Abstract
The synthesis of two 5′-end (4-dimethylamino)azobenzene conjugated G-quadruplex forming aptamers, the thrombin binding aptamer (TBA) and the HIV-1 integrase aptamer (T30695), was performed. Their structural behavior was investigated by means of UV, CD, fluorescence spectroscopy, and gel electrophoresis techniques in K+-containing buffers and water-ethanol blends. Particularly, we observed that the presence of the 5′-(4-dimethylamino)azobenzene moiety leads TBA to form multimers instead of the typical monomolecular chair-like G-quadruplex and almost hampers T30695 G-quadruplex monomers to dimerize. Fluorescence studies evidenced that both the conjugated G-quadruplexes possess unique fluorescence features when excited at wavelengths corresponding to the UV absorption of the conjugated moiety. Furthermore, a preliminary investigation of the trans-cis conversion of the dye incorporated at the 5′-end of TBA and T30695 showed that, unlike the free dye, in K+-containing water-ethanol-triethylamine blend the trans-to-cis conversion was almost undetectable by means of a standard UV spectrophotometer.
Highlights
The higher-order noncanonical G-quadruplex structures (Qs) arising from the reverseHoogsteen-like pairing of four guanines (G-tetrad) are the most frequently studied DNA structures.Their involvement in important biological functions, such as telomere maintenance [1,2,3], DNA-protein recognition [4,5] and protein inhibition [6,7] has been supposed
The stability of the new phosphoramidite found in each cycle of the automated solid-phase synthesis under standard chemical conditions was verified before its incorporation at the 50 -end of the two selected aptamer sequences, executing a coupling step with standard solid supports in controlled pore glass (CPG) functionalized with G or T
T30695 and thrombin binding aptamer (TBA) were first synthesized by automated solid phase synthesis and, still anchored to the solid support, coupled manually with compound 7 using two coupling cycles
Summary
The higher-order noncanonical G-quadruplex structures (Qs) arising from the reverseHoogsteen-like pairing of four guanines (G-tetrad) are the most frequently studied DNA structures.Their involvement in important biological functions, such as telomere maintenance [1,2,3], DNA-protein recognition [4,5] and protein inhibition [6,7] has been supposed. The higher-order noncanonical G-quadruplex structures (Qs) arising from the reverse. Hoogsteen-like pairing of four guanines (G-tetrad) are the most frequently studied DNA structures. Their involvement in important biological functions, such as telomere maintenance [1,2,3], DNA-protein recognition [4,5] and protein inhibition [6,7] has been supposed. Qs are often modified with suitable molecules in order to tune their stability or to provide them with specific properties such as fluorescence, chemical resistance, etc.
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