Biologically active molecules with a "light switch"

Infrared Studies of Small Azobenzene Peptides: Unexpectedly Slow Reactions on the Time Range of Minutes

Infrared absorption experiments on light-triggered azobenzene peptides have been performed below and above the freezing point of the solvent dimethyl sulfoxide (DMSO). Even 20 K below the freezing point, illumination of the azobenzene chromophore resulted in IR absorption changes indicative of light-induced structural rearrangements of the peptide. In addition, new conformational states could be found at low temperature, which involve the formation of additional hydrogen bonds. In one sample the new low-temperature state survived melting and reheating and disappeared at 298 K only on the time scale of 10 min. The observations indicate that at low temperatures the peptide, together with traces of water present in the sample, forms a shell in the vicinity of the chromophore that facilitates internal motion even in the rigid cage of frozen DMSO.

Controlled Release of Volatiles under Mild Reaction Conditions: From Nature to Everyday Products

Volatile organic compounds serve in nature as semiochemicals for communication between species, and are often used as flavors and fragrances in our everyday life. The quite limited longevity of olfactive perception has led to the development of pro-perfumes or pro-fragrances--ideally nonvolatile and odorless fragrance precursors which release the active volatiles by bond cleavage. Only a limited amount of reaction conditions, such as hydrolysis, temperature changes, as well as the action of light, oxygen, enzymes, or microorganisms, can be used to liberate the many different chemical functionalities. This Review describes the controlled chemical release of fragrances and discusses additional challenges such as precursor stability during product storage as well as some aspects concerning toxicity and biodegradability. As the same systems can be applied in different areas of research, the scope of this Review covers fragrance delivery as well as the controlled release of volatiles in general.

Photoinduced C−N Bond Cleavage in 2-Azido-1,3-diphenyl-propan-1-one Derivatives: Photorelease of Hydrazoic Acid

Photolysis of 3-azido-1,3-diphenyl-propan-1-one (1a) in toluene yields 1,3-diphenyl-propen-1-one (2), whereas irradiation of 3-azido-2,2-dimethyl-1,3-diphenyl-propan-1-one (1b) results in the formation of mainly 2,2-dimethyl-1,3-diphenyl-propan-1-one. Laser flash photolysis (308 nm) of 1a,b in acetonitrile reveals a transient absorption (lambda max = approximately 310 nm) due to the formation of radicals 4a and 4b, respectively, which have lifetimes of approximately 14 micros at ambient temperature. TD-DFT calculations (B3LYP/6-31+G(d)) reveal that the first and second excited states of the triplet ketone (T1K (n,pi*) and T2K (pi,pi*)) in azide 1a are almost degenerate, at approximately 74 and 76 kcal/mol above the ground state (S0), respectively. Similarly, azide 1b has T1K and T2K 75 and 82 kcal/mol above S0, respectively. The calculated transition state for cleaving the C-N bond is located 71 and 74 kcal/mol above S0 in azides 1a and 1b, respectively. The calculated bond dissociation energies for breaking the C-N bond are 55 and 58 kcal/mol for azides 1a and 1b, respectively, making C-N bond breakage accessible from T1K in azides 1 at ambient temperature. In comparison, the irradiation of azides 1 in argon matrices at 14 K lead to the formation of the corresponding triplet alkyl nitrenes (1-n), via intramolecular energy transfer from T2K. The characterization of 1-n was supported by isotope labeling, IR spectroscopy, and molecular modeling.

Photoresponsive Change of Oxygen-Binding Affinity of a Cobalt Schiff-Base Complex with an Axially Coordinating Stilbazole Residue of a Copolymer

The reversible binding reaction of oxygen to N,N'-ethylene bis(salicylideneiminato) cobalt(II) (CoS), to which a photoisomerizable stilbazole residue of copolymer 1 coordinated, was investigated. The E form of the stilbazole residues coordinating to CoS, (E)-1-CoS, showed photoisomerization into the Z form, (Z)-1-CoS, on direct ultraviolet irradiation and negligible reverse isomerization. The oxygen-binding equilibrium constant (K) values for (E)-1-CoS and (Z)-1-CoS in toluene were 3.3 x 10(-2) mmHg-1 and 4.8 x 10(-3) mmHg(-1), respectively, at 10 degrees C. Although the pK(a) values of the E and Z forms of the stilbazole residue were similar, the oxygen-binding affinity of (Z)-1-CoS was small in terms of the linear correlation of the logarithm of K (ln K) versus the pK(a). Steric hindrance of the polymer chain of 1 on the coordination of the stilbazole residue of (Z)-1 to CoS was thought to cause the small K. A photoresponsive change of apparent oxygen-binding affinity of 1-CoS along with the E/Z isomerization of the stilbazole residues was observed. The ratio of (Z)-1-CoS converted from (E)-1-CoS by the ultraviolet irradiation could be estimated from analysis of absorption spectra for the oxygen binding of a resulting mixture of (E)-1-CoS and (Z)-1-CoS.

Caged O-phosphorothioyl amino acids as building blocks for Fmoc-based solid phase peptide synthesis

The synthesis of 1-(2-nitrophenylethyl) caged O-phosphorothioylserine, -threonine and -tyrosine derivatives is reported. These amino acid building blocks can be directly incorporated into peptides by Fmoc-based solid phase synthesis as their pentafluorophenyl esters or as symmetric anhydrides. Upon irradiation with UV light, the thiophosphate group, representing a hydrolysis resistant phosphate analog, is revealed.

Synthesis of oligo-RNAs with photocaged adenosine 2′-hydroxyls

This protocol describes a general method for the preparation of RNAs in which the reactivity or hydrogen-bonding properties of the molecule are modified in a photoreversible fashion by use of a caging strategy. A single caged adenosine, modified at the 2' position as a nitro-benzyl ether, can be incorporated into short RNAs by chemical synthesis or into long RNAs by a combination of chemical and enzymatic synthesis. The modified RNAs can be uncaged by photolysis under a variety of conditions including the use of a laser or xenon lamp, and the course of this uncaging reaction may be readily followed by HPLC or thin-layer chromatography.

Photochemical DNA activation

A new photocaged nucleoside was synthesized and incorporated into DNA with the use of standard synthesis conditions. This approach enabled the disruption of specific H-bonds and allowed for the analysis of their contribution to the activity of a DNAzyme. Brief irradiation with nonphotodamaging UV light led to rapid decaging and almost quantitative restoration of DNAzyme activity. The developed strategy has the potential to find widespread application in the light-induced regulation of oligonucleotide function.

2-Oxoalkyl caged oligonucleotides: one-electron reductive activation into emergence of ordinary hybridization property by hypoxic X-irradiation

Ionizing radiation triggers the activation of caged oligodeoxynucleotides (ODNs) with a 2-oxoalkyl leaving group to give the corresponding normal uncaged strands. We designed and synthesized ODNs caged by a 2-oxopropyl group at a given thymine N(3) position (d(oxo)T) to evaluate their one-electron reduction characteristics. Upon hypoxic X-radiolysis in aqueous solution, the caged ODNs released the 2-oxopropyl group to produce the corresponding uncaged ODNs. Digestion by a restriction enzyme Swa I revealed that caged ODN pre-irradiated in hypoxia could form an ordinary duplex with its complementary strand.

Chemical biology of steroid and nuclear hormone receptors

The nuclear hormone receptors are ligand-gated transcription factors that modulate gene expression by directly acting upon genomic DNA, and have been of profound interest across all biological disciplines. Recent advancements in this area have included the expansion of transgene activation through ligand-receptor engineering, drug development from structural design and the exploitation of innate ligand-specific associations towards developing novel conditional protein-based recombinant and diagnostic tools. These advancements come on the heels of exciting new modes of hormone action that challenge and expand upon the classic paradigms of hormone receptor function.

Photochemical control of biological processes

Photochemical regulation of biological processes offers a high level of control to study intracellular mechanisms with unprecedented spatial and temporal resolution. This report summarizes the advances made in recent years, focusing predominantly on the in vivo regulation of gene function using irradiation with UV light. The majority of the described applications entail the utilization of photocaging groups installed either on a small molecule modulator of biomolecular function or directly on a biological macromolecule itself.

Regulating gene expression with light-activated oligonucleotides

Since the development of light-responsive amino acids, the activity of numerous biomolecules has been photomodulated in biochemical, biophysical, and cellular assays. Biological problems of even greater complexity motivate the development of quantitative methods for controlling gene activity with high spatial and temporal resolution, using light as an external trigger. Photoresponsive DNA and RNA oligonucleotides would optimally serve this purpose, but have proven difficult to expand from proofs-of-concept to in vivo experiments. Until recently, the development of this technology was limited by the synthesis of oligonucleotides whose function could be significantly modulated with near-UV light. New synthetic protocols and strategies for both up- and down-regulating gene activity finally make it possible to address biological considerations. In the near future, we can expect photoresponsive DNA and RNA molecules that are relatively non-toxic, nuclease-resistant, and maintain their specificity and activity in vivo. Quantitative, laser-initiated methods for controlling DNA and RNA function will illuminate new areas in cell and developmental biology.