Basis for the Right-Handed Helical Sense of Double-Stranded DNA:  Formation of the Right-Handed Helix byl-Oligonucleotides Fixed in Low-antiGlycosyl Conformation

2001 ◽  
Vol 123 (20) ◽  
pp. 4845-4846 ◽  
Author(s):  
Hidehito Urata ◽  
Hidetaka Miyagoshi ◽  
Tetsuya Kumashiro ◽  
Keiji Mori ◽  
Keiko Shoji ◽  
...  
Keyword(s):  
Double Stranded Dna ◽  
The Right

scholarly journals Biological Nanomotors with a Revolution, Linear, or Rotation Motion Mechanism

2016 ◽  
Vol 80 (1) ◽  
pp. 161-186 ◽  
Author(s):  
Peixuan Guo ◽  
Hiroyuki Noji ◽  
Christopher M. Yengo ◽  
Zhengyi Zhao ◽  
Ian Grainge
Keyword(s):  
Close Contact ◽  
Motion Mechanism ◽  
Channel Size ◽  
Left Handed ◽  
Double Stranded Dna ◽  
Directional Movement ◽  
Two Factors ◽  
Rotation Motion ◽  
The Right ◽  
Small Channels

SUMMARYThe ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. In 2013, a third type of biomotor, revolution without rotation (http://rnanano.osu.edu/movie.html), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded DNA (dsDNA) bacteriophages. This review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and energy usage rate, in a variety of well-studied motors, including FoF1ATPase, helicases, viral dsDNA-packaging motors, bacterial chromosome translocases, myosin, kinesin, and dynein. In particular, dsDNA translocases are used to illustrate how these features relate to the motion mechanism and how nature elegantly evolved a revolution mechanism to avoid coiling and tangling during lengthy dsDNA genome transportation in cell division. Motor chirality and channel size are two factors that distinguish rotation motors from revolution motors. Rotation motors use right-handed channels to drive the right-handed dsDNA, similar to the way a nut drives the bolt with threads in same orientation; revolution motors use left-handed motor channels to revolve the right-handed dsDNA. Rotation motors use small channels (<2 nm in diameter) for the close contact of the channel wall with single-stranded DNA (ssDNA) or the 2-nm dsDNA bolt; revolution motors use larger channels (>3 nm) with room for the bolt to revolve. Binding and hydrolysis of ATP are linked to different conformational entropy changes in the motor that lead to altered affinity for the substrate and allow work to be done, for example, helicase unwinding of DNA or translocase directional movement of DNA.

scholarly journals Sticker Systems Over Monoids

2014 ◽  
Vol 8 (3) ◽  
Author(s):  
N.A. Mohd Sebry ◽  
N. Z. A. Hamzah ◽  
N.H. Sarmin ◽  
W.H. Fong ◽  
S. Turaev
Keyword(s):  
Neutral Element ◽  
Arbitrary Length ◽  
Double Stranded Dna ◽  
Enumerable Language ◽  
Successful Experiment ◽  
Sticker System ◽  
Sticky Ends ◽  
Generative Mechanism ◽  
Current Sequence ◽  
The Right

Molecular computing has gained many interests among researchers since Head introduced the first theoretical model for DNA based computation using the splicing operation in 1987. Another model for DNA computing was proposed by using the sticker operation which Adlemanused in his successful experiment for the computation of Hamiltonian paths in a graph: a double stranded DNA sequence is composed by prolonging to the left and to the right a sequence of (single or double) symbols by using given single stranded strings or even more complex dominoes with sticky ends, gluing these ends together with the sticky ends of the current sequence according to a complementarity relation. According to this sticker operation, a language generative mechanism, called a sticker system, can be defined: a set of (incomplete) double-stranded sequences (axioms) and a set of pairs of single or double-stranded complementary sequences are given. The initial sequences are prolonged to the left and to the right by using sequences from the latter set, respectively. The iterations of these prolongations produce “computations” of possibly arbitrary length. These processes stop when a complete double stranded sequence is obtained. Sticker systems will generate only regular languages without restrictions. Additional restrictions can be imposed on the matching pairs of strands to obtain more powerful languages. Several types of sticker systems are shown to have the same power as regular grammars; one type is found to represent all linear languages whereas another one is proved to be able to represent any recursively enumerable language. The main aim of this research is to introduce and study sticker systems over monoids in which with each sticker operation, an element of a monoid is associated and a complete double stranded sequence is considered to be valid if the computation of the associated elements of the monoid produces the neutral element. Moreover, the sticker system over monoids is defined in this study.

Defining cosQ, the Site Required for Termination of Bacteriophage λ DNA Packaging

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 495-506 ◽  
Author(s):  
Douglas J Wieczorek ◽  
Michael Feiss
Keyword(s):  
Insertional Mutagenesis ◽  
Dna Looping ◽  
Saturation Mutagenesis ◽  
Bacteriophage Λ ◽  
Recognition Sequence ◽  
Optimal Sequence ◽  
Bottom Strand ◽  
Double Stranded Dna ◽  
The Right ◽  
Half Site

Abstract Bacteriophage λ is a double-stranded DNA virus that processes concatemeric DNA into virion chromosomes by cutting at specific recognition sites termed cos. A cos is composed of three subsites: cosN, the nicking site; cosB, required for packaging initiation; and cosQ, required for termination of chromosome packaging. During packaging termination, nicking of the bottom strand of cosN depends on cosQ, suggesting that cosQ is needed to deliver terminase to the bottom strand of cosN to carry out nicking. In the present work, saturation mutagenesis showed that a 7-bp segment comprises cosQ. A proposal that cosQ function requires an optimal sequence match between cosQ and cosNR, the right cosN half-site, was tested by constructing double cosQ mutants; the behavior of the double mutants was inconsistent with the proposal. Substitutions in the 17-bp region between cosQ and cosN resulted in no major defects in chromosome packaging. Insertional mutagenesis indicated that proper spacing between cosQ and cosN is required. The lethality of integral helical insertions eliminated a model in which DNA looping enables cosQ to deliver a gpA protomer for nicking at cosN. The 7 bp of cosQ coincide exactly with the recognition sequence for the Escherichia coli restriction endonuclease, EcoO109I.

scholarly journals Machine Learning to Improve the Sensing of Biomolecules by Conical Track-Etched Nanopore

Biosensors ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 140
Author(s):  
Nathan Meyer ◽  
Jean-Marc Janot ◽  
Mathilde Lepoitevin ◽  
Michaël Smietana ◽  
Jean-Jacques Vasseur ◽  
...  
Keyword(s):  
Machine Learning ◽  
Support Vector Machines ◽  
Aspect Ratio ◽  
Dwell Time ◽  
Support Vector ◽  
Double Stranded Dna ◽  
Vector Machines ◽  
Conical Nanopores ◽  
Data Points ◽  
The Right

Single nanopore is a powerful platform to detect, discriminate and identify biomacromolecules. Among the different devices, the conical nanopores obtained by the track-etched technique on a polymer film are stable and easy to functionalize. However, these advantages are hampered by their high aspect ratio that avoids the discrimination of similar samples. Using machine learning, we demonstrate an improved resolution so that it can identify short single- and double-stranded DNA (10- and 40-mers). We have characterized each current blockade event by the relative intensity, dwell time, surface area and both the right and left slope. We show an overlap of the relative current blockade amplitudes and dwell time distributions that prevents their identification. We define the different parameters that characterize the events as features and the type of DNA sample as the target. By applying support-vector machines to discriminate each sample, we show accuracy between 50% and 72% by using two features that distinctly classify the data points. Finally, we achieved an increased accuracy (up to 82%) when five features were implemented.

Investor-State Dispute Settlement under NAFTA Chapter 11: The Shape of Things to Come?

1998 ◽  
Vol 35 ◽  
pp. 263-290
Author(s):  
J. Anthony VanDuzer
Keyword(s):  
Free Trade Agreement ◽  
Dispute Settlement ◽  
Trade Agreement ◽  
Minimum Standards ◽  
The North ◽  
State Behaviour ◽  
Nafta Chapter 11 ◽  
To Come ◽  
The Right

SummaryRecently, there has been a proliferation of international agreements imposing minimum standards on states in respect of their treatment of foreign investors and allowing investors to initiate dispute settlement proceedings where a state violates these standards. Of greatest significance to Canada is Chapter 11 of the North American Free Trade Agreement, which provides both standards for state behaviour and the right to initiate binding arbitration. Since 1996, four cases have been brought under Chapter 11. This note describes the Chapter 11 process and suggests some of the issues that may arise as it is increasingly resorted to by investors.

What face familiarity feelings say about the lateralization of specific entities within the core system

2019 ◽  
Vol 42 ◽  
Author(s):  
Guido Gainotti
Keyword(s):  
Temporal Lobe ◽  
Memory System ◽  
Core System ◽  
The Core ◽  
Memory Traces ◽  
Specific Memory ◽  
Target Article ◽  
Temporal Structures ◽  
The Right

Abstract The target article carefully describes the memory system, centered on the temporal lobe that builds specific memory traces. It does not, however, mention the laterality effects that exist within this system. This commentary briefly surveys evidence showing that clear asymmetries exist within the temporal lobe structures subserving the core system and that the right temporal structures mainly underpin face familiarity feelings.

Study of charge transfer in FeTi

1983 ◽  
Vol 41 ◽  
pp. 296-297
Author(s):  
J. Taft∅
Keyword(s):  
Charge Transfer ◽  
Charge Distribution ◽  
Electron Scattering ◽  
Periodic System ◽  
Electron Distribution ◽  
Scattering Amplitude ◽  
Transition Elements ◽  
Hartree Fock ◽  
Cscl Structure ◽  
The Right

It is well known that for reflections corresponding to large interplanar spacings (i.e., sin θ/λ small), the electron scattering amplitude, f, is sensitive to the ionicity and to the charge distribution around the atoms. We have used this in order to obtain information about the charge distribution in FeTi, which is a candidate for storage of hydrogen. Our goal is to study the changes in electron distribution in the presence of hydrogen, and also the ionicity of hydrogen in metals, but so far our study has been limited to pure FeTi. FeTi has the CsCl structure and thus Fe and Ti scatter with a phase difference of π into the 100-ref lections. Because Fe (Z = 26) is higher in the periodic system than Ti (Z = 22), an immediate “guess” would be that Fe has a larger scattering amplitude than Ti. However, relativistic Hartree-Fock calculations show that the opposite is the case for the 100-reflection. An explanation for this may be sought in the stronger localization of the d-electrons of the first row transition elements when moving to the right in the periodic table. The tabulated difference between fTi (100) and ffe (100) is small, however, and based on the values of the scattering amplitude for isolated atoms, the kinematical intensity of the 100-reflection is only 5.10-4 of the intensity of the 200-reflection.

New Dimensions in Freeze-Etching

1969 ◽  
Vol 27 ◽  
pp. 202-203 ◽  
Author(s):  
Russell L. Steere ◽  
Michael Moseley
Keyword(s):  
Fracture Surfaces ◽  
Aluminum Specimen ◽  
Specimen Holder ◽  
Freeze Etching ◽  
The Right

A redesigned specimen holder and cap have made possible the freeze-etching of both fracture surfaces of a frozen fractured specimen. In principal, the procedure involves freezing a specimen between two specimen holders (as shown in A, Fig. 1, and the left side of Fig. 2). The aluminum specimen holders and brass cap are constructed so that the upper specimen holder can be forced loose, turned over, and pressed down firmly against the specimen stage to a position represented by B, Fig. 1, and the right side of Fig. 2.

Adrenocorticotropin Production by a Mammary Carcinoma

1977 ◽  
Vol 35 ◽  
pp. 462-463
Author(s):  
K.S. McCarty ◽  
N.R. Wallace ◽  
W. Litaker ◽  
S. Wells ◽  
G. Eisenbarth
Keyword(s):  
Adrenocorticotropic Hormone ◽  
Small Cell ◽  
Hormone Production ◽  
Carcinoma Of The Breast ◽  
Ectopic Acth ◽  
Ultrastructural Studies ◽  
Subcutaneous Metastases ◽  
Ectopic Acth Production ◽  
The Right ◽  
Pituitary Carcinomas

The production of adrenocorticotropic hormone by non-pituitary carcinomas has been documented in several tumors, most frequently small cell carcinoma of the lung, islet cell carcinomas of the pancreas, thymomas and carcinoids. Electron microscopy of these tumors reveals typical membrane-limited "neurosecretory" granules. Confirmation of the granules as adrenocorticotropin (ACTH) requires the use of OsO4 as a primary fixative to give the characteristic cored granule appearance in conjunction with immunohistochemical demonstration of the hormone peptide. Because of the rarity of ectopic ACTH production by mammary carcinomas and the absence of appropriate ultrastructural studies in the two examples of such ectopic hormone production in the literature of which we are aware (1,2), we present biochemical and ultrastructural data from a carcinoma of the breast with apparent ACTH production.The patient had her primary tumor in the right breast in 1969. The tumor recurred as visceral and subcutaneous metastases in 1976 and again in 1977.

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