-Aminopurine (2AP) is a structural isomer of adenine (A), in which the amino group is at C2 instead of C6, and can form stable Watson-Crick (WC) type base pairs with thymine (T) (Figure 1). [1,2] While natural nucleobases do not emit at all, 2AP shows appreciable fluorescence. More importantly, its fluorescence quantum yield decreases 100-fold upon duplex formation. [3] Numerous studies exploit 2AP fluorescence to investigate problems in structural biology and biophysics: methyltransferase-induced base flipping, [4][5][6] conformational changes and enzymatic cleavage of the hammerhead ribozyme, [7,8] promoter binding and clearance of T7 RNA polymerase, [9,10] binding and strand separation of primertemplate DNA by T4 DNA polymerase, [11][12][13] and chargetransfer mechanisms in DNA coupled to polar solvation. [14][15][16] Alternatively, structural changes can be monitored by a lowenergy circular dichroism band observed with 2AP, as was demonstrated with RNA and DNA hairpin loops. [17,18] The high number of publications relating to 2AP reflects its importance in studies of biological macromolecules.When structural transitions in biological systems are examined with a molecular probe, the assumption is that the modified system behaves like the natural one. Consequently the introduction of the probe must leave the structure and dynamics unchanged. Fluorophore-induced perturbations have been analyzed by solution NMR spectroscopy in many cases. [19][20][21][22][23] With 2AP, however, the changes are so small that the results in the original studies were inconclusive. [24,25] With high-field spectrometers and an expanded set of NMR parameters at hand we can now investigate 2AP-induced changes in detail.We present herein the NMR solution structure and basepair dynamics of two 13-mer DNA duplexes (Figure 1) with X = A in the reference sequence and X = 2AP in the modified sample (in the following called 13merRef and 13mer2AP, respectively). The only change introduced into the helix is the position of the amino group in A and 2AP. To what extent are structure and dynamics affected by this change? To answer this question we employed 2D NMR spectroscopy and measurements of residual dipolar couplings (RDC) in conjunction with simulated annealing calculations to determine the solution structure, selective NMR T 1 experiments to evaluate base-pair dynamics, and temperature-dependent absorption and fluorescence spectroscopy to characterize local melting. By combining information from these different approaches the effect of a single substitution A!2AP can be evaluated.All NMR resonances except for the severely overlapped H5'/H5'' signals could be assigned by intra-and internucleotide NOEs.[26] WC base-pairing of 2AP is evidenced by the imino proton signal of T20 which is observed-though broadened-for 13mer2AP at 298 K. [26] In contrast to an earlier report, [24] all cross peaks expected for regular B-DNA are present in the NOESY spectra of both samples. However, for the diagonal imino proton signal for T20, fast decay with increa...

Blending in: A triazole‐modified DNA duplex is perturbed in structure and dynamics, but this is delocalized over five base pairs. The conformation remains B‐DNA and hydrogen bonds between the DNA phosphate oxygen and polymerases can be mimicked by the triazole nitrogen (see figure). The results explain the surprising biocompatibility of triazole‐linked DNA.

An artificial base pair in the center of a duplex DNA oligomer, formed by 2,4-diaminopyrimidine and fluorescent 4-aminophthalimide C-nucleosides, is characterized spectroscopically, with a view towards its use in femtosecond solvation dynamics. Quantum-chemical calculations predict H-bonding energy equivalent to A:T. UV-vis absorption spectra provide insight into local melting at the 4-aminophthalimide modification site. Increase of temperature to nearly the melting temperature of the duplex leads to better hybridisation of the fluorescent nucleoside, contrary to native base pairs. This unusual observation is explained by the NMR solution structure of the duplex. Two conformations are adopted by the artificial pair due to backbone constraints, having either two or one interbase hydrogen bonds. In the latter, hydrogen bonding sites remain accessible for water solvation. The time-resolved dynamic Stokes' shift of 4-aminophthalimide fluorescence is consistent with that of a mixture of a slow and fast species. From the observations, the optimal linkage between 4-aminophthalimide and 2-deoxyribose for fitting into the duplex B-DNA structure is deduced.

Riding the waves: In a DNA–ligand complex, the time‐dependent Stokes shift shows initial oscillation. Molecular dynamics simulations help assign this ripple to coherent in/out motion of the ligand together with breathing of the minor groove (see picture).

A 13mer DNA duplex containing the artificial 4-aminophthalimide:2,4-diaminopyrimidine (4AP:DAP) base pair in the central position was characterized by optical and NMR spectroscopy. The fluorescence of 4AP in the duplex has a large Stokes shift of Δλ=124 nm and a quantum yield of Φ =24 %. The NMR structure shows that two interstrand hydrogen bonds are formed and confirms the artificial base pairing. In contrast, the 4-N,N-dimethylaminophthalimide moiety prefers the syn conformation in DNA. The fluorescence intensity of this chromophore in DNA is very low and the NMR structure shows no significant interaction with DAP. Primer-extension experiments with DNA polymerases showed that not only is the 4AP C nucleotide incorporated at the desired position opposite DAP in the template, but also that the polymerase is able to progress past this position to give the full-length product. The observed selectivity supports the NMR results.