Formation of sugar radicals in RNA model systems and oligomers via excitation of guanine cation radical

In previous work, we have shown that photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of DNA and its model compounds at 143 K results in the formation of neutral sugar radicals with substantial yield. In this report, we present electron spin resonance (ESR) and theoretical (DFT) evidence regarding the formation of sugar radicals after photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of one-electron-oxidized RNA model compounds (nucleosides, nucleotides and oligomers) at 143 K. Specific sugar radicals C5'*, C3'* and C1'* were identified employing derivatives of Guo deuterated at specific sites in the sugar moiety, namely, C1'-, C2'-, C3'- and C5'-. These results suggest C2'* is not formed upon photoexcitation of G*+ in one-electron-oxidized Guo and deuterated Guo derivatives. Phosphate substitution at C5'- (i.e., in 5-GMP) hinders formation of C5'* via photoexcitation at 143 K but not at 77 K. For the RNA-oligomers studied, we observe on photoexcitation of oligomer-G*+ the formation of mainly C1'* and an unidentified radical with a ca. 28 G doublet. The hyperfine coupling constants of each of the possible sugar radicals were calculated employing the DFT B3LYP/6-31G* approach for comparison to experiment. This work shows that formation of specific neutral sugar radicals occurs via photoexcitation of guanine cation radical (G*+) in RNA systems but not by photoexcitation of its N1 deprotonated species (G(-H)*). Thus, our mechanism regarding neutral sugar formation via photoexcitation of base cation radicals in DNA appears to be valid for RNA systems as well.

Oligoribonucleotide analogues containing a mixed backbone of phosphodiester and formacetal internucleoside linkages, together with vicinal 2'-O-methyl groups

Oligoribonucleotides containing formacetal internucleoside linkages have been prepared and studied by UV melting experiments. In RNA duplexes, the formacetal substitution is stabilizing (Deltat(m)=0 to +0.9 degrees C per modification) at physiological salt concentrations (0.1 M) but destabilizing (Deltat(m)=-0.4 to -0.8 degrees C per modification) at high salt concentrations (1 M); this suggests that reduction of electrostatic repulsion contributes substantially to the stabilization. The presence of 2'-O-Me substituents increases the stabilities of the duplexes (Deltat(m)=+0.5 to +1.1 degrees C per modification). The positive effects of formacetals and 2'-O-Me groups were independent and additive. (1)H NMR studies on monomeric model compounds containing 3'-(ethyl phosphate) or 3'-O-ethoxymethyl groups showed that the formacetal and 2'-O-Me substitutions shift the conformational equilibria of the ribose residues towards the North conformers by 5 to 12 %. Although the preference for the North conformers qualitatively correlates with increased duplex stabilities, changes in thermodynamic parameters (DeltaH degrees and TDeltaS degrees ) for formation of oligonucleotide duplexes and differences in dependence on concentrations of sodium acetate, sodium chloride and sodium perchlorate suggest that solvation effects are also important for the duplex stabilities. Overall the formacetal linkages fit well in A-type RNA duplexes, making them potentially interesting modifications for RNA-based gene-control strategies (e.g., antisense and RNA interference).

Fragmentation pathway studies of oligonucleotides in matrix-assisted laser desorption/ionization mass spectrometry by charge tagging and H/D exchange

The desorption and decompositions of synthesized oligonucleotides bearing fixed charge sites have been investigated by linear, delayed-extraction, reflecting and post-source decay mode matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. In contrast to the conventional [M + H]+ forms of unmodified molecules where a proton is likely attached to a nucleobase, here the charge is fixed at one of the termini. In this case the observed fragment ions always incorporate the charge-tag. H/D exchange experiments provide no evidence for intramolecular migration of protons on the phosphate backbone to initiate the fragmentation event. New unique pathways of proton migration from the ribose have been elucidated and are rationalized by a charge-remote fragmentation pathway.

Structural differences in the NOE-derived structure of G-T mismatched DNA relative to normal DNA are correlated with differences in (13)C relaxation-based internal dynamics

Detailed description of the characteristics of mismatched DNA that are distinct from normal DNA is vital to the understanding of how mismatch repair proteins are able to recognize and repair these DNA lesions. To this end, we have used nuclear Overhauser effect spectroscopy (NOESY)-based distance restraints and (13)C relaxation measurements to solve the solution structures and measure some of the internal dynamics of the G-T mismatched DNA oligomer d(CCATGCGTGG)(2) (GT) and its parent DNA sequence d(CCACGCGTGG)(2) (GC). In GT, the mismatched G7 is structurally perturbed much more than the mismatched T4 relative to their corresponding bases in GC. The degree of G7 displacement differs from previous high-resolution structures of G-T mismatch-containing B-DNA, suggesting a dependence of G-T mismatch-induced structural perturbation on sequence context. The internal dynamics of GC and GT differ on multiple timescales. The mismatched G7 of GT contains spins that decrease significantly in order in GT compared to GC, while spins in C6, T8, and A3 have significantly higher order in GT compared to GC. Linear correlations between helical parameters of GC and GT and the order of C-1' and aromatic methine carbon atoms relate differences in internal dynamics to the structures quantitatively. The dynamic differences between the normal and mismatched DNA signify changes in local flexibility that may be exploited by the mismatch repair system to bind mismatched DNA preferentially while ignoring normal DNA.

The hydrogen bonding and hydration of 2'-OH in adenosine and adenosine 3'-ethyl phosphate

The 2'-OH group has major structural implications in the recognition, processing, and catalytic properties of RNA. We report here intra- and intermolecular H-bonding of 2'-OH in adenosine 3'-ethyl phosphate (1), 3'-deoxyadenosine (2), and adenosine (3) by both temperature- and concentration-dependent NMR studies, as well as by detailed endo ((3)J(H,H)) and exocyclic ((3)J(H,OH)) coupling constant analyses. We have also examined the nature of hydration and exchange processes of 2'-OH with water by a combination of NOESY and ROESY experiments in DMSO-d(6) containing 2 mol % HOD. The NMR-constrained molecular modeling (by molecular mechanics as well as by ab initio methods both in the gas and solution phase) has been used to characterize the energy minima among the four alternative dihedrals possible from the solution of the Karplus equation for (3)J(H2',OH) and (3)J(H3',OH) to delineate the preferred orientation of 2'-O-H proton in 1 and 2 as well as for 2'/3'-O-H protons in 3. The NMR line shape analysis of 2'-OH gave the DeltaG(H-bond)(298K) of 7.5 kJ mol(-1) for 1 and 8.4 kJ mol(-1) for 3; similar analyses of the methylene protons of 3'-ethyl phosphate moiety in 1 also gave comparable DeltaG(H-bond)(298K) of 7.3 kJ mol(-1). The donor nature of the 2'-OH in the intramolecular H-bonding in 3 is evident from its relatively reduced flexibility [-TDeltaS++](2'-OH) = -17.9(+/-0.5) kJ mol(-1)] because of the loss of conformational freedom owing to the intramolecular 2'O-H...O3' H-bonding, compared to the acceptor 3'-OH in 3 [-TDeltaS++](3'-OH) = -19.8 (+/- 0.6) kJ mol(-1)] at 298 K. The presence of intramolecular 2'-OH...O3' H-bonding in 3 is also corroborated by the existence of weak long-range (4)J(H2',OH3') in 3 (i.e., W conformation of H2'-C2'-C3'-O3'-H) as well as by (3)J(H,OH) dependent orientation of the 2'- and 3'-OH groups. The ROESY spectra for 1 and 3 at 308 K, in DMSO-d(6), show a clear positive ROE contact of both 2'- and 3'-OH with water. The presence of a hydrophilic 3'-phosphate group in 1 causes a much higher water activity in the vicinity of its 2'-OH, which in turn causes the 2'-OH to exchange faster, culminating in a shorter exchange lifetime (tau) for 2'-OH proton with HOD in 1 (tau2'-OH: 489 ms) compared to that in 3 (tau2'-OH: 6897 ms). The activation energy (E(a)) of the exchange with the bound-water for 2'- and 3'-OH in 3 (48.3 and 45.0 kJ mol(-1), respectively) is higher compared to that of 2'-OH in 1 (31.9 kJ mol(-1)), thereby showing that the kinetic availability of hydrated 2'-OH in 1 for any inter- and intramolecular interactions, in general, is owing to the vicinal 3'-phosphate residue. It also suggests that 2'-OH in native RNA can mediate other inter- or intramolecular interactions only in competition with the bound-water, depending upon the specific chemical nature and spatial orientation of other functions with potential for hydrogen bonding in the neighborhood. This availability of the bound water around 2'-OH in RNA would, however, be dictated by whether the vicinal phosphate is exposed to the bulk water or not. This implies that relatively poor hydration around a specific 2'-OH across a polyribonucleotide chain, owing to some hydrophobic microenvironmental pocket around that hydroxyl, may make it more accessible to interact with other donor or acceptor functions for H-bonding interactions, which might then cause the RNA to fold in a specific manner generating a new motif leading to specific recognition and function. Alternatively, a differential hydration of a specific 2'-OH may modulate its nucleophilicity to undergo stereospecific transesterification reaction as encountered in ubiquitous splicing of pre-mRNA to processed RNA or RNA catalysis, in general.

NMR evidence for mechanical coupling of phosphate B(I)-B(II) transitions with deoxyribose conformational exchange in DNA

The conformational exchange of the phosphate and deoxyribose groups of the DNA oligomers d(GCGTACGC)(2) and d(CGCTAGCG)(2) have been investigated using a combination of homonuclear and heteronuclear NMR techniques. Two-state exchange between phosphate B(I) and B(II) conformations and deoxyribose N and S conformations was expressed as percent population of the major conformer, %B(I) or %S. Sequence context-dependent variations in %B(I) and %S were observed. The positions of the phosphate and deoxyribose equilibria provide a quantitative measure of the ps to ns timescale dynamic exchange processes in the DNA backbone. Linear correlations between %B(I), %S, and previously calculated model free (13)C order parameters (S(2)) were observed. The %B(I) of the phosphates were found to be correlated to the S(2) of the flanking C3' and C4' atoms. The %B(I) was also found to be correlated with the %S and C1' S(2) of the deoxyribose ring 5' of the phosphates. The %B(I) of opposing phosphates is correlated, while the %B(I) of sequential phosphates is anti-correlated. These correlations suggest that conformational exchange processes in DNA are coupled to each other and are modulated by DNA base sequence, which may have important implications for DNA-protein interactions.

Synthesis of abasic locked nucleic acid and two seco-LNA derivatives and evaluation of their hybridization properties compared with their more flexible DNA counterparts

To investigate the structural basis of the unique hybridization properties of LNA (locked nucleic acid) three novel LNA derivatives with modified carbohydrate parts were synthesized and evaluated with respect to duplex stabilities. The abasic LNA monomer (X(L), Figure 1) with the rigid carbohydrate moiety of LNA but no nucleobase attached showed no enhanced duplex stabilities compared to its more flexible abasic DNA counterpart (X, Figure 1). These results suggest that the exceptional hybridization properties of LNA primarily originate from improved intrastrand nucleobase stacking and not backbone preorganization. Two monocyclic seco-LNA derivatives, obtained by cleavage of the C1'-O4' bond of an LNA monomer or complete removal of the O4'-furanose oxygen atom (Z(L) and dZ(L), respectively, Figure 1), were compared to their acyclic DNA counterpart (Z, Figure 1). Even though they are more constrained than Z, the seco-LNA derivatives Z(L) and dZ(L) destabilize duplex formation even more than the flexible seco-DNA monomer Z.