.
Liu
Zhiqiang
Z
Liu
Shuying
S
Bentzley
Catherine M
CM
Bruist
Michael F
MF
D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001120:Arginine / Q000031:analogs & derivatives* / Q000737:chemistry; D005583:Fourier Analysis; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D044366:Transition Temperature
D052157:Aptamers, Nucleotide; C069339:argininamide; D001120:Arginine