2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence

We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short ( approximately 50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is substituted by an abasic site analog. The corresponding cocrystal structure shows 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not essential for base flipping. However, in this structure, a shift of the 3' neighbor of the target base into the vacancy left after base flipping is observed, apparently replicating a stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide quenching measurements of M.TaqI complexes in solution provide evidence for an alternative binding site for the extra-helical target base within M.TaqI and suggest that the partner thymine assists in delivering the target base into the active site.     

Coupling of a Nucleoside with DNA by a Methyltransferase

How to outwit a methyltransferase: Methyltransferases (Mtases) catalyze the transfer of the activated methyl group from the cofactor S-adenosyl-L -methionine ( 1 ) to acceptors R within a large variety of biomolecules. Through the use of the cofactor analogue 2 a whole nucleoside was coupled to DNA in a Mtase-catalyzed reaction.     

Optogalvanic spectroscopy of metastable states in Yb+

The metastable ²F_7/2 and ²D_3/2 states of Yb⁺ are of interest for applications in metrology and quantum information and also act as dark states in laser cooling. These metastable states are commonly repumped to the ground state via the 638.6 nm ²F_7/2–¹D[5/2]_5/2 and 935.2?nm ²D_3/2–³D[3/2]_1/2 transitions. We have performed optogalvanic spectroscopy of these transitions in Yb⁺ ions generated in a discharge. We measure the pressure broadening coefficient for the 638.6 nm transition to be 70±10?MHz?mbar^?1. We place an upper bound of 375 MHz/nucleon on the 638.6 nm isotope splitting and show that our observations are consistent with theory for the hyperfine splitting. Our measurements of the 935.2 nm transition extend those made by Sugiyama et al., showing well-resolved isotope and hyperfine splitting (Sugiyama and Yoda in IEEE Trans. Instrum. Meas. 44: 140, 1995). We obtain high signal-to-noise, sufficient for laser stabilisation applications (Streed et al. in Appl. Phys. Lett. 93: 071103, 2008).     

Natural J-coupling analysis: interpretation of scalar J-couplings in terms of natural bond orbitals.

The natural J-coupling (NJC) method presented here analyzes the Fermi contact portion of J-coupling in the framework of finite perturbation theory applied to ab initio/density function theory (DFT) wave functions, to compute individual and pairwise orbital contributions to the net J-coupling. The approach is based on the concepts and formalisms of natural bond orbital (NBO) methods. Computed coupling contributions can be classified as Lewis (individual orbital contributions corresponding to the natural Lewis structure of the molecule), delocalization (resulting from pairwise donor-acceptor interactions), and residual repolarization (corresponding to correlation-like interactions). This approach is illustrated by an analysis of the angular and distance dependences of the contributions to vicinal (3)J(HH) couplings in ethane and to the long-range (6)J(HH) couplings in pentane. The results indicate that approximately 70% or more of the net J-coupling is propagated by steric exchange antisymmetry interactions between Lewis orbitals (predominantly sigma bonding orbitals). Hyperconjugative sigma to sigma delocalization interactions account for the remainder of the coupling. Calculated pairwise-steric and hyperconjugative-delocalization energies provide a means for relating coupling mechanisms to molecular energetics. In this way, J-coupling contributions can be related directly to the localized features of the molecular electronic structure in order to explain measured J-coupling patterns and to predict J-coupling trends that have yet to be measured.     

Design of a new fluorescent cofactor for DNA methyltransferases and sequence-specific labeling of DNA

Sequence-specific labeling of DNA is of immense interest for analytical and functional studies of DNA. We present a novel approach for sequence-specific labeling of DNA using a newly designed fluorescent cofactor for the DNA methyltransferase from Thermus aquaticus (M.TaqI). Naturally, M.TaqI catalyzes the nucleophilic attack of the exocyclic amino group of adenine within the double-stranded 5'-TCGA-3' DNA sequence onto the methyl group of the cofactor S-adenosyl-L-methionine (AdoMet) leading to methyl group transfer. The design of a new fluorescent cofactor for covalent labeling of DNA was based on three criteria: (1) Replacement of the methionine side chain of the natural cofactor AdoMet by an aziridinyl residue leads to M.TaqI-catalyzed nucleophilic ring opening and coupling of the whole nucleoside to DNA. (2) The adenosyl moiety is the molecular anchor for cofactor binding. (3) Attachment of a fluorophore via a flexible linker to the 8-position of the adenosyl moiety does not block cofactor binding. According to these criteria the new fluorescent cofactor 8-amino[1'-(N'-dansyl)-4'-aminobutyl]-5'-(1-aziridinyl)-5'-deoxyadenosine (3) was synthesized. 3 binds about 4-fold better than the natural cofactor AdoMet to M.TaqI and is coupled with a short duplex oligodeoxynucleotide by M.TaqI. The identity of the expected modified nucleoside was verified by electrospray ionization mass spectrometry after enzymatic fragmentation of the product duplex. In addition, the new cofactor 3 was used to sequence-specifically label plasmid DNA in a M.TaqI-catalyzed reaction.     

Natural resonance theory: III. Chemical applications

We describe quantitative numerical applications of the natural resonance theory (NRT) to a variety of chemical bonding types, in order to demonstrate the generality and practicality of the method for a wide range of chemical systems. Illustrative applications are presented for (1) benzene and polycyclic aromatics; (2) CO₂, formate, and related acyclic species; (3) ionic and polar compounds; (4) coordinate covalent compounds and complexes; (5) hypervalent and electron-deficient species; (6) noncovalent H-bonded complex; and (7) a model Diels-Alder chemical reaction surface. The examples exhibit the general harmony of NRT weightings with qualitative resonance-theoretic concepts and illustrate how these concepts can be extended to many new types of chemical phenomena at a quanitative ab initio level. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 628–646, 1998     

Piezoelectricity of porous polytetrafluoroethylene single- and multiple-film electrets containing high charge densities of both polarities

Single-film bipolar electrets of porous polytetrafluoroethylene are generated by means of a two-step corona-charging process at elevated temperatures. Quasi-static direct piezoelectric coefficients of up to 0.15 nC/N have been observed on these films. In addition, multiple-layer stacks of porous and non-porous polytetrafluoroethylene films with monopolar charge were also investigated. While the piezoelectric responses of the stacks were not as high as those of the single films, the multiple-film arrangements may have other advantages such as better electrical shielding or tunable mechanical properties and adjustable acoustical impedance. Our new results are discussed in the context of the emerging field of porous polymer electrets with many potential device applications.