Information Gathering and Processing with Fluorescent Molecules

Molecular information gathering and processing – a young field of applied chemistry - is undergoing good growth. The progress is occurring both in terms of conceptual development and in terms of the strengthening of older concepts with new examples. This review critically surveys these two broad avenues. We consider some cases where molecules emulate one of the building blocks of electronic logic gates. We then examine molecular emulation of various Boolean logic gates carrying one, two or three inputs. Some single-input gates are popular information gathering devices. Special systems, such as ‘lab-on-a-molecule’ and molecular keypad locks, also receive attention. A situation deviating from the Boolean blueprint is also discussed. Some pointers are offered for maintaining the upward curve of the field.

Fluorescent PET (Photoinduced Electron Transfer) Sensors with Targeting/Anchoring Modules as Molecular Versions of Submarine Periscopes for Mapping Membrane-Bounded Protons

The two families of fluorescent PET (photoinduced electron transfer) sensors (1-9) show that the effective proton density near the surface of several micelle membranes changes over 2-3 orders of magnitude as the microlocation of the sensor (with respect to the membrane) is altered via hydrophobic tuning.

'Off-On' Fluorescent Sensors for Physiological levels of Magnesium Ions based on Photoinduced Electron Transfer (PET) which also behave as OR Logic Gates

The fluorescence of molecules 1-3 is enhanced by factors of up to 67 in the presence of magnesium and calcium ions in neutral water which allows the selective monitoring of magnesium ions under simulated physiological conditions and permits the construction of truth tables with OR logic when these molecules are viewed as ion input-photon output molecuIar devices.

Fluorescent Signalling of the Brain Neurotransmitter Gamma Amino Butyric Acid and Related Amino Acid Zwitterions

Fluorescent PET (photoinduced electron transfer) sensor 1 with monoaza-18-crown-6 ether and guanidinium receptor units shows a significant fluorescence enhancement with y-aminobutyric acid (GABA) in mixed aqueous solution.

Direct Visual Indication of pH Windows: 'Off-On-Off' Fluorescent PET (Photoinduced Electron Transfer) Sensors/Switches

1–3, which contain a fluorophore and two proton receptors with opposite PET (photoinduced electron transfer) characteristics, only display strong fluorescence within a pH window whose position and width are tunable.

Arenedicarboximide Building Blocks for Fluorescent Photoinduced Electron Transfer pH Sensors Applicable with Different Media and Communication Wavelengths

N-(aminoalkyl)-4-chloronaphthalene-
1,8-dicarboximides 1, N-
(aminoalkyl)-4-acetamidonaphthalene-
1,8-dicarboximides 3 and N,N'-bis(aminoalkyl)-
perylene-3,4:9,10-tetracarboxydiimides
4 show good fluorescent off ±
on switching in aqueous alcoholic solution
with protons as required for fluorescent
PET sensor design. The excitation
wavelengths lie in the ultraviolet
(lmaxˆ345 and 351 nm) for 1 and 3 and
in the blue-green (lmaxˆ528, 492 and
461 nm) for 4; the emission wavelengths
lie in the violet (lmaxˆ408 nm) for 1, in
the blue (lmaxˆ474 nm) for 3 and in the
yellow-orange (lmaxˆ543 and 583 nm)
for 4. Compound 4b shows substantial
fluorescence enhancement with protons
when immobilized in a poly(vinylchloride)
matrix, provided that 2-nitrophenyloctyl
ether plasticizer and potassium
tetrakis(4-chlorophenyl)borate additive
are present to prevent dye crystallization
and to facilitate proton diffusion
into the membrane, respectively.

4-Amino-1,8-naphthalimide-based Tröger's bases as high affinity DNA targeting fluorescent supramolecular scaffolds

The synthesis and photophysical and biological investigation of fluorescent 1,8-naphthalimide conjugated Troger's bases 1-3 are described. These structures bind strongly to DNA in competitive media at pH 7.4, with concomitant modulation in their fluorescence emission. These structures also undergo rapid cellular uptake, being localized within the nucleus within a few hours, and are cytotoxic against HL60 and (chronic myeloid leukemia) K562 cell lines.

Fluorescent Logic Systems for Sensing and Molecular Computation: Structure-Activity Relationships in Edge-Detection

Molecular logic-based computation continues to throw up new applications in sensing and switching, the newest of which is the edge detection of objects. The scope of this phenomenon is mapped out by the use of structure-activity relationships, where several structures of the molecules and of the objects are examined. The different angles and curvatures of the objects are followed with good-fidelity in the visualized edges, even when the objects are in reverse video.

Measurement of Local Sodium Ion Levels near Micellar Surfaces with Fluorescent PET (Photoinduced Electron Transfer) Sensors

Na+ near membranes controls our nerve signals, besides several other crucial bioprocesses. We demonstrate that fluorescent PET (photoinduced electron transfer) sensor molecules target Na+ in nanospaces near micellar membranes with excellent discrimination against H+. They find that Na+ near anionic micelles is concentrated by factors of upto 160. Sensor molecules which are not held tight to the micelle surface find a Na+ amplification factor of 8 only. These findings are strengthened by the employment of control compounds whose PET processes are permanently ‘on’ or permanently ‘off’.

Highly CO2 sensitive extruded fluorescent plastic indicator film based on HPTS

Highly-sensitive optical fluorescent extruded plastic films are reported for the detection of gaseous and dissolved CO2. The pH-sensitive fluorescent dye used is 8-Hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS, PTS-) coated on the surface of hydrophilic fumed silica and the base is tetrabutylammonium hydroxide (TBAH). The above components are used to create an HPTS pigment (i.e. HPTS/SiO2/TBAH) with a high CO2 sensitivity (%CO2(S=1/2) = 0.16%) and fast 50% response (t50↓) = 2 s and recovery (t50↑) = 5 s times. Highly CO2-sensitive plastic films are then fabricated, via the extrusion of the HPTS pigment powder in low-density polyethylene (LDPE). As with the HPTS-pigment, the luminescence intensity (at 515 nm) and absorbance (at 475 nm) of the HPTS plastic film decreases as the %CO2 in the ambient gas phase increases. The HPTS plastic film exhibits a high CO2 sensitivity, %CO2(S=1/2), of 0.29%, but a response time ˂2 min and recovery time ˂40 min, which is slower than that of the HPTS pigment. The HPTS plastic film is very stable under ambient conditions, (with a shelf life ˃ six month when stored in the dark but under otherwise ambient conditions). Moreover, the HPTS-film is stable in water, salt solution and even in acid (pH=2), and in each of these media it can be used to detect dissolved CO2.

Interactions between pyrazole derived enantiomers and Chiralcel OJ: Prediction of enantiomer absolute configurations and elution order by molecular dynamics simulations

The separation of enantiomers and confirmation of their absolute configurations is significant in the development of chiral drugs. The interactions between the enantiomers of chiral pyrazole derivative and polysaccharide-based chiral stationary phase cellulose tris(4-methylbenzoate) (Chiralcel OJ) in seven solvents and under different temperature were studied using molecular dynamics simulations. The results show that solvent effect has remarkable influence on the interactions. Structure analysis discloses that the different interactions between two isomers and chiral stationary phase are dependent on the nature of solvents, which may invert the elution order. The computational method in the present study can be used to predict the elution order and the absolute configurations of enantiomers in HPLC separations and therefore would be valuable in development of chiral drugs.

Using the fluorescent properties of STO-609 as a tool to assist structure-function analyses of recombinant CaMKK2

Calcium/calmodulin-dependent kinase kinase 2 (CaMKK2) has been implicated in the regulation of metabolic activity in cancer and immune cells, and affects whole-body metabolism by regulating ghrelin-signalling in the hypothalamus. This has led to efforts to develop specific CaMKK2 inhibitors, and STO-609 is the standardly used CaMKK2 inhibitor to date. We have developed a novel fluorescence-based assay by exploiting the intrinsic fluorescence properties of STO-609. Here, we report an in vitro binding constant of KD ∼17 nM between STO-609 and purified CaMKK2 or CaMKK2:Calmodulin complex. Whereas high concentrations of ATP were able to displace STO-609 from the kinase, GTP was unable to achieve this confirming the specificity of this association. Recent structural studies on the kinase domain of CaMKK2 had implicated a number of amino acids involved in the binding of STO-609. Our fluorescent assay enabled us to confirm that Phe(267) is critically important for this association since mutation of this residue to a glycine abolished the binding of STO-609. An ATP replacement assay, as well as the mutation of the 'gatekeeper' amino acid Phe(267)Gly, confirmed the specificity of the assay and once more confirmed the strong binding of STO-609 to the kinase. In further characterising the purified kinase and kinase-calmodulin complex we identified a number of phosphorylation sites some of which corroborated previously reported CaMKK2 phosphorylation and some of which, particularly in the activation segment, were novel phosphorylation events. In conclusion, the intrinsic fluorescent properties of STO-609 provide a great opportunity to utilise this drug to label the ATP-binding pocket and probe the impact of mutations and other regulatory modifications and interactions on the pocket. It is however clear that the number of phosphorylation sites on CaMKK2 will pose a challenge in studying the impact of phosphorylation on the pocket unless the field can develop approaches to control the spectrum of modifications that occur during recombinant protein expression in E. coli.