RNA polymerase as a molecular machine

Structure and function of DNA-dependent RNA polymerase is considered in terms of a conveying molecular machine. The use of mechanical energy and mechanical devices, such as "power-stroke motor", is supposed unlikely in the conveying function of RNA polymerase, as well as other molecular machines. Brownian motion and thermal mobility of macromolecules and their parts are postulated as the only motive impulse at the molecular level. Binding of substrates and subsequent chemical reaction as the energy input may provide successive selection and fixation of alternative conformational states of the enzyme complex thus providing the directionality of the conveyance ("Brownian ratchet mechanism"). The following sequence of events "substrate binding--fixation of a certain conformational state--chemical reaction--fixation of an alternative conformational state--translocation (dissociation and downstream reassociation) of product-template duplex" is proposed as the principal scheme of the forward movement of RNA polymerase along DNA template.     

Cell molecular computer. VII. Cell biophysics and realistic or information physics (1)]

Living organisms measure many parameters in order to have orientation in the outer medium. That is why biophysics cannot use the ordinary laws of physics and must take into account the influence on the phenomena to be studied not only of a measurement but also of a calculation process in the real physical and biophysical device predicting the future. Science taking into account the effects of the calculating process-realistical or informative (RI) physics-has different (laws) for different times, distances and numbers of measuring and predicting parameters. RI-physics deals with unreproducible events and considers only such time intervals and distances for which the prediction can be made on the basis of earlier measurements and calculations according to the laws with optimal difficulty. It is suggested that the living cell uses the laws which are close to these optimal (limiting) laws of RI-physics. Physics and quantum mechanics can be considered as a limiting case of RI-physics. In this case values of distances and times are large enough and the number of simultaneously measured independent parameters is such that the heat effect of the calculating device would become negligible. Molecular cell computer (MCC) [I] cannot calculate the interaction of a great quantity of different molecules, using the equations of quantum mechanics because the expense of the (price of action) would be very large and both MCC and the surrounding world could change.     

Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking

Biomolecular nanomechanical devices are of great interest as tools for the processing and manipulation of molecules, thereby mimicking the function of nature’s enzymes. DNA nanotechnology provides the capability to build molecular analogs of mechanical machine elements such as joints and hinges via sequence-programmable self-assembly, which are otherwise known from traditional mechanical engineering. Relative to their size, these molecular machine elements typically do not reach the same relative precision and reproducibility that we know from their macroscopic counterparts; however, as they are scaled down to molecular sizes, physical effects typically not considered by mechanical engineers such as Brownian motion, intramolecular forces, and the molecular roughness of the devices begin to dominate their behavior. In order to investigate the effect of different design choices on the roughness of the mechanical energy landscapes of DNA nanodevices in greater detail, we here study an exemplary DNA origami-based structure, a modularly designed rotor-stator arrangement, which resembles a rotatable nanorobotic arm. Using fluorescence tracking microscopy, we follow the motion of individual rotors and record their corresponding energy landscapes. We then utilize the modular construction of the device to exchange its constituent parts individually and systematically test the effect of different design variants on the movement patterns. This allows us to identify the design parameters that most strongly affect the shape of the energy landscapes of the systems. Taking into account these insights, we are able to create devices with significantly flatter energy landscapes, which translates to mechanical nanodevices with improved performance and behaviors more closely resembling those of their macroscopic counterparts.     

On-line integration of computer controlled diagnostic devices and medical information systems in undergraduate medical physics education for physicians

We designed and evaluated an innovative computer-aided-learning environment based on the on-line integration of computer controlled medical diagnostic devices and a medical information system for use in the preclinical medical physics education of medical students. Our learning system simulates the actual clinical environment in a hospital or primary care unit. It uses a commercial medical information system for on-line storage and processing of clinical type data acquired during physics laboratory classes. Every student adopts two roles, the role of ‘patient’ and the role of ‘physician’. As a ‘physician’ the student operates the medical devices to clinically assess ‘patient’ colleagues and records all results in an electronic ‘patient’ record. We also introduced an innovative approach to the use of supportive education materials, based on the methods of adaptive e-learning. A survey of student feedback is included and statistically evaluated.The results from the student feedback confirm the positive response of the latter to this novel implementation of medical physics and informatics in preclinical education. This approach not only significantly improves learning of medical physics and informatics skills but has the added advantage that it facilitates students’ transition from preclinical to clinical subjects.     

Reconstruction of long polynucleotide sequences from fragments using the Iskra-226 personal computer]

An algorithm for reconstructing long DNA sequences, i.e. arranging all overlapping gel readings in the contigs, and the corresponding BASIC programme for personal computer "Iskra-226" (USSR) are described. The contig construction begins with the search for all fragments overlapping the basic (longest) one follower by determination of coordinates of 5' ends of the overlapping fragments. Then the gel reading with minimal 5' end coordinate and the gel reading with maximal 3' end coordinate are selected and used as basic ones at the next assembly steps. The procedure is finished when no gel reading overlapping the basic one can be found. All gel readings entered the contig are ignored at the next steps of the assembly. Finally, one or several contigs consisted of DNA fragments are obtained. Effectiveness of the algorithm was tested on a model based on the multiple assembly of the nucleotide sequence, encoding the Na, K-ATPase alpha-subunit of pig kidney. The programme does not call for user's participation and can comprise contigs up to 10,000 nucleotides long.     

Physics of Ion Channels

We review the basic physics involved in transport of ions across membrane channels in cells. Electrochemical forces that control the diffusion of ions are discussed both from microscopic and macroscopic perspectives. A case is made for use of Brownian dynamics as the minimal phenomenological model that provides a bridge between experiments and more fundamental theoretical approaches. Application of Brownian and molecular dynamics methods to channels with known molecular structures is discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Brain-controlled interfaces: movement restoration with neural prosthetics

Brain-controlled interfaces are devices that capture brain transmissions involved in a subject's intention to act, with the potential to restore communication and movement to those who are immobilized. Current devices record electrical activity from the scalp, on the surface of the brain, and within the cerebral cortex. These signals are being translated to command signals driving prosthetic limbs and computer displays. Somatosensory feedback is being added to this control as generated behaviors become more complex. New technology to engineer the tissue-electrode interface, electrode design, and extraction algorithms to transform the recorded signal to movement will help translate exciting laboratory demonstrations to patient practice in the near future.     

Information concerning the mechanism of electrophoretic DNA separation provided by quantitative video-epifluorescence microscopy

Changes in conformation, length, and mobility of individual DNA molecules during agarose gel electrophbresis were measured using video micrographs obtained by epifluorescence microscopy. Globular, V-shaped, and linear conformations of DNA are found. The mobility, upon transformation from the globular to the V-shaped conformation, decreases, suggesting a collision with a gel fiber. The duration of interaction between DNA and gel fiber is proportional to the length of DNA. Hypothetically, this proportionality underlies the size separation of DNA by agarose gel electrophoresis. DNA release from the gel fiber appears to involve the movement of the arms of the V-shaped molecule around the gel fiber. Concomitant with this movement is a length reduction the degree of which is constant for DNA of various lengths in a particular buffer milieu. The luminant densitometric profiles of DNA molecules in the V conformation show maxima at the ends and apex of the V. The unequal distribution of nucleotides along the DNA chain appears to provide the driving force for the molecular movement around the gel fiber.     

Calculation of the solution properties of flexible macromolecules: methods and applications

While the prediction of hydrodynamic properties of rigid particles is nowadays feasible using simple and efficient computer programs, the calculation of such properties and, in general, the dynamic behavior of flexible macromolecules has not reached a similar situation. Although the theories are available, usually the computational work is done using solutions specific for each problem. We intend to develop computer programs that would greatly facilitate the task of predicting solution behavior of flexible macromolecules. In this paper, we first present an overview of the two approaches that are most practical: the Monte Carlo rigid-body treatment, and the Brownian dynamics simulation technique. The Monte Carlo procedure is based on the calculation of properties for instantaneous conformations of the macromolecule that are regarded as if they were instantaneously rigid. We describe how a Monte Carlo program can be interfaced to the programs in the HYDRO suite for rigid particles, and provide an example of such calculation, for a hypothetical particle: a protein with two domains connected by a flexible linker. We also describe briefly the essentials of Brownian dynamics, and propose a general mechanical model that includes several kinds of intramolecular interactions, such as bending, internal rotation, excluded volume effects, etc. We provide an example of the application of this methodology to the dynamics of a semiflexible, wormlike DNA.     

Rotation and structure of FoF1-ATP synthase

F(o)F(1)-ATP synthase is one of the most ubiquitous enzymes; it is found widely in the biological world, including the plasma membrane of bacteria, inner membrane of mitochondria and thylakoid membrane of chloroplasts. However, this enzyme has a unique mechanism of action: it is composed of two mechanical rotary motors, each driven by ATP hydrolysis or proton flux down the membrane potential of protons. The two molecular motors interconvert the chemical energy of ATP hydrolysis and proton electrochemical potential via the mechanical rotation of the rotary shaft. This unique energy transmission mechanism is not found in other biological systems. Although there are other similar man-made systems like hydroelectric generators, F(o)F(1)-ATP synthase operates on the nanometre scale and works with extremely high efficiency. Therefore, this enzyme has attracted significant attention in a wide variety of fields from bioenergetics and biophysics to chemistry, physics and nanoscience. This review summarizes the latest findings about the two motors of F(o)F(1)-ATP synthase as well as a brief historical background.     

Brownian dynamics simulation of knot diffusion along a stretched DNA molecule

Manipulation of individual DNA molecules by optical tweezers has made it possible to tie these molecules into knots. After stretching the DNA molecules the knots become highly localized. In their recent study, Quake and co-authors investigated diffusion of such knots along stretched DNA molecules. We used these data to test the accuracy of a Brownian dynamics simulation of DNA bending motion. We simulated stretched DNA molecules with knots 3(1), 4(1), and 7(1), and determined their diffusion coefficients. Comparison of the simulated and experimental results shows that Brownian dynamics simulation is capable of predicting the rates of large-scale DNA rearrangements within a factor of 2.     

Parallel mechanisms of epigenetic reprogramming in the germline

Germ cells possess the extraordinary and unique capacity to give rise to a new organism and create an enduring link between all generations. To acquire this property, primordial germ cells (PGCs) transit through an unprecedented programme of sequential epigenetic events that culminates in an epigenomic basal state that is the foundation of totipotency. This process is underpinned by genome-wide DNA demethylation, which may occur through several overlapping pathways, including conversion to 5-hydroxymethylcytosine. We propose that the epigenetic programme in PGCs operates through multiple parallel mechanisms to ensure robustness at the level of individual cells while also being flexible through functional redundancy to guarantee high fidelity of the process. Gaining a better understanding of the molecular mechanisms that direct epigenetic reprogramming in PGCs will enhance our ability to manipulate epigenetic memory, cell-fate decisions and applications in regenerative medicine.     

Distinct Merkel Cell Polyomavirus Molecular Features in Tumour and Non Tumour Specimens from Patients with Merkel Cell Carcinoma

Merkel Cell Polyomavirus (MCPyV) is associated with Merkel Cell carcinoma (MCC), a rare, aggressive skin cancer with neuroendocrine features. The causal role of MCPyV is highly suggested by monoclonal integration of its genome and expression of the viral large T (LT) antigen in MCC cells. We investigated and characterized MCPyV molecular features in MCC, respiratory, urine and blood samples from 33 patients by quantitative PCR, sequencing and detection of integrated viral DNA. We examined associations between either MCPyV viral load in primary MCC or MCPyV DNAemia and survival. Results were interpreted with respect to the viral molecular signature in each compartment. Patients with MCC containing more than 1 viral genome copy per cell had a longer period in complete remission than patients with less than 1 copy per cell (34 vs 10 months, P = 0.037). Peripheral blood mononuclear cells (PBMC) contained MCPyV more frequently in patients sampled with disease than in patients in complete remission (60% vs 11%, P = 0.00083). Moreover, the detection of MCPyV in at least one PBMC sample during follow-up was associated with a shorter overall survival (P = 0.003). Sequencing of viral DNA from MCC and non MCC samples characterized common single nucleotide polymorphisms defining 8 patient specific strains. However, specific molecular signatures truncating MCPyV LT were observed in 8/12 MCC cases but not in respiratory and urinary samples from 15 patients. New integration sites were identified in 4 MCC cases. Finally, mutated-integrated forms of MCPyV were detected in PBMC of two patients with disseminated MCC disease, indicating circulation of metastatic cells. We conclude that MCPyV molecular features in primary MCC tumour and PBMC may help to predict the course of the disease.     

Linguistics of nucleotide sequences. II: Stationary words in genetic texts and the zonal structure of DNA

Words are irregularly distributed in genetic texts. The analysis of this irregularity leads to the notion of stationary and non-stationary words. The polyW and polyS tracts are shown to be the most non-stationary words in genetic texts (here W-[A,T], S-[G,C], a polyW tract is a sequence of A,T nucleotides and a polyS tract is a sequence of G,C nucleotides. The distribution of stationary words suggests a method for partitioning DNA into zones. The zones obtained in the case of the phage are interpreted in the light of the Dowe hypothesis of the modular structure of bacteriophage genomes.     

Chemomechanical coupling of the forward and backward steps of single kinesin molecules

The molecular motor kinesin travels processively along a microtubule in a stepwise manner. Here we have studied the chemomechanical coupling of the hydrolysis of ATP to the mechanical work of kinesin by analysing the individual stepwise movements according to the directionality of the movements. Kinesin molecules move primarily in the forward direction and only occasionally in the backward direction. The hydrolysis of a single ATP molecule is coupled to either the forward or the backward movement. This bidirectional movement is well described by a model of Brownian motion assuming an asymmetric potential of activation energy. Thus, the stepwise movement along the microtubule is most probably due to Brownian motion that is biased towards the forward direction by chemical energy stored in ATP molecules.     

Linguistics of Nucleotide Sequences II: Stationary Words in Genetic Texts and the Zonal Structure of DNA

Abstract

Words are irregularly distributed in genetic texts. The analysis of this irregularity leads to the notion of stationary and non-stationary words. The polyW and polyS tracts are shown to be the most non-stationary words in genetic texts (here W-(AT), S-{G,C}, a polyW tract is a sequence of AT nucleotides and a polyS tract is a sequence of G,C nucleotides. The distribution of stationary words suggests a method for partitioning DNA into zones. The zones obtained in the case of the phage are interpreted in the light of the Dowe hypothesis of the modular structure of bacteriophage genomes.     

Molecular charge contact biosensing based on the interaction of biologically modified magnetic beads with an ion-sensitive field effect transistor

In this article, we report a novel method of biomolecular recognition based on the molecular charge contact (MCC). As one of the MCC biosensing method, the interaction between DNA-coated magnetic beads and a silicon-based semiconductor, an ion-sensitive field effect transistor (ISFET) could be detected for DNA molecular recognition events using the principle of the field effect, which enables detecting ionic or molecular charges. After DNA-coated magnetic beads had been introduced and brought in contact with the gate surface by a magnet, the threshold voltage of the ISFET was shifted in the positive direction by immobilization, hybridization and extension reaction of DNA molecules on magnetic beads. This positive shift was based on the increase in negative charges of the phosphate groups in them. Then, the ISFET device could be reused a couple of dozen times continuously and cost-effectively because the oligonucleotide probes were tethered to the magnetic beads, but this was not done directly on the gate surface of the ISFET. Moreover, the MCC biosensing method enabled discrimination of a single nucleotide polymorphism. By creating an interaction of magnetic beads with the semiconductor, we can expect enhancement of the reaction efficiency in a solution and reuse of the device by separating the reaction field from the sensing substrate.     

The primary structure of rat ribosomal proteins: the amino acid sequences of L27a and L28 and corrections in the sequences of S4 and S12

The amino acid sequences of rat ribosomal proteins L27a and L28 were deduced from the sequences of nucleotides in recombinant cDNAs and confirmed from the NH2-terminal amino acid sequences of the proteins. L27a contains 147 amino acids (the NH2-terminal methionine is removed after translation of the mRNA) and has a molecular weight of 16 476. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 18-22 copies of the L27a gene. The mRNA for the protein is about 600 nucleotides in length. L27a is homologous to mouse L27a (there are 3 amino acid changes) and to yeast L29. Rat ribosomal protein L28 has 136 amino acids (its NH2-terminal methionine is also processed after translation) and has a molecular weight of 15 707. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 9 or 10 copies of the L28 gene. The mRNA for the protein is about 640 nucleotides in length. L28 contains a possible internal duplication of 9 residues. Corrections are recorded in the sequences reported before for rat ribosomal proteins S4 and S12.     

Stabilization of duplex DNA and RNA by dangling ends studied by free energy simulations

Single unpaired nucleotides at the end of double‐stranded nucleic acids, termed dangling ends, can contribute to duplex stability. Umbrella sampling free energy simulations of dangling cytosine and guanine nucleotides at the end of duplex and single stranded RNA and DNA molecules have been used to investigate the molecular origin of dangling end effects. In unrestraint simulations, the dangling end nucleotides stayed close to placements observed in experimental structures. Calculated free energy contributions associated with the presence of dangling nucleotides were in reasonable agreement with experiment predicting the general trend of a more stabilizing effect of purine vs. pyrimidine dangling ends. In addition, the calculations indicate a more significant stabilizing effect of dangling ends at the 5′‐end vs. 3′‐end in case of DNA and the opposite trend in case of RNA. Both electrostatic and van der Waals interactions contribute to the duplex stabilizing effect of dangling end nucleotides. The free energy simulation scheme could also be used to design dangling end nucleotides that result in enhanced duplex stabilization. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 418–427, 2014.