Probing structure and function with alternative nucleic acids bearing 2',5'-linked, zwitterionic, and isocytosine-isoguanine components

The development of isoguanosine: from discovery, synthesis, and modification to supramolecular structures and potential applications

First systematical review of isoguanosine, an unnatural base, as an isomer of guanosine shows significant differences in diverse properties.

Parallel DNA double helices incorporating isoG or m5isoC bases studied by FTIR, CD and molecular modeling

FTIR spectroscopy has been used to follow the formation of parallel stranded DNA duplexes incorporating isoG or m5isoC bases and determine their base pairing scheme. The results are discussed in comparison with data concerning anti-parallel duplexes with comparable base composition and sequence. In duplexes containing A-T and isoG-C or m5isoC-G base pairs shifts of the thymine C2=O2 and C4=O4 carbonyl stretching vibrations (to lower and higher wavenumbers, respectively, when compared to their positions in classical cis Watson-Crick (WC) base pairs) reflect the formation of trans Watson-Crick A-T base pairs. All carbonyl groups of cytosines, m5isocytosines, guanines and isoguanines are found to be involved in hydrogen bonds, indicative of the formation of isoG-C and m5isoC-G base pairs with three hydrogen bonds. Molecular modeling shows that both structures form regular right handed helices with C2'endo sugar puckers. The role of the water content on the helical conformation of the parallel duplexes has been studied by FTIR and CD. It is found that a conformational transition similar to the B --> A transition observed for anti-parallel duplexes induced by a decrease of the water content of the samples can occur for these parallel duplexes. Their helical flexibility has been evidenced by FTIR studies on hydrated films by the emergence of absorption bands characteristic of A type geometry, in particular by an S-type --> N-type repuckering of the deoxyribose. All sugars in the parallel duplex with alternating d(isoG-A)/d(C-T) sequence can adopt an N-type geometry in low water content conditions. The conformational transition of the parallel hairpin duplex with alternating d(isoG-A)/d(C-T) sequence was followed by circular dichroism in water/trifluoroethanol solutions and its free energy at 0 degrees C was estimated to be 6.6 +/- 0.3 kcal mol(-1).

Photochemical syn-anti isomerization reactions in N2-hydroxyisocytosines--an experimental matrix isolation and theoretical study

N2-hydroxyisocytosine and 1-methyl-N2-hydroxyisocytosine were studied using a matrix isolation technique combined with infrared absorption spectroscopy. For N2-hydroxyisocytosine isolated in an Ar matrix (at 10 K), two imino-oxo isomers, one with the hydroxyimino =N-OH group directed toward the N1-H group (the form called further anti) and the second with the =N-OH group directed toward N3-H (syn), were observed in the ratio 1.4:1. The syn isomer is converted totally to the anti form after UV (lambda > 295 nm) irradiation of the matrix. A small amount of the N(3)H-hydroxy-amino tautomer of N2-hydroxyisocytosine was also detected in the matrix. This form did not react photochemically. For 1-methyl-N2-hydroxyisocytosine, only the syn form of the imino-oxo tautomer was observed after deposition of the matrix. UV (lambda > 295 nm) irradiation induced a photoreaction converting this isomer into the anti form. After 15% of the starting material had been converted into the product, a photostationary state was achieved, and no further progress of the reaction was observed. Subsequent UV irradiation (lambda > 335 nm) caused a back reaction, leading to a disappearance of the anti form and to the recovery of the initial syn isomer. All isomers were identified by comparing their experimental IR spectra with the spectra theoretically calculated at the DFT(B3LYP)/6-31G(d,p) level, where DFT is the density functional theory. Good agreement between the observed and predicted patterns of the spectral lines allowed for reliable identification. The experimental IR spectra were interpreted and discussed. The relative energies of the 12 isomers of N2-hydroxyisocytosine were calculated at the MP2/6-31G(d,p) and MP4//MP2/6-31G(d,p) levels. For six isomers of 1-methyl-N2-hydroxyisocytosine, the calculations were carried out at the MP2/6-31G(d,p) level. The anti form of the imino-oxo tautomer of N-hydroxyisocytosine and the syn form of the imino-oxo tautomer of 1-methyl-N2-hydroxyisocytosine were predicted to be the most stable.