DNA Aptamers are Functional Molecular Recognition Sensors in Protic Ionic Liquids

Abstract

The function and structural changes of an AMP molecular aptamer beacon and its molecular recognition capacity for its target, adenosine monophosphate (AMP), was systematically explored in solution with a protic ionic liquid, ethylammonium nitrate (EAN). It could be proven that up to 2 M of EAN in TBS buffer, the AMP molecular aptamer beacon was still capable of recognizing AMP while also maintaining its specificity. The specificity was proven by using the guanosine monophosphate (GMP) as target; GMP is structurally similar to AMP but was not recognized by the aptamer. We also found that in highly concentrated EAN solutions the overall amount of double stranded DNA formed, as well as its respective thermal stability, diminished gradually, but surprisingly the hybridization rate (kh ) of single stranded DNA was significantly accelerated in the presence of EAN. The latter may have important implications in DNA technology for the design of biosensing and DNA-based nanodevices in nonconventional solvents, such as ionic liquids.

Active biopolymers in green non-conventional media: a sustainable tool for developing clean chemical processes

“…91 Related to this characteristic of molecular biosensing through structural changes in DNA sequences, aptamers are single stranded nucleic acids (ssDNA or RNA) that specifically recognize desired targets, such as proteins, amino acids, antibiotics or small molecules. 92 In this way, Machado et al 93 have studied the influence of ethylammonium nitrate on the capacity of molecular recognition of an AMP aptamer molecular beacon. At high concentrations, this IL reduced the thermal stability of the intramolecular dsDNA structure of the probe, and accelerates the hybridization rate of ssDNA.…”

Aqueous ionic liquids in comparison with standard co-solutes

“…In the latter case, novel magnetic ILs turn out to be particularly interesting for the purpose of effective extraction and preservation of DNA (Clark et al 2015a(Clark et al , b, 2016. For industrial purposes, ILs are being currently applied in DNA-based biosensors (Chen et al 2013;Sun et al 2013;Machado et al 2014), or to assist a vast variety of methods in genetic manipulations, including genomic sequencing (Kulkarni and Mukherjee 2016), cloning (Li et al 2013b), or gene delivery and transformation (Zhang et al 2009;Soni et al 2015). Moreover, replacement of standard aqueous solutions by ILs as solvents and catalysts for laboratory purposes enabled to overcome certain technological limitations associated with DNA nanotechnology (Nishimura et al 2005;Dandia et al 2013) due to enhanced DNA stability and solubility in ILs (Zhang et al 2009;Sharma et al 2015;Jumbri et al 2016;Mishra et al 2016).…”

Ionic liquids as solvents of polar and non-polar solutes: affinity and coordination

“…Typical ILs are composed of, but not limited to, an organic cation (most often an alkyl-substituted imidazolium, a pyridinium or a quaternary ammonium ion) and an inorganic anion. 1 In particular, solvent properties of methylimidazolium-based ILs have been widely studied, as media for chemical reactions, catalysis, 2,3 gas separation 4 and for the solvation of bigger systems such as DNA, [5][6][7][8][9][10] nanotubes, 2 or enzymes. [11][12][13][14][15][16][17] Apart from the wealth of experimental research conducted on the properties of methylimidazolium based ILs, [18][19][20][21][22][23][24][25][26][27][28][29] a great effort has been made by theoreticians to provide insight into their physicochemical properties, [30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45]…”