Tuesday, April 8, 2008

2,500 Researchers, 1 Large Hadron Collider, 1 New Snapshot Of The Universe

Deep in the bowels of the earth --100 metres below ground in Geneva, Switzerland -- lies a supermachine of 27 km circumference called the Large Hadron Collider (LHC) that has been built to unlock the mysteries of the universe.

Claude Leroy, a Université de Montréal physics professor, was among the 2,500 scientists from 37 countries recruited to help design, test and build the ATLAS detector at the supermachine that will provide a new perspective into what occurred at the time of the Big Bang and immediately after. Designed for CERN, the European Organization for Nuclear Research, the ATLAS detector, the largest among the four detectors operating at the supermachine in question, is 46 metres in length, 25 metres in height and 7000 tonnes in weight -- or the size of three football fields.

Prof. Leroy was responsible for the radiation and irradiation studies conducted to ensure the ATLAS detector will run smoothly. His investigations also led to the creation of MPX, a small device attached throughout the supermachine and ATLAS that uses pixel silicon detectors to perform real-time measurements of the spectral characteristics and composition of radiation inside and around the ATLAS detector. The small devices essentially capture images of what's inside the detector and its environment, such neutrons and photons, a world-first.

He also participated in physics studies that targeted the production of heavy leptons, excited leptons, quarks and supersymmetry, in particular the study of neutralinos as dark matter candidates. Prof. Leroy's experiments were critical in ensuring the viability of the ATLAS detector at the core of the supermachine, which is the world's biggest particles physics detector. Indeed, before the LHC can be started up, some 38,000 tons of equipment of the supermachine must be cooled down to minus 456 degrees Fahrenheit for the magnets to operate in a superconducting state. This will be achieved by using liquid helium for magnet. Parts of the ATLAS calorimeters use liquid argon cooled at minus 312 degrees Fahrenheit. "The radiation field produced by the operation of the machine and ATLAS is stronger than a nuclear reactor, so it is vital that its design master all aspects of physics," said Prof. Leroy.

Supermachine's Big Bang

The LHC will recreate conditions akin to the Big Bang -- which many scientists believe gave birth to the universe -- by colliding two beams of particles at close to the speed of light. Since it is estimated that only 4 percent of the universe has been charted, the supermachine will help answer the following questions in physics when it is turned on in summer 2008:

  1. What is the unknown 96 percent of the universe made of?
  2. Why do particles have mass?
  3. Why does nature prefer matter over antimatter?
  4. What lies beyond Earth's dimension?

http://www.sciencedaily.com/releases/2008/03/080331122534.htm

Large Hadron Collider world’s largest particle accelerator

It must be unequivocally stated at the outset that the chances of the danger described below actually happening is extremely remote. Having said that, however, it is a fact that two people in the US are pursuing a lawsuit in a federal court in Hawaii to stop scientists from turning on the world’s largest particle accelerator later this year. The men believe that the Large Hadron Collider, as it’s called, which is capable of recreating conditions that existed a trillionth of a second after the Big Bang could also create a small black hole capable of swallowing up the Earth and, in time, parts of the universe too — if not the whole of it.

The scientists involved with the construction and deployment of the $8 billion project that has the potential to revolutionise physics and our understanding of the universe, don’t deny that black holes might, in fact, be created when the machine’s cranked up. But they say these will be microscopic in size and will decay and evaporate in next to no time before any serious swallowing can begin.

However, a spokesperson of the Collider group also said: “Assuming our wildest fantasies, how much matter can one of these black holes consume in a second, in a year or even in several billion years? A black hole we make would only consume a tiny fraction of a gram of matter from Earth. There’s no possibility of causing any damage to the Earth.”

The scientists are almost certainly right — especially since they speak after having addressed such concerns by initiating two safety studies earlier and a third anonymous one last year. Nevertheless, where the well-being of the Earth is concerned (actually its very existence in this case) along with all life on it, no amount of safeguards is too much. One has only to see the havoc of global warming caused by burning fossil fuels indiscriminately to realise that unchecked by-products can have a runaway cascading effect. In this case it won’t even be like a factory that can’t dispose of its by-product. Instead, the by-product will dispose of the factory — and everything else.

It is, of course, a grand tribute to human intelligence that scientific endeavour can unlock the ultimate mysteries of the universe and, in doing so, relate itself to the rest of existence. But it would be far more than merely ironic to find that in trying to discover our beginnings we deliver our ends.

http://economictimes.indiatimes.com/News/News_By_Industry/Where_one_cant_be_too_careful/articleshow/2933635.cms

Large Hadron Collider (LHC)

Back in the old days before terrorists and tsunamis, it was always the labcoat-wearing mad scientists who were going to destroy the Earth in one of their crazy experiments. In the movies, scientists were always the ideal scapegoats - bald apart from two tufts of hair, certifiably mad, and without a friend in the world. Well, scientists are back in the firing line again. As the Large Hadron Collider (LHC) in Europe gets closer to completion, there is a paranoid groundswell telling the world that this science experiment will unleash uncontrollable forces, wreck the planet and kill us all.

The LHC has actually been designed to answer some of the big questions in physics, such as, what is mass. There are so many questions. For example, think about some of the sub-atomic particles, such as electrons and quarks. They are just points - they have no size. And in between them, there is a vacuum. So these sub-atomic particles are mathematical figments floating in nothing. Even worse, these mathematical figments have weird properties like charge, and mass. The LHC, when it switches on in late 2008, will help solve some of these crazy mysteries. To do this, it will recreate some of the titanic energies found immediately after the Big Bang.

The Large in LHC is not an exaggeration - it's enormous. It's an underground tunnel, shaped like a ring, that straddles the borders of Switzerland and France. Over 2500 scientists from 37 countries are labouring to build just one of its four detectors - which by itself, has more iron than the Eiffel Tower. The LHC will generate so much raw data that if it were stored on CDs, the stack would grow at 1.6 kilometres per month. The project will employ about half of all the particle physicists in the world.

Its name tells you what it does. 'Hadrons' are microscopic particles (such as the protons or neutrons in the core of an atom) that in turn, are made of even smaller sub-atomic particles. The LHC will collide beams of protons together. And hopefully the products of the collision will include the long sought after Higgs Particle, which is thought to endow everything in the universe with the strange property we call 'mass'.

The protons will travel at 99.99991% of the speed of light through pipes 27 kilometres in circumference, buried 50-100 metres underground. At that speed, the protons will have the energy of an express train. They will be kept travelling in a curved path by the largest array of superconducting magnets ever built, cooled by 130 tonnes of liquid helium. The liquid helium will be colder than the temperature of deep space.

You've probably heard that mass and energy can be turned into each other. In a nuclear weapon, a small amount of mass is turned into a huge amount of energy. In the LHC, the opposite happens - energy is turned into mass. In a bizarre example of how mass and energy can be interchanged, two small fast-moving protons will collide to make much-heavier slower particles - as though two nippy Cessna planes collided to make a lumbering bus. The energy in the 'speed' of the protons will hopefully be converted to the mass of the Higgs Particle.

Over the last decade, uninformed scare-mongers have spread disaster scenarios, with the LHC destroying the Earth, and even the universe. They say (quite correctly) that it's theoretically possible for the LHC to create mini-black holes. They then conveniently ignore the rest of the same theory that points out that the black holes would evaporate almost immediately. Instead, they wrongly claim that the mini-black holes would rapidly eat the Earth.

The scare-mongers also claim that the colliding protons in the LHC have enormous energies, and so something totally unforeseen in our current theories might happen. Well, cosmic rays with energies many tens of millions of times greater than the speeding protons in the LHC have been smashing into all the planets and moons in our solar system for billions of years - and we're all still here. So let's give it a whirl, and see what we find.

http://www.abc.net.au/science/articles/2008/04/08/2211092.htm?site=science/greatmomentsinscience&topic=latest

Sharp LC42XL2E 42" Full HD Slimline LCD TV

PRODUCT FEATURES:

42 inch Aquos Full High Definition LCD TV with built-in digital tuner (DVB-T) and dynamic contrast ratio of 10000:1

100Hz Double frame drive. Slim frame and super thin design

De-Juddering picture enhancement technology, 4ms response time and 3x HDMI outputs

10bit Signal processing for smoother color gradients

Highlights of the Sharp 42" Full HD Slimline LCD TV

  • 42 inch Aquos Full High Definition LCD TV with built-in digital tuner (DVB-T) and dynamic contrast ratio of 10000:1
  • 100Hz Double frame drive. Slim frame and super thin design
  • De-Juddering picture enhancement technology, 4ms response time and 3x HDMI outputs
  • 10bit Signal processing for smoother color gradients

Specifications

Freeview Built In
Yes
HDMI Inputs
3

Aerial

Type
None

Audio System

Features
Auto volume adjustment
Output Power / Total
30 Watt
Sound Effects (JA)
SRS TruSurround XT
Sound Output Mode
Stereo
Speakers Included
2 speakers
Surround Mode
Built-in

Battery

Type
None

Digital Storage Media

Type
None

Dimensions & Weight

Comments (JA)
Without stand
Depth
9.6 cm
Height
64.6 cm
Width
100 cm

DVD

Type
None

Header

Manufacturer
Sharp
Model
42XL2E
Product Line
Sharp LC

Power Device

Form Factor
Internal
Frequency Required
50 Hz
Nominal Voltage
AC 230V
Power Consumption Operational
242 Watt
Power Consumption Stand by / Sleep
0.5 Watt
Type
Power supply

Radio System

Type
None

Remote Control

Technology
Infrared
Type
Remote control

Remote Control (2nd)

Type
None

Stands & Mounts

Stand Design
Tabletop
Stand Included
Built-in

Television

Backlight Life
60,000 hour(s)
Brightness
450 cd/m2
Comb Filter
3D-Y/C digital
Diagonal Size
42 in
Diagonal Size (cm)
107 cm
Digital Television Certification
HD ready 1080p
Display Format
1080p (FullHD)
Features
On-screen menu
TruD technology
HD Ready
Yes
Image Aspect Ratio
16:9
Image Contrast Ratio
2000:1
PC Interface
VGA (HD-15)
Pixel Response Time
4 ms
Progressive Scan
Progressive scanning (line doubling)
Resolution
1920 x 1080
Series
Aquos
Technology
TFT active matrix
Type
LCD TV
Video Interface
Component
Composite
HDMI
S-Video
SCART
Viewing Angle
176 degrees
Viewing Angle (Vertical)
176 degrees
Widescreen
Widescreen

TV Tuner

Analogue TV Tuner
PAL
SECAM
Digital TV Service
FREEVIEW
Digital TV Tuner
DVB-T
Stereo Reception System
A2
NICAM
Teletext
Yes
Tuners Configuration
1x analogue
1x digital
TV Tuner Presence
Built-in

http://www.dabs.com/productview.aspx?quicklinx=4QLP

LC42XL2E 42 inch 100Hz HD Ready 1080P Slimline LCD TV

42 inch Aquos HD Ready 1080P LCD TV with built-in digital tuner (DVB-T) and dynamic contrast ratio of 10000:1. 100Hz Double frame drive. Slim frame and super thin design. De-Juddering picture enhancement technology, 4ms response time and 3x HDMI outputs. 10bit Signal processing for smoother colour gradients. 24Hz Compatible.



Specification

Screen size (inches): 42

HD technology: HD Ready 1080P

IDTV Freeview DVB tuner: Yes

Wall mountable: Yes

Teletext built in: Yes

Aspect ratio: 16:9

Screen resolution (pixels): 1920 x 1080

Response time (ms): 4

Brightness (cd/m2): 450

Contrast ratio: 2000:1


http://www.sharp.co.uk/invt/lc42xl2e







Sharp LC-42XL2E - 42" Widescreen 1080P Full HD LCD TV - With 100hz & Freeview

Product Features

  • Full HD 1080P LCD Television
  • Screen Size:42
  • Tuner Type:Analogue with Freeview
  • Teletext:Smartext with EPG
  • Nicam sound system
  • 42 inch Aquos HD Ready 1080P LCD TV
  • Built-in digital tuner (DVB-T)
  • Dynamic contrast ratio of 10000:1
  • 100Hz Double frame drive
  • Slim frame and super thin design
  • De-Juddering picture enhancement technology
  • 4ms response time
  • 3x HDMI outputs
  • 10bit Signal processing for smoother colour gradients
  • 24Hz Compatible

Technical Details


Screen size (inches): 42
HD technology: 1080P Full HD + HD Ready
IDTV Freeview DVB tuner: Yes
Wall mountable: Yes
Teletext built in: Yes
Aspect ratio: 16:9
Screen resolution (pixels): 1920 x 1080
Response time (ms): 4
Brightness (cd/m2): 450
Contrast ratio: 2000:1
Diagonal visible screen size (cm): 107
Picture and Text: Yes
Audio technology: SRS TruSurroundXT
Audio output (watts): 15W + 15W
Speaker system: Integrated
Integral tuner / av box: Integrated PAL/SECAM
Input port 1: HDMI x 3
Input port 2: SCART x 2
Input port 3: Composite RCA /S-Video Mini Din
Input port 4: Component RCA
Input port 5: PC 15pin D
Input port 7: RS232C
Output port 1: Audio (RCA)
Output port 2: Digital Audio (Optical)
Panel life (hours): 60,000
Power consumption (Watt): 242
Standby power consumption (Watt): 0.5
Power source: AC 220V-240V, 50Hz
Viewing angle (degrees): 176
DVB: Yes
Freeview: Yes
Advanced Super view LCD: Yes
3D-Y/C: Yes
4-Wavelength Backlight: Yes
Surround Sound: Yes
Clear Voice System: Yes
Top-up TV card slot: Yes
Component Terminal: Yes
Analog RGB for PC: Yes
Other features: Auto volume control
integrated PAL/SECAM tuner
DCE (Dynamic Contrast Enhancement)
Accessories included: Universal remote control, cables, manual
Outside dimensions - width (in mm): 1004
Outside dimensions - height (in mm): 646
Outside dimensions - depth (in mm): 95.8
Outside dimensions - depth incl stand (in mm): 305.1
Outside dimensions - width incl stand (in mm): 1004
Outside dimensions - height incl stand (in mm): 708
Weight of panel and speakers (kg): 26.5

http://www.amazon.co.uk/Sharp-LC-42XL2E-Widescreen-1080P-Freeview/dp/tech-data/B000WJ4WYE/ref=de_a_smtd/026-1885744-2754809

SHARP LC 42XL2E

SHARP LC 42XL2E

Premium Slim-line 42" XL2 Series Full HD 1080p LCD with 100Hz, Freeview, 3 x HDMI, PC Input and Aquos Link Also available in larger 46" screen size LC-46XL2E Product Features: Gloss Black Full High Definition 42" 107cmV 16:9 Wide Screen LCD TV Full HD Ready 1080p with 1920x1080 resolution Accepts 1080p, 1080i and 720p HD signal formats 3 x HDMI Digital Link for superb digital pictures and sound Advanced Super View non-reflective LCD panel with 60,000 backlight lifespan RGB Plus - Primary Red, Green & Blue colours are enhanced by two further shades of Red & Green; Provides much more natural and realistic colour shades Optical Picture...


Product Description Sharp LC 42XL2E - 42" LCD TV
Product Type LCD TV
Diagonal Size 42" - widescreen
Dimensions (WxDxH) 100 cm x 9.6 cm x 64.6 cm - without stand
Digital Television Certification HD ready 1080p
Resolution 1920 x 1080
Display Format 1080p (FullHD)
Digital TV Service FREEVIEW
Video Interface Component, composite, HDMI, S-Video, SCART
PC Interface VGA (HD-15)
Technology TFT active matrix
Progressive Scan Yes
Image Aspect Ratio 16:9
TV Tuner 1x analogue, 1x digital
Digital TV Tuner DVB-T
Analogue TV Tuner PAL, SECAM
Features On-screen menu, TruD technology
Sound Output Mode Stereo
Speaker System 2 speakers
Sound Effects SRS TruSurround XT
Stereo Reception System NICAM, A2
Remote Control Remote control - infrared
Power AC 230V ( 50 Hz )


Product Type 42" LCD TV
Series Aquos
Digital Television Certification HD ready 1080p
TV Tuner 1x analogue, 1x digital
Video Interface Component, composite, HDMI, S-Video, SCART
PC Interface VGA (HD-15)
Dimensions Without stand
Width 100 cm
Depth 9.6 cm
Height 64.6 cm
Display
Diagonal Size 42" - widescreen
Technology TFT active matrix
Resolution 1920 x 1080
Display Format 1080p (FullHD)
Image Aspect Ratio 16:9
Image Contrast Ratio 2000:1
Brightness 450 cd/m2
Progressive Scan Progressive scanning (line doubling)
Viewing Angle 176 degrees
Viewing Angle (Vertical) 176 degrees
Pixel Response Time 4 ms
Backlight Life 60,000 hour(s)
Comb Filter 3D-Y/C digital
Features On-screen menu, TruD technology
TV Tuner
Analogue TV Tuner PAL, SECAM
Stereo Reception System NICAM, A2
Digital TV Tuner
Digital TV Tuner DVB-T
Digital TV Service FREEVIEW
Video Features
HD Ready Yes
Teletext Yes
Remote Control
Type Remote control - infrared
Audio System
Sound Output Mode Stereo
Surround Mode Built-in
Sound Effects SRS TruSurround XT
Speakers Included 2 speakers
Output Power / Total 30 Watt
Features Auto volume adjustment
Speaker(s) 2 x right/left channel speaker - built-in - 15 Watt
Connections
Connector Type 3 x HDMI ( 19 pin HDMI Type A ) ¦ 2 x SCART ( 21 PIN SCART ) ¦ 1 x composite video/audio input ( RCA phono x 3 ) ¦ 1 x S-Video input ( 4 PIN mini-DIN ) ¦ 1 x component video input ( RCA phono x 3 ) ¦ 1 x VGA input ( 15 PIN HD D-Sub (HD-15) ) ¦ 1 x serial ¦ 1 x audio line-out ( RCA phono x 2 ) ¦ 1 x digital audio output (optical) ( TOS Link )
Stands & Mounts
Stand Included Built-in
Stand Design Tabletop
Power
Power Device Power supply - internal
Voltage Required AC 230V ( 50 Hz )
Power Consumption Stand by / Sleep 0.5 Watt
Power Consumption Operational 242 Watt
Dimensions & Weight Details
Dimensions & Weight Details Panel without stand - 100 cm x 9.6 cm x 70.8 cm ¦ Panel with stand - 100 cm x 30.5 cm x 64.6 cm x 26.5 kg



http://www.twenga.co.uk/specs-LC-42XL2E-SHARP-LCD-TV-193898

Potent stimulation of transcription-coupled DNA supercoiling by sequence-specific DNA-binding proteins

Transcription by RNA polymerase can stimulate localized DNA supercoiling in Escherichia coli. In vivo, there is extensive experimental support for a "twin-domain" model in which positive DNA supercoils are generated ahead of a translocating RNA polymerase complex and negative supercoils are formed behind it. Negative supercoils accumulate in the template DNA because the positive supercoils are preferentially removed by cellular topoisomerase action. Yet, in vitro, clear and convincing support for the twin-domain mechanism has been lacking. In this article, we reconcile this inconsistency by showing that, in a defined in vitro system with plasmid DNA templates, a variety of sequence-specific DNA-binding proteins, such as the bacteriophage lambda O replication initiator or the E. coli lactose or galactose repressors, strikingly stimulate transcription-coupled DNA supercoiling. We demonstrate further that this stimulation requires the presence in the DNA template of a recognition sequence for the relevant DNA-binding protein and depends on the production of long RNA chains by an RNA polymerase. Our data are most consistent with a model in which specific DNA-binding proteins facilitate a twin-domain mechanism to enhance DNA supercoiling during transcription. More precisely, we suggest that some nucleoprotein complexes, perhaps those that contain sharply bent DNA, can form barriers that impede the diffusion and merger of independent chromosomal supercoil domains. Localization of DNA supercoils by nucleoprotein complexes may serve as a general mechanism for modulating DNA transactions that are sensitive to DNA superhelicity.

http://www.pnas.org/cgi/content/abstract/99/14/9139

Crucial Role for DNA Supercoiling in Mu Transposition

DNA supercoiling plays an indispensable role in an early step of bacteriophage Mu transposition. This step involves formation of a nucleoprotein complex in which the Mu ends synapse and undergo two concerted single-strand cleavages. We describe a kinetic analysis of the role of supercoiling in the Mu-end synapsis reaction as measured by the cleavage assay. We observe a dependence of the reaction rate on superhelical density as well as on the length of Mu donor plasmid DNA. The reaction has a high activation enthalpy ({approx}67 kcal/mol). These results imply that the free energy of supercoiling is used directly to lower the activation barrier of the rate-limiting step of the reaction. Only the free energy of supercoiling associated with DNA outside the Mu ends appears to be utilized, implying that the Mu ends come together before the supercoiling energy is used. Our results suggest an essential function for the bacterial sequences attached to the ends of Mu virion DNA.

http://www.pnas.org/cgi/content/abstract/91/2/699

Supercoiling

What’s knotty about DNA? Under an electron microscope DNA looks like a long thin "knotted" strand that is tightly packed inside the cell nucleus. To visualize this, imagine packing 200 km of fishing line inside a basketball without tangling it! Amazingly, the cells in your body do the equivalent of this by supercoiling the DNA. Supercoiling is a very smart form of compact storage that allows for easy manipulation.

supercoiling.gif (7435 bytes)To illustrate supercoiling, take a long elastic band, cut it, hold one end tight and twist the other end as many times as possible (about 100 times!). Now without untwisting the elastic band, bring the ends together. You will end up with a supercoiled band, see diagram. When you bring the two end pieces together the elastic band tries to unwind, by untwisting about the centreline. However, this is not possible because you are still holding the ends, so it compromises by writhing around in space (like a well used phone cord).

The mathematical formula Lk=Tw+Wr can be used to describe this process. Lk, the linking number, represents the number of times one strand winds around the other, Tw is the twist or the amount of rotation about the centre line and Wr, the writhe, describes how hard it is to straighten out the curve. When the curve is straightened out the writhe, Wr, is zero and the twist, Tw, is high. You can feel the elastic band trying to untwist. When the elastic band is relaxed it supercoils. The twist Tw is now very small and the writhe Wr is high.

anglebeta.gif (2260 bytes)Supercoiling allows for easy manipulation and so easy access to the information coded in the DNA. When a cell is copying a DNA strand it will uncoil a strand, copy it and then recoil it. In order to obtain a more workable interpretation of the stresses in the DNA, David Stump and Peter Watson in the Mathematics Department of the University of Queensland have obtained mathematical formulas for the Twist and Writhe depending on the length of the strand and the angle beta (see figure). This then gives (through the formula above) the Linking number or the number of times one strand winds around the other.These results can then be used to explain the pictures, taken by an electron microscope, of the tiny strands of DNA coiling and uncoiling

http://www.maths.uq.edu.au/~infinity/Infinity7/supercoiling.html

DNA Supercoiling as a Pattern for Understanding Psycho-social Twistedness

The review here of twistedness in DNA provides a technical basis for the discussion in the main paper (Engaging with Questions of Higher Order: cognitive vigilance required for higher degrees of twistedness, 2004).

The insights in the main paper regarding "twistedness" reflect an intuitive understanding of complexity which calls for deeper insight to understand how twistedness works and why it may be vitally important in some psycho-social processes -- as well as being highly problematic in others. Part of the difficulty in approaching this matter is that "twistedness" is in most cases used unthinkingly as a pejorative term to characterize a pattern which is felt to inhibit right-thinking and clarity. The argument here is that, given its importance at every scale in nature, from the organization of nebula to the organization of the human cell, there is a case for distinguishing various forms of twistedness and understanding their function. This could be especially valuable to reconciling apparently irreconcilable understandings in society.

The merit of focusing on the nature and function of twisting in DNA is that it provides a rich natural template. It offers a sense of the degree of complexity that it may be required to master in order to comprehend how twistedness "works" in practice. It might also be argued that, as a process active in every human body and inherent to human life, humans may well have some kind of profound intuitive understanding of how it works and the "rightness" of such working. Some of the very explicit dynamics of this process may also offer patterns for understanding how the inhibiting effects of "twistedness" may be addressed when they are perceived to be a constraint on human development.

Understanding of how DNA works has been much enriched by concepts from topology -- as a branch of mathematics that deals with structural properties that are unchanged by deformations such as stretching and bending. This use of mathematics is especially important because there is no experimental way to observe the dynamics of enzymatic action directly, notably with respect to knotting and coiling of DNA (see De Witt Sumners. Lifting the Curtain: Using Topology to Probe the Hidden Action of Enzymes, 1995; Xiaoyan R. Bao, et al. Behavior of Complex Knots in Single DNA Molecules, 2003).

http://www.laetusinpraesens.org/docs00s/dnahelix.php are very long and thin. There is over a metre of DNA in every human cell in a space of some 0.0006 centimetres diametre. If DNA were constrained to be linear it would not fit into a cell. It must therefore fold many times to fit within the confines of a cell. The DNA is composed of 10** base pairs. This density of packing results in tangles and knots in the DNA that are essential to enable the cell to divide (involving transcription and replication).

http://www.laetusinpraesens.org/docs00s/dnahelix.php

DNA supercoil

In a "relaxed" double-helical segment of DNA, the two strands twist around the helical axis once every 10.4 base pairs of sequence. Adding or subtracting twists, as some enzymes can do, imposes strain. If a DNA segment under twist strain were to be closed into a circle by joining its two ends and then it is allowed to move freely, the circular DNA would contort into new shape, such as a simple figure-eight. Such a contortion is a supercoil.

The simple figure eight is the simplest supercoil, and is the shape a circular DNA assumes to accommodate one too many or one too few helical twists. The two lobes of the figure eight will appear rotated either clockwise or counterclockwise with respect to one another, depending on whether the helix is over or underwound. For each additional helical twist being accommodated, the lobes will show one more rotation about their axis.

The noun form "supercoil" is rarely used in the context of DNA topology. Instead, global contortions of a circular DNA, such as the rotation of the figure-eight lobes above, are referred to as writhe. The above example illustrates that twist and writhe are interconvertible. "Supercoiling" is an abstract mathematical property, and represents the sum of twist and writhe. The twist is the number of helical turns in the DNA and the writhe is the number of times the double helix crosses over on itself (these are the supercoils). The relationship of twist, writhe and supercoiling is expressed as the equation:

S = T + W.

Extra helical twists are positive and lead to positive supercoiling, while subtractive twisting causes negative supercoiling. Many topoisomerase enzymes sense supercoiling and either generate or dissipate it as they change DNA topology. DNA of most organisms is negatively supercoiled.

In part because chromosomes may be very large, segments in the middle may act as if their ends are anchored. As a result, they may be unable to distribute excess twist to the rest of the chromosome or to absorb twist to recover from underwinding--the segments may become supercoiled, in other words. In response to supercoiling, they will assume an amount of writhe, just as if their ends were joined.

Supercoiled DNA forms two structures; a plectoneme or a toroid, or a combination of both. A negatively supercoiled DNA molecule will produce either a one-start left-handed helix, the toroid, or a two-start right-handed helix with terminal loops, the plectoneme. Plectonemes are typically more common in nature, and this is the shape most bacterial plasmids will take. For larger molecules it is common for hybrid structures to form - a loop on a toroid can extend into a plectoneme. If all the loops on a toroid extend then it becomes a branch point in the plectonemic structure.

Image:Circular DNA Supercoiling.png
Size of this preview: 392 × 599 pixels


Supercoiled structure of circular DNA molecules with low writhe. Note that the helical nature of the DNA duplex is omitted for clarity.

Image:Linear DNA Supercoiling.png
Size of this preview: 800 × 474 pixels



Supercoiled structure of linear DNA molecules with constrained ends. Note that the helical nature of the DNA duplex is omitted for clarity


http://en.wikipedia.org/wiki/DNA_supercoil

DNA supercoiling

Varying levels of positive and negative supercoiling differently affect the efficiency with which topoisomerase II catenates and decatenates DNA

Type II DNA topoisomerases catalyze the transport of one DNA double helix through another. Here, by using a non-hydrolyzable analog of ATP, I examined the single-step DNA transport preferences of the yeast type II topoisomerase bound to positively and negatively supercoiled DNA rings. I found that negative supercoiling favors decatenation of DNA rings more than positive supercoiling. Conversely, positive supercoiling favors the catenation and knotting of DNA rings more than negative supercoiling. This vectorial effect of DNA supercoiling handedness supports a model in which type II topoisomerases can recognize three DNA segments, and highlights a novel influence of DNA supercoiling in global DNA topology.

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457D7V9-6&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=c0fd136de40dfc9683a0e8e90f21d368