Excited‐State Dynamics of Isolated DNA Bases: A Case Study of Adenine

We present a summary of recent advances in the understanding of the UV photophysics of the isolated DNA base adenine, emphasizing a discussion of the mechanisms behind the ultrafast relaxation following excitation to the ππ* band. Drawing on our femtosecond time‐resolved photoelectron spectroscopy experiments, we discuss differences in the ultrafast relaxation of adenine and 9‐methyladenine and consider the relative merits of the various proposed mechanisms.     

Mechanism of UV-induced formation of Dewar lesions in DNA

The importance of a backbone: The mechanism of formation of Dewar lesions has been investigated by using femtosecond IR spectroscopy and ab?initio calculations of the exited state. The 4π?electrocyclization is rather slow, occurs with an unusual high quantum yield, and--surprisingly--is controlled by the phosphate backbone.     

A Rotational BODIPY Nucleotide: An Environment‐Sensitive Fluorescence‐Lifetime Probe for DNA Interactions and Applications in Live‐Cell Microscopy

Fluorescent probes for detecting the physical properties of cellular structures have become valuable tools in life sciences. The fluorescence lifetime of molecular rotors can be used to report on variations in local molecular packing or viscosity. We used a nucleoside linked to a meso‐substituted BODIPY fluorescent molecular rotor ( dC^bdp ) to sense changes in DNA microenvironment both in vitro and in living cells. DNA incorporating dC^bdp can respond to interactions with DNA‐binding proteins and lipids by changes in the fluorescence lifetimes in the range 0.5–2.2 ns. We can directly visualize changes in the local environment of exogenous DNA during transfection of living cells. Relatively long fluorescence lifetimes and extensive contrast for detecting changes in the microenvironment together with good photostability and versatility for DNA synthesis make this probe suitable for analysis of DNA‐associated processes, cellular structures, and also DNA‐based nanomaterials.     

Chiral Selectivity in the Binding of [4]Helicene Derivatives to Double‐Stranded DNA

The interaction of a series of chiral cationic [4]helicene derivatives, which differ by their substituents, with double‐stranded DNA has been investigated by using a combination of spectroscopic techniques, including time‐resolved fluorescence, fluorescence anisotropy, and linear dichroism. Addition of DNA to helicene solutions results to a hypochromic shift of the visible absorption bands, an increase of fluorescence quantum yield and lifetime, a slowing down of fluorescence anisotropy decay, and a linear dichroism in flow‐oriented DNA, which unambiguously points to the binding of these dyes to DNA. Both helicene monomers and dimeric aggregates, which form at higher concentration, bind to DNA, the former most probably upon intercalation and the latter upon groove binding. The binding constant depends substantially on the dye substituents and is, in all cases, larger with the M than the P enantiomer, by factors ranging from 1.2 to 2.3, depending on the dye.     

Reversal of a Single Base‐Pair Step Controls Guanine Photo‐Oxidation by an Intercalating Ruthenium(II) Dipyridophenazine Complex

Small changes in DNA sequence can often have major biological effects. Here the rates and yields of guanine photo‐oxidation by Λ‐[Ru(TAP)₂(dppz)]²⁺ have been compared in 5′‐{CCGG AT CCGG}₂ and 5′‐{CCGG TA CCGG}₂ using pico/nanosecond transient visible and time‐resolved IR (TRIR) spectroscopy. The inefficiency of electron transfer in the TA sequence is consistent with the 5′‐TA‐3′ versus 5′‐AT‐3′ binding preference predicted by X‐ray crystallography. The TRIR spectra also reveal the differences in binding sites in the two oligonucleotides.     

Intramolecular excimer formation and delayed fluorescence in sterically constrained pyrene dimers

The synthesis is described for a series of five molecular dyads comprising pyrene-based terminals covalently linked through a 1,3-disubstituted phenylene spacer. The extent of through-space communication between the pyrene units is modulated by steric interactions imposed by bulky moieties attached at the 6,8-positions of each pyrene unit. For the control compound, only hydrogen atoms occupy the 6,8 positions (DP1), whereas the remaining compounds incorporate ethynylene groups terminated with either triisopropylsilyl (DP2), 1-tert-butylbenzene (DP3), 2,6-di-tert-butylbenzene (DP4) or 1-tert-butyl-3,5-dimethylbenzene (DP5) units. Each compound shows a mixture of monomer and excimer fluorescence in fluid solution at room temperature, but only monomer emission in a glassy matrix at 77 K. The ratio of monomer to excimer fluorescence depends markedly on the molecular structure; DP1 is heavily biased in favour of the excimer and DP4 is enriched with monomer fluorescence. Photophysical properties, including laser induced and delayed fluorescence data, are reported for each compound. Delayed fluorescence occurs by both intramolecular and bimolecular steps, but these events take place on different timescales. The possibility is raised for using intramolecular triplet-triplet annihilation as a means of molecular imaging.     

Structural heterogeneity in DNA: temperature dependence of 2-aminopurine fluorescence in dinucleotides.

The fluorescent base analogue 2-aminopurine is a sensitive probe for local dynamics of DNA. Its fluorescence is quenched by interaction with the neighboring bases, but the underlying mechanisms are still under investigation. We studied 2-aminopurine fluorescence in dinucleotides with each of the natural bases. Consistently, two of the four fluorescence-decay components depend strongly on temperature. Our results indicate that these components are due to the excited-state dynamics of a single conformational state. We propose a variation of the gating model in which transient unstacking occurs in the excited state.     

Progress in the optimization of chiral cyclophane synthetic receptors for shape selective molecular recognition in aqueous media through hydrophobic association

Three new synthetic receptors based on Tr?ger’s base are prepared and evaluated. These three receptors are structural isomers of a successful receptor reported earlier from this laboratory, and they are all far inferior to that original receptor. Two of these receptors fail almost entirely and do so for an interesting reason. In water (not in other solvents) they collapse, forming a deflated structure. Collapsed or “sicklied” receptors do not bind to alicyclic or hydrophobic substrates in water because an important component of the driving force, the high energy waters solvating the interior of the macrocyclic structure, is lost when the receptor collapses. The results clearly illustrate how important it is to use computational methods that include good aqueous solvation models when designing new cyclophane receptors.     

The excited-state chemistry of protochlorophyllide a: a time-resolved fluorescence study.

The excited-state processes of protochlorophyllide a, the precursor of chlorophyll a in chlorophyll biosynthesis, are studied using picosecond time-resolved fluorescence spectroscopy. Following excitation into the Soret band, two distinct fluorescence components, with emission maxima at 640 and 647 nm, are observed. The 640 nm emitting component appears within the time resolution of the experiment and then decays with a time constant of 27 ps. In contrast, the 647 nm emitting component is built up with a 3.5 ps rise time and undergoes a subsequent decay with a time constant of 3.5 ns. The 3.5 ps rise kinetics are attributed to relaxations in the electronically excited state preceding the nanosecond fluorescence, which is ascribed to emission out of the thermally equilibrated S(1) state. The 27 ps fluorescence, which appears within the experimental response of the streak camera, is suggested to originate from a second minimum on the excited-state potential-energy surface. The population of the secondary excited state is suggested to reflect a very fast motion out of the Franck-Condon region along a reaction coordinate different from the one connecting the Franck-Condon region with the S(1) potential-energy minimum. The 27 ps-component is an emissive intermediate on the reactive excited-state pathway, as its decay yields the intermediate photoproduct, which has been identified previously (J. Phys. Chem. B 2006, 110, 4399-4406). No emission of the photoproduct is observed. The results of the time-resolved fluorescence study allow a detailed spectral characterization of the emission of the excited states in protochlorophyllide a, and the refinement of the kinetic model deduced from ultrafast absorption measurements.     

Protease Probes that Enable Excimer Signaling upon Scission

Peptide‐based probes that fluoresce upon proteolytic cleavage are invaluable tools for monitoring protease activity. The read‐out of protease activity through pyrene excimer signaling would be a valuable asset because the large Stokes shift and the long lifetime of the excimer emission facilitate measurements in autofluorescent media such as blood serum. However, proteolytic cleavage abolishes rather than installs the proximity relationships required for excimer signaling. Herein, we introduce a new probe architecture to enable the switching on of pyrene excimer emission upon proteolytic scission. The method relies on hairpin‐structured peptide nucleic acid (PNA)/peptide hybrids with pyrene units and anthraquinone‐based quencher residues positioned in a zipper‐like arrangement within the PNA stem. The excimer hairpin peptide beacons afforded up to a 50‐fold enhancement of the pyrene excimer emission. Time‐resolved measurements allowed the detection of matrix metalloprotease 7 in human blood serum.     

Contributions of the distance-dependent reorganization energy and proton-transfer to the hole-transfer process in DNA

A kinetic study of the single-step hole transfer in DNA was performed by measuring time-resolved transient absorption. DNA molecules with various sequences were designed and conjugated with naphthalimide (NI) and phenothiazine (PTZ) to investigate the sequence and distance dependence of the single-step hole transfer between guanines (Gs). Hole injection into DNA was accomplished by excitation of the NI site with a 355 nm laser pulse, and the kinetics of the hole-transfer process were investigated by monitoring the transient absorption of the PTZ radical cation (PTZ.+). Kinetic analysis of the time profile of PTZ.+ based on the kinetic model showed that the distance dependence of the hole-transfer process was significantly influenced by the DNA sequence. Results of temperature- and isotope-effect experiments demonstrated that the activation energy increased as the number of bridge bases separating the Gs increased. This is because of the distance-dependent reorganization energy and contribution of the proton-transfer process to the hole transfer in DNA.