G-quadruplex induced stabilization by 2'-deoxy-2'-fluoro-D-arabinonucleic acids (2'F-ANA)

The impact of 2'-deoxy-2'-fluoroarabinonucleotide residues (2'F-araN) on different G-quadruplexes derived from a thrombin-binding DNA aptamer d(G(2)T(2)G(2)TGTG(2)T(2)G(2)), an anti-HIV phosphorothioate aptamer PS-d(T(2)G(4)T(2)) and a DNA telomeric sequence d( G(4)T(4)G(4)) via UV thermal melting (T-m) and circular dichroism ( CD) experiments has been investigated. Generally, replacement of deoxyguanosines that adopt the anti conformation (antiguanines) with 2'F-araG can stabilize G-quartets and maintain the quadruplex conformation, while replacement of syn-guanines with 2'F-araG is not favored and results in a dramatic switch to an alternative quadruplex conformation. It was found that incorporation of 2'F-araG or T residues into a thrombin-binding DNA G-quadruplex stabilizes the complex (Delta T-m up to similar to+3 degrees C/2' F- araN modification); 2'F-araN units also increased the half-life in 10% fetal bovine serum (FBS) up to 48-fold. Two modified thrombin-binding aptamers (PG13 and PG14) show an approximately 4-fold increase in binding affinity to thrombin, as assessed via a nitrocellulose filter binding assay, both with increased thermal stability (similar to 1 degrees C/2'F-ANA modification increase in T-m) and nuclease resistance (4-7-fold) as well. Therefore, the 2'-deoxy-2'-fluoro-D-arabinonucleic acid (2'F-ANA) modification is well suited to tune ( and improve) the physicochemical and biological properties of naturally occurring DNA G-quartets.