2-aminopurine fluorescent probe

The photophysical properties of adenine have intrigued chemists from early on. Broo studied adenine and 2-aminopurine (2AP) in order to understand their differences in photophysical properties. Adenine like all natural nucleobases has very short excited state lifetimes and low quantum yields of fluorescence, while 2AP, which differs from adenine in the position of the amino group, has long lifetimes and strong fluorescence, making it a very useful fluorescent probe. In Broo s work it was observed that the first excited state is a nn at vertical excitation but crosses with an nn state which becomes the Si state adiabatically at the minimum. The large out-of-plane distortion on the nn state opens up a deactivation channel in adenine compared to 2AP. In 2AP, on the other hand, the Si state always has a 7T7r character. 

Among fluorescence probes of nucleic acid structure, dynamics, and folding, 2-aminopurine (2AP) is unique in that its introduction into an RNA can often be done with little perturbation of the RNA structure. Whereas other fluorescent nucleotide analogs have higher quantum yields than 2AP, their modifications have the potential to disrupt secondary and... 

Three fluorescent purine analogs will be described here 2-aminopurine (2AP) [183] and 8-vinyladenine (8VAD), both of which mimic adenine, and N1,N6-ethenoadenine (e-AD). Their structures are shown in Figure 11-15. 2AP is probably the most widely used fluorescent DNA base analog, being utilized as a probe for DNA conformational dynamics [184, 185], due to the environmental specificity of... 

Rachofsky EL, Osman R, Ross JBA (2001) Probing structure and dynamics of DNA with 2-aminopurine effects of local environment on fluorescence. Biochem 40 946-956... 

The fluorescence lifetimes of the four natural DNA bases within the femtosecond range are too short to be useful as spectroscopic probes to characterize the solvation dynamics of DNA (31). The minor groove binder Hoechst 33258, the fluorescent adenine analog 2-Aminopurine (2Ap), and the base pair mimic coumarine 102-abasic site are better probes because they exhibit longer lifetimes and better solvatochromic properties. Of the two base pair analogs, the coumarine 102-abasic site base pair mimic disrupts the native DNA structure more than the adenine analog 2Ap. However, the spectroscopic characteristics of the former are superior to those of 2Ap for probing solvation dynamics. 

DNA polymerase incorporation of the mutagenic 2-hydroxy-dA has been examined and found to lead to GC- AT transition mutations." The synthesis, incorporation and repair of etheno-dA adducts have been reported." The use of a C2-alkaryl modified adenosine gave rise to enhanced stability towards a mutant UlA protein in which a conserved phenylalanine was substituted for alanine. ° 2-Aminopurine (2-AP) has been widely used because of its fluorescent properties. However, 2-AP dinucleotide also exhibits a distinct positive CD band at 326 nm, and this property has been used to probe changes in local conformation of ODNs containing (2-AP)2 by CD measurements." ... 

Figure 2.11 Fluorescent purines. Two very useful non-invasive DNA (base fluorophores that can be included by solid phase DNA synthesis are 2-aminopurine (left) and 3-methyl-isoxanthopterin (right). The fluorescence quantum yield depends on the base stacking, and both bases are useful probes of conformational change/state in DNA.

Boc- and Fmoc-terminated fluorescent fluorescein PNA monomer units were synthesized by means of solid-phase synthesis, and the products had photophysical properties comparable to nonmodifled fluorescein conjugates. 2-Aminopurine (2-ap) was the first fluorophore incorporated into a PNA strand for the purpose of examining PNA-DNA complexation via fluctuation in fluorescence emission. A more sophisticated sensing design was introduced by Seitz et al. that utilized the intercalator dye thiazole orange, termed a forced intercalation probe (FIT probe), for the determination of base pair mismatches within a duplex. ... 

To directly probe charge-transfer reactions between two DNA bases, two fluorescent analogues of adenine, 2-aminopurine (A2) and l,N -ethenoadenine (A ), were employed as photooxidants (Figure ID) [16]. In aqueous solution, both of these bases are efficiently quenched by deazaguanine (Z) and guaifine (G), with only small amounts of quenching observed with inosine (I). 

The main N2-modified adenosine used is 2-aminopurine, which is frequently used as an adenine surrogate because it maintains hydrogen bonding with thymine and is fluorescent. Applications of this analogue are described in section 3.5. A synthesis of the E. coli tRNA anticodon arm containing 2-methyladenosine has been reported,and the role of 2-methyladenosine in the anticodon loop of E. coli tRNA has been reported. A spin label has been attached to the C2-position of adenine to probe oligonucleotide structures by EPR. ... 

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