Background: 8-OxoG is a major oxidative lesion in DNA and is associated with cancer. Results: Kinetic and mass spectrometric studies demonstrate that human polymerase bypasses 8-oxoG in a largely error-free manner. Conclusion: Arginine 61 from the finger domain plays a key role in error-free bypass at the insertion stage. Significance: In addition to photo-adducts and cisplatinated DNA, polymerase might also be involved in accurate bypass of 8-oxoG in vivo.

The way it is: Incorporation of 2′‐deoxy‐2′‐fluororibonucleotides (2′‐F RNA) into RNA oligomers leads to a marked increase in duplex stability. Using NMR spectroscopy (see picture) with native (red circles) and 2′‐F modified (black squares) RNA duplexes, and UV melting and osmotic stress experiments the higher stability of 2′‐F RNA relative to RNA is shown to be the result of both increased Watson–Crick H‐bonding strength and favorable base stacking.

Background: Abasic sites are the most common lesion in DNA. Results: Kinetic and mass spectrometric assays demonstrate that human polymerase (pol) preferentially inserts A and G opposite an abasic site. Conclusion: Crystal structures reveal H-bonding between incoming ATP and GTP and the 5Ј-phosphate of the abasic moiety. Significance: Abasic site bypass by pol follows a "purine rule" for insertion, with formation of frameshifts.

Background: Arg-61 and Gln-38 of human DNA polymerase (hpol) play important roles in the catalytic reaction. Results: Mutations R61M or Q38A/R61A dramatically disrupt the activity of hpol . Conclusion: Polarized water molecules can mimic and partially compensate for the missing side chains of Arg-61 and Gln-38 in the Q38A/R61A mutant. Significance: The positioning and positive charge of Arg-61 synergistically contribute to the activity of hpol , with additional effects of Gln-38.

Binding target strands with single base selectivity at a terminal position is difficult with natural DNA or RNA hybridization probes. Nature uses a degenerate genetic code that is based on RNA:RNA codon:anticodon duplexes tolerating wobble base pairs at the terminus. The importance of short RNA strands in regulatory processes in the cell make it desirable to develop receptor-like approaches for high fidelity binding, even at the very 3'-terminus of a probe. Here, we report the three-dimensional structure of a DNA duplex with a 3'-terminal 2'-anthraquinoylamido-2'-deoxyuridine (Uaq) residue that was solved by NMR and restrained molecular dynamics. The Uaq residue binds the 5'-terminus of the target strand through a combination of pi-stacking, hydrogen bonding, and interactions in the minor groove. The acylated aminonucleoside is the best molecular cap for 3'-termini reported to date. The Uaq motif assists binding of DNA strands, but is particularly effective in enhancing the affinity for RNA target strands, with a DeltaT(m) in the UV melting point of up to +18.2 degrees C per residue. Increased base pairing selectivity is induced for all sequence motifs tested, even in cases where unmodified duplexes show no preference for the canonical base pair at all. A single mismatched nucleobase facing the 3'-terminus gives DeltaDeltaT(m) values as large as -23.9 degrees C (RNA) or -29.5 degrees C (DNA). The 5'-phosphoramidite of the Uaq cap reported here allows for routine incorporation during automated syntheses.

F macht stabil: Der Einbau von 2′‐Desoxy‐2′‐fluorribonucleotiden (2′‐F‐RNA) in RNA‐Oligomere erhöht die Stabilität der resultierenden Doppelstränge deutlich. NMR‐Spektroskopie mit nativen (rote Kreise) und 2′‐F‐modifizierten RNA‐Doppelsträngen (schwarze Quadrate) sowie UV‐Schmelzexperimente zeigen, dass die höhere Stabilität für 2′‐F‐RNA im Vergleich zu RNA sowohl auf stärkere Wasserstoffbrücken der Watson‐Crick‐Paare als auch auf eine günstige Basenstapelung zurückgeht.

The thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli strain relies on the four building blocks 5-chloro-2′-deoxyuridine (ClU), A, C and G instead of the standard T, A, C, G alphabet [Marlière,P., Patrouix,J., Döring,V., Herdewijn,P., Tricot,S., Cruveiller,S., Bouzon,M. and Mutzel,R. (2011) Chemical evolution of a bacterium’s genome. Angew. Chem. Int. Ed., 50, 7109–7114]. The residual fraction of T in the DNA of adapted bacteria was <2% and the switch from T to ClU was accompanied by a massive number of mutations, including >1500 A to G or G to A transitions in a culture. The former is most likely due to wobble base pairing between ClU and G, which may be more common for ClU than T. To identify potential changes in the geometries of base pairs and duplexes as a result of replacement of T by ClU, we determined four crystal structures of a B-form DNA dodecamer duplex containing ClU:A or ClU:G base pairs. The structures reveal nearly identical geometries of these pairs compared with T:A or T:G, respectively, and no consequences for stability and cleavage by an endonuclease (EcoRI). The lack of significant changes in the geometry of ClU:A and ClU:G base pairs relative to the corresponding native pairs is consistent with the sustained unlimited self-reproduction of E. coli strains with virtually complete T→ClU genome substitution.

1,N 6-Ethenodeoxyadenosine (1,N 6 -⑀dA) is the major etheno lesion formed in the reaction of DNA with epoxides substituted with good leaving groups (e.g. vinyl chloride epoxide). This lesion is also formed endogenously in DNA from lipid oxidation. Recombinant human DNA polymerase (hpol ) can replicate oligonucleotide templates containing 1,N 6 -⑀dA. In steady-state kinetic analysis, hpol preferred to incorporate dATP and dGTP, compared with dTTP. Mass spectral analysis of incorporation products also showed preferred purine (A, G) incorporation and extensive ؊1 frameshifts, suggesting pairing of the inserted purine and slippage before further replication. Five x-ray crystal structures of hpol ternary complexes were determined, three at the insertion and two at the extension stage. Two insertion complexes revealed incoming non-hydrolyzable dATP or dGTP analogs not pairing with but instead in a staggered configuration relative to 1,N 6 -⑀dA in the anti conformation, thus opposite the 5-T in the template, explaining the proclivity for frameshift misincorporation. In another insertion complex, dTTP was positioned opposite 1,N 6 -⑀dA, and the adduct base was in the syn conformation, with formation of two hydrogen bonds. At the extension stage, with either an incorporated dA or dT opposite 1,N 6 -⑀dA and 2-deoxythymidine-5-[(␣,␤)-imido-]triphosphate opposite the 5-A, the 3-terminal nucleoside of the primer was disordered, consistent with the tendency not to incorporate dTTP opposite 1,N 6 -⑀dA. Collectively, the results show a preference for purine pairing opposite 1,N 6 -⑀dA and for ؊1 frameshifts.