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All structures within living cells must form at the right time and place. This includes condensates such as the nucleolus, Cajal bodies and stress granules, which form via liquid-liquid phase separation of biomolecules, particularly proteins enriched in intrinsically disordered regions (IDRs).sup.1,2. In non-living systems, the initial stages of nucleated phase separation arise when thermal fluctuations overcome an energy barrier due to surface tension. This phenomenon can be modelled by classical nucleation theory (CNT), which describes how the rate of droplet nucleation depends on the degree of supersaturation, whereas the location at which droplets appear is controlled by interfacial heterogeneities.sup.3,4. However, it remains unknown whether this framework applies in living cells, owing to the multicomponent and highly complex nature of the intracellular environment, including the presence of diverse IDRs, whose specificity of biomolecular interactions is unclear.sup.5-8. Here we show that despite this complexity, nucleation in living cells occurs through a physical process similar to that in inanimate materials, but the efficacy of nucleation sites can be tuned by their biomolecular features. By quantitatively characterizing the nucleation kinetics of endogenous and biomimetic condensates in living cells, we find that key features of condensate nucleation can be quantitatively understood through a CNT-like theoretical framework. Nucleation rates can be substantially enhanced by compatible biomolecular (IDR) seeds, and the kinetics of cellular processes can impact condensate nucleation rates and specificity of location. This quantitative framework sheds light on the intracellular nucleation landscape, and paves the way for engineering synthetic condensates precisely positioned in space and time. Experiments using endogenous and biomimetic condensates in cells show that nucleation in cells resembles the physical process in inanimate materials, but is tuned by biomolecular features., Author(s): Shunsuke F. Shimobayashi [sup.1] , Pierre Ronceray [sup.2] [sup.3] , David W. Sanders [sup.1] , Mikko P. Haataja [sup.4] [sup.5] , Clifford P. Brangwynne [sup.1] [sup.5] [sup.6] Author Affiliations: [...]

The article discusses the field of nanomedicine and how it aims to use the properties and physical characteristics of nanomaterials for the diagnosis and treatment of diseases at the molecular level. The properties of nanomaterials, their principal medical applications and future possibilities for this emerging field are highlighted.

A central challenge in systems biology today is to understand the network of interactions among biomolecules and, especially, the organizing principles underlying such networks. Recent analysis of known networks has identified small motifs that occur ubiquitously, suggesting that larger networks might be constructed in the manner of electronic circuits by assembling groups of these smaller modules. Using a unique process-based approach to analyzing such networks, we show for two cell-cycle networks that each of these networks contains a giant backbone motif spanning all the network nodes that provides the main functional response. The backbone is in fact the smallest network capable of providing the desired functionality. Furthermore, the remaining edges in the network form smaller motifs whose role is to confer stability properties rather than provide function. The process-based approach used in the above analysis has additional benefits: It is scalable, analytic (resulting in a single analyzable expression that describes the behavior), and computationally efficient (all possible minimal networks for a biological process can be identified and enumerated). biological network | Boolean network | modulization and motif | process centric analysis doi/ 10.1073/pnas.0914180107

Binding-induced biomolecular switches are used throughout nature and, increasingly, throughout biotechnology for the detection of chemical moieties and the subsequent transduction of this detection into useful outputs. Here we show that the thermodynamics of these switches are quantitatively described by a simple 3-state population-shift model, in which the equilibrium between a nonbinding, nonsignaling state and the binding-competent, signaling state is shifted toward the latter upon target binding. Because of this, their performance is determined by the tradeoff inherent to their switching thermodynamics; while a switching equilibrium constant favoring the nonbinding, nonsignaling, conformation ensures a larger signal change (more molecules are poised to respond), it also reduces affinity (binding must overcome a more unfavorable conformational free energy). We then derive and employ the relationship between switching thermodynamics and switch signaling to rationally tune the dynamic range and detection limit of a representative structure-switching biosensor, a molecular beacon, over 4 orders of magnitude. These findings demonstrate that the performance of biomolecular switches can be rationally tuned via mutations that alter their switching thermodynamics and suggest a mechanism by which the performance of naturally occurring switches may have evolved. allostery | ligand-induced conformational change | pre-existing equilibrium | rational design, sensitivity | riboswitches

The ability to charge huge biomolecules without breaking them apart has made matrix-assisted laser desorption/ionization (MALDI) mass spectrometry an indispensable tool for biomolecular analysis. Conventional, empirically selected matrices produce abundant matrix ion clusters in the low-mass region ( clinical diagnostic | matrix design | positive/negative ions | ion-formation model | MALDI

Biomolecular computing is the computational method that uses the potential of DNA as a parallel computing device. DNA computing can be used to solve NP-complete problems. An appropriate application of DNA computation is large-scale evaluation of parallel computation models such as Boolean Circuits. In this study, we present a molecular-based algorithm for evaluation of Nand-based Boolean Circuits. The contribution of this paper is that the proposed algorithm has been implemented using only three molecular operations and the number of passes in each level is decreased to less than half of previously addressed in the literature. Thus, the proposed algorithm is much easier to implement in the laboratory. Key words: DNA computing, simulation, Boolean circuit, parallel computation, modeling, complexity, INTRODUCTION Molecular computing was emerged in 1994 by original paper of Adleman (8). He proposed an algorithm for solving Hamiltonian Path Problem using molecular operations. Adleman's experiment ushered in a [...]

We have developed a simple method using a magnetic bar array to anchor nonmagnetic biomolecules for time-lapse analysis and identification. Biomolecules of interest are attached, using linker molecules, to the superparamagnetic beads which are in turn captured at gaps of the magnetic bar array. This micro-array system can be used for various studies and applications such as yeast growth studies, as illustrated in this work, and pyrosequencing. The technology is applicable to a wide variety of biomolecules using the suitable linker molecules, with the merits of low lost and reusability. Index Terms--CoPt magnetic film, linker molecule, magnetic array, paramagnetic bead, yeast growth.

Here, we report a previously undescribed approach for controlling metal ion coordination geometry in biomolecules by reorientating amino acid side chains through substitution of L- to D-amino acids. These diastereopeptides allow us to manipulate the spatial orientation of amino acid side chains to alter the sterics of metal binding pockets. We have used this approach to design the de novo metallopeptide, Cd[(TRIL12[L.sub.D]L16C).sup.-.3], which is an example of Cd(II) bound to 3 L-Cys as exclusively trigonal Cd[S.sub.3], as characterized by a combination of [sup.113]Cd NMR and [sup.111m]Cd PAC spectroscopy. We subsequently show that the physical properties of such a site, such as the high [pK.sup.a2] for Cd(II) binding of 15.1, is due to the nature of the coordination number and not the ligating group. Furthermore this approach allowed for the design of a construct, GRANDL12[L.sub.D]L16CL26AL30C, capable of independently binding 2 equivalents of Cd(II) to 2 very similar Cys sites as exclusively 3- and 4-, Cd[S.sub.3] and Cd[S.sub.3]O, respectively. Demonstrating that we are capable of controlling the Cd(II) coordination number in these 2 sites solely by varying the nature of a noncoordinating second coordination sphere amino acid, with D-leucine and L-alanine resulting in exclusively 3- and 4-coordinate structures, respectively. Cd(II) was found to selectively bind to the 4-coordinate Cd[S.sub.3]O site, demonstrating that a protein can be designed that displays metal-binding selectivity based solely on coordination number control and not on the chemical identity of coordinating ligands. cadmium | coiled-coil peptides | D-amino acids | de novo metallopeptide design

We report the use of individual gold nanorods as plasmonic transducers to detect the binding of streptavidin to individual biotin-conjugated nanorods in real time on a surface. Label-free detection at the single-nanorod level was performed by tracking the wavelength shift of the nanorod-localized surface plasmon resonant scattering spectrum using a dark-field microspectroscopy system. The lowest streptavidin concentration that was experimentally measured was 1 nM, which is a factor of 1000-fold lower than the previously reported detection limit for streptavidin binding by biotinylated single plasmonic nanostructures. We believe that the current optical setup is able to reliably measure wavelength shifts as small as 0.3 nm. Binding of streptavidin at 1 nM concentration induces a mean resonant wavelength shift of 0.59 nm suggesting that we are currently operating at close to the limit of detection of the system.

The Poisson-Nernst-Planck approach is used for studying the effects of ion and substrate concentrations on the reaction rate and rate coefficient in biomolecular system, especially for acetylcholine consumption process by acetylcholinesterase. The results have estimated reaction rates at various conditions and have shown that the concentrations of charged substrates should be coupled with the electrostatic computation for describing neurotransmission and other reaction processes.

A new fluorescence imaging system is described for visualizing biomolecules within living biological samples by using time-resolved, long-lived luminescence microscopy (TRLLM). The changes of intracelluar ionic zinc [(Zn.sup.2]) concentration is monitored by using a [Zn.sup.2}-selective luminescent [Eu.sup.3} chemosensor [Eu-7].

Fourier transform infrared (FTIR) spectroscopy provides a unique molecular fingerprint of tissue from endogenous sources of light absorption; however, specific molecular components of the overall FTIR signature of precancer have not been characterized. In attenuated total reflectance mode, infrared light penetrates only a few microns of the tissue surface, and the influence of water on the spectra can be minimized, allowing for the analyses of the molecular composition of tissues. Here, spectra were collected from 98 excised specimens of the distal esophagus, including 38 squamous, 38 intestinal metaplasia (Barrett's), and 22 gastric, obtained endoscopically from 32 patients. We show that DNA, protein, glycogen, and glycoprotein comprise the principal sources of infrared absorption in the 950- to 1,800-[cm.sup.-1] regime. The concentrations of these biomolecules can be quantified by using a partial least-squares fit and used to classify disease states with high sensitivity, specificity, and accuracy. Moreover, use of FTIR to detect premalignant (dysplastic) mucosa results in a sensitivity, specificity, positive predictive value, and total accuracy of 92%, 80%, 92%, and 89%, respectively, and leads to a better interobserver agreement between two gastrointestinal pathologists for dysplasia ([kappa] = 0.72) versus histology alone ([kappa] = 0.52). Here, we demonstrate that the concentration of specific biomolecules can be determined from the FTIR spectra collected in attenuated total reflectance mode and can be used for predicting the underlying histopathology, which will contribute to the early detection and rapid staging of many diseases. dysplasia | pathology | optical biopsy | diagnostics

The theoretical and experimental studies of silica formation are conducted utilizing biological and model organic additives to understand the roles of hydroxyl-containing biomolecules in biosilicification. The results demonstrate that in aqueous systems, the effect of hydroxyl-containing additives is negligible.

To overcome several problems in affinity capillary electrophoresis (ACE), i.e., low detectability, need for sample derivatization, and difficulty in the fixation of affinity ligands (ALs), mulfifunctional magnetic particles (MFMPs) were prepared by immobilizing both fluorescent molecules and ALs for low-density lipoproteins onto the surface of magnetic polymer microspheres with a polyelectrolyte multilayer coating technique and applied to the ACE analysis. The prepared MFMPs showed a remarkable change in the electrophoretic mobility ([[micro].sub.ep]) by the addition of low-density lipoproteins (LDL), whereas for high-density lipoproteins (HDL), [[micro].sub.ep] of the MFMPs kept constant, so that it was confirmed that the MFMPs possess an affinity with LDL. On the other hand, the MFMPs can be trapped by the magnetic field even under a higher electric field for electrophoresis. By a successive on-off control of the magnetic field, online preconcentration of the LDL bound MFMPs and the selective separation of LDL from HDL were successfully achieved. In the ACE analysis of LDL employing UV detection, an 82-fold increase in the sensitivity was obtained by the oncapillary sample preconcentration using the MFMPs. When laser induced-fluorescence detection was employed, furthermore, the limit of detection for LDL was improved to the order of subpicomolar.

The halogen bond, a noncovalent interaction involving polarizable chlorine, bromine, or iodine molecular substituents, is now being exploited to control the assembly of small molecules in the design of supramolecular complexes and new materials. We demonstrate that a halogen bond formed between a brominated uracil and phosphate oxygen can be engineered to direct the conformation of a biological molecule, in this case to define the conformational isomer of a four-stranded DNA junction when placed in direct competition against a classic hydrogen bond. As a result, this bromine interaction is estimated to be [approximately equal to] 2-5 kcal/mol stronger than the analogous hydrogen bond in this environment, depending on the geometry of the halogen bond. This study helps to establish halogen bonding as a potential tool for the rational design and construction of molecular materials with DNA and other biological macromolecules. biomolecular engineering | DNA structure | molecular interactions

How to effectively mix small volumes of liquids within microplate wells is a still underestimated and often neglected challenge. The method the authors introduce here relies on violent turbulent motion [...]

The ability to present biomolecules on the highly organized structure of M13 filamentous bacteriophage is a unique advantage. Where previously this viral template was shown to direct the orientation and nucleation of nanocrystals and materials, here we apply it in the context of single-molecule (SM) biophysics. Genetically engineered constructs were used to display different reactive species at each of the filament ends and along the major capsid, and the resulting hetero-functional particles were shown to consistently tether microscopic beads in solution. With this system, we report the development of a SM assay based on M13 bacteriophage. We also report the quantitative characterization of the biopolymer's elasticity by using an optical trap with nanometerscale position resolution. Expanding the fluctuating rod limit of the wormlike chain to incorporate enthalpic polymer stretching yielded a model capable of accurately capturing the full range of extensions. Fits of the force-extension measurements gave a mean persistence length of [approximately equal to] 1,265 nm, lending SM support for a shorter filamentous bacteriophage persistence length than previously thought. Furthermore, a predicted stretching modulus roughly two times that of dsDNA, coupled with the system's linkage versatility and load-bearing capability, makes the M13 template an attractive candidate for use in tethered bead architectures. optical tweezers | single molecule | wormlike chain

We report on a biomolecular sieving system based on the use of ordered colloidal arrays to define the sieve structure within a microfluidic device. A facile microfluidic colloidal self-assembly strategy has been developed to create ordered, robust, three-dimensional nanofluidic sieves within microfluidic devices, with which fast separation of DNA and proteins of a wide size range was achieved. Compared to conventional colloidal deposition procedures, such as vertical deposition, this approach features much faster assembling speed, the absence of drying-caused cracks that may jeopardize the separation performance, and better flexibility to couple with current microfabrication techniques. The flexibility of pore size enabled by this methodology provides separation of biomolecules with a wide size distribution, ranging from proteins (20-200 kDa) to dsDNA (0.05-50 kbp). Under moderate electric fields, complete separation can be finished in minutes, with separation efficiency comparable to gel/polymer-filled or micro-/nanofabricated microsystems. To our knowledge, this is the first demonstration of size separation of biomolecules within self-assembled ordered colloidal lattices embedded within a microfluidic system.

The concept of intermittent-contact-mode frequency and force modulation atomic force microscopy (FFM-AFM) is used to measure the cross-sectional scan of a single bacteriorhodopsin molecule within atomistic and classical simulations. The analysis has shown that its cross-section can be measured without any damage, in contrast to conventional tapping-mode AFM.

We characterize a new geometry for single-molecule detection with flow for use with a submilliliter drop of sample on an inverted confocal microscope. The solution is sucked into a glass capillary positioned above the ellipsoidal confocal volume so that molecules traverse the longest axis of the ellipsoid for greatest photon yield. Decreased spacing between the capillary tip and laser focus gives increased flow speed, as measured by fluorescence correlation spectroscopy, but also increased background from capillary autofluorescence. Flow can alleviate localized triplet and photobleaching effects and speed single-molecule sampling rates for fluorescence fluctuation spectroscopy determinations of slowly diffusing biomolecules in pharmaceutical drug discovery research. OCIS codes: 300.2530, 300.6280, 180.1790, 180.2520.

Electrocapture is a multifunctional microfluidic tool that can be used for concentration, sample cleanup, multistep reactions, and separation of biomolecules. Herein, we investigate the mechanisms underlying the electrocapture principle. A microfluidic electrocapture device was found to be capable of generating regions of different electric field, which are maintained in the flow by electric and hydrodynamic forces, with the zones of lower electric field strength upstream of those with higher strength. In addition to detection of the local electric fields by direct measurements, the existence of the zones was observed by the capture of a solution containing Coomassie and myogiobin. The two molecules were captured at different spots in a steady-state manner and were released (separated) at different electric fields. Considering these observations and the experimental values for the electric field strengths, flow velocities, and electrophoretic mobilities of DNA, proteins, and peptides, it is concluded that the macromolecules are captured between the field zones by a stacking mechanism.

Several new methods are presented that make slow exchange phenomena in biological macromolecules amenable to study via singlet-state nuclear magnetic resonance (NMR) spectroscopy. Results show that the lifetimes of [T.sub.S] of singlet states of pairs of protons in a partially deuterated saccharide are longer than the longitudinal proton relaxation times [T.sub.1] in the same compound.

We have extended the method of single-molecule fluorescence, two-color coincidence detection (TCCD) to detect coincident events due to a low fraction of a complex against a background of chance coincident events, due to monomers. We developed two complementary methods to determine the number of chance coincident events using the experimental data and without the need for additional experiments. We show that the subtraction of the chance coincidence level is essential for accurate quantification of the relative number of complexes and their stoichiometry. By performing experiments on model samples made from fluorophore-labeled duplex DNA and free dye, a linear dependence on the fraction of duplex DNA was found, independent of the level or ratio of free dye, with quantification down to a level of 0.5% and 500 fM duplex DNA. The method was then used to measure the equilibrium dissociation constant and offrate of a 9-mer duplex DNA, demonstrating the application of this method to systems with nanomolar dissociation constants. These improvements to the method of TCCD analysis significantly extend the application of TCCD to weakly bound complexes and large multicomponent biomolecular systems.

This paper presents a ricin detection method based on ricin's inhibitory effects on protein synthesis. Biological synthesis (expression) of a protein includes the steps of gene transcription (DNA [right arrow] RNA) and protein translation (RNA [right arrow] proteins); these reactions can be coupled into a one-step operation and carded out in a cell-free medium. Ricin is known to inhibit protein synthesis by interacting with 28S ribosome RNA; the inhibitory effect is exploited as the sensing mechanism in this work. For each copy of DNA, thousands of copies of proteins can be produced. As a result, the inhibitory effects of ricin are amplified, leading to a significantly enhanced detection signal (the difference between the positive control and samples). An array of protein expression units is developed to accommodate positive/negative controls and multiple samples. The array device contains a solution without any reagent captured on a solid surface, offering flexibility without comprising the activities of biomolecules. The miniaturized well-in-a-well design possesses a mechanism to supply nutrients continuously and remove byproducts, leading to higher protein expression yields and thus larger detection signals (lower detection limit) when ricin is present. We demonstrate the production of green fluorescent protein and luciferase in the device. A calibration curve has been obtained between the luciferase expression yield and the ricin concentration, showing a detection limit of 0.01 nM (0.3 ng/mL) ricin. The nested-well device is also used for measuring the toxicity level of ricin after physical or chemical treatment.

We present a method to distinguish authentic ancient DNA from contaminating DNA in a human bone. This is achieved by taking account of the spatial distribution of the various sequence families within the bone and the extent of degradation of the template DNAs, as revealed by the error content of the sequences. To demonstrate the veracity of the method, we handled two ancient human tibiae in order to contaminate them with modern DNA, and then subjected segments of the bones to various decontaminating treatments, including removal of the outer 1-2 mm, before extracting DNA, cloning, and obtaining a total of 107 mitochondrial DNA sequences. Sequences resulting from the deliberate contamination were located exclusively in the outer 1-2 mm of the bones, and only one of these 27 sequences contained an error that could be ascribed to DNA degradation. A second, much smaller set of relatively error-free sequences, which we ascribe to contamination during excavation or curation, was also located exclusively in the outer 1-2 mm. In contrast, a family of 72 sequences, displaying extensive degradation products but identifiable as haplogroup U5ala, was distributed throughout one of the bones and represents the authentic ancient DNA content of this specimen. KEY WORDS biomolecular archaeology; mitochondrial DNA; haplogroups

Surface plasmon-resonance analysis using a Biacore biosensor is a powerful tool for the detailed study of biomolecular interactions. The authors examined the methods of immobilizing proteins on the surface of [...]

Biomolecules often undergo large-amplitude motions when they bind or release other molecules. Unlike macroscopic machines, these biomolecular machines can partially disassemble (unfold) and then reassemble (fold) during such transitions. Here we put forward a minimal structure-based model, the 'multiple-basin model,' that can directly be used for molecular dynamics simulation of even very large biomolecular systems so long as the endpoints of the conformational change are known. We investigate the model by simulating large-scale motions of four proteins: glutamine-binding protein, S100A6, dihydrofolate reductase, and HIV-1 protease. The mechanisms of conformational transition depend on the protein basin topologies and change with temperature near the folding transition. The conformational transition rate varies linearly with driving force over a fairly large range. This linearity appears to be a consequence of partial unfolding during the conformational transition. conformational transition | cracking | partial unfolding | funnel

Here we present the detection of ultralow concentrations of biomolecules in a device made from a polycarbonate membrane containing a network of gold nanowires and using a 'contactless' impedance tomoscopy technique. The sensor comprises a thin dielectric layer with two parallel band electrodes on the one side and a micro-channel containing gold nanowires onto which the adsorption of antibodies occurs. Upon applying a high-frequency ac voltage between the two electrodes, the adsorption process occurring at the surface of the gold nanowires can be followed through contactless impedance measurements. The configuration allows the real-time detection of biomolecules with a bulk concentration in the picomolar range.

Helices are among the simplest shapes that are observed in the filamentary and molecular structures of nature. The local mechanical properties of such structures are often modeled by a uniform elastic potential energy dependent on bending and twist, which is what we term a rod model. Our first result is to complete the semi-inverse classification, initiated by Kirchhoff, of all infinite, helical equilibria of inextensible, unshearable uniform rods with elastic energies that are a general quadratic function of the flexures and twist. Specifically, we demonstrate that all uniform helical equilibria can be found by means of an explicit planar construction in terms of the intersections of certain circles and hyperbolas. Second, we demonstrate that the same helical centerlines persist as equilibria in the presence of realistic distributed forces modeling nonlocal interactions as those that arise, for example, for charged linear molecules and for filaments of finite thickness exhibiting self-contact. Third, in the absence of any external loading, we demonstrate how to construct explicitly two helical equilibria, precisely one of each handedness, that are the only local energy minimizers subject to a nonconvex constraint of self-avoidance. biomolecules | differential geometry | elasticity | filaments | rods

Carotenoids (Car) act as 'wires' that discharge unwanted electrons in the reaction center of higher plants. One step in this 'side-path' electron conduction is thought to be mediated by Car oxidation. We have carried out direct measurements of the conductance of single-Car molecules under potential control in a membrane-mimicking environment, and we found that when Car are oxidized conductance is enhanced and the electronic decay constant ([beta]) is decreased. However, the neutral molecule may already be conductive enough to account for observed electron transfer rates. carotenoid | molecular electronics | photosynthesis | potential control single molecule

We have recently introduced a quantum mechanical polarizable force field (QMPFF) fitted solely to high-level quantum mechanical data for simulations of biomolecular systems. Here, we present an improved form of the force field, QMPFF2, and apply it to simulations of liquid water. The results of the simulations show excellent agreement with a variety of experimental thermodynamic and structural data, as good or better than that provided by specialized water potentials. In particular, QMPFF2 is the only ab initio force field to accurately reproduce the anomalous temperature dependence of water density to our knowledge. The ability of the same force field to successfully simulate the properties of both organic molecules and water suggests it will be useful for simulations of proteins and protein-ligand interactions in the aqueous environment.

Understanding the mechanism of fast transitions between conformed states of large biomolecules is central to reconciling the dichotomy between the relatively high speed of metabolic processes and slow (random-walk based) estimates on the speed of biomolecular processes, Here we use the dynamical systems approach to suggest that the reduced time of transition between different conformations is due to features of the dynamics of molecules that are a consequence of their structural features. Long-range and local effects both play a role. Long-range molecular forces account for the robustness of final states and nonlinear processes that channel localized, bounded disturbances into collective, modal motions. Local interconnections provide fast transition dynamics. These properties are shared by a class of networked systems with strong local interconnections and long-range nonlinear forces that thus exhibit flexibility and robustness at the same time. coupled oscillator model | resonance | dynamics of biomolecules

We demonstrate the formation of charged molecular packets and their transport within optically created electrical force-field traps in a pH-buffered electrolyte. We call this process photoelectrophoretic localization and transport (PELT). The electrolyte is in contact with a photoconductive semiconductor electrode and a counterelectrode that are connected through an external circuit. A light beam directed to coordinates on the photoconductive electrode surface produces a photocurrent within the circuit and electrolyte. Within the electrolyte, the photocurrent creates localized force-field traps centered at the illuminated coordinates. Charged molecules, including polypeptides and proteins, electrophoretically accumulate into the traps and subsequently can be transported in the electrolyte by moving the traps over the photoconductive electrode in response to movement of the light beam. The molecules in a single trap can be divided into aliquots, and the aliquots can be directed along multiple routes simultaneously by using multiple light beams. This photoelectrophoretic transport of charged molecules by PELT resembles the electrostatic transport of electrons within force-field wells of solid-state charge-coupled devices. The molecules, however, travel in a liquid electrolyte rather than a solid. Furthermore, we have used PELT to position amphoteric biomolecules in three dimensions. A 3D pH gradient was created in an electrolyte medium by controlling the illumination position on a photoconductive anode where protons were generated electrolytically. Photoelectrophoretic transport of amphoteric molecules through the pH gradient resulted in accumulation of the molecules at their apparent 3D isoelectric coordinates in the medium. electrophoresis | light | mass spectrometry | protein transport | proteomics