
The Mechanical properties of DNA are closly related to its molecular structure and the reletive weekness of the hydrogen bonds that hold strands of DNA together compared to the strength of the bonds within each strand. ===Strands association and dissociation=== The hydrogen bonds between the strands of the double helix are weak enough that they can be easily separated by enzymes. Enzymes known as helicases unwind the strands to facilitate the advance of sequence-reading enzymes such as DNA polymerase. The unwinding requires that helicases chemically cleave the phosphate backbone of one of the strands so that it can swivel around the other. The strands can also be separated by gentle heating, as used in PCR, provided they have fewer than about 10,000 base pairs (10 kilobase pairs, or 10 kbp). The intertwining of the DNA strands makes long segments difficult to separate. ===Circular DNA=== When the ends of a piece of double-helical DNA are joined so that it forms a circle, as in plasmid DNA, the strands are knot theory knotted. This means they cannot be separated by gentle heating or by any process that does not involve breaking a strand. The task of unknotting topologically linked strands of DNA falls to enzymes known as topoisomerases. Some of these enzymes unknot circular DNA by cleaving two strands so that another double-stranded segment can pass through. Unknotting is required for the replication of circular DNA as well as for various types of recombination in linear DNA. ===Great length versus tiny breadth=== The narrow breadth of the double helix makes it impossible to detect by conventional transmission electron microscope, except by heavy staining. At the same time, the DNA found in many cells can be macroscopic in length -- approximately 5 centimetres long for strands in a human chromosome. Consequently, cells must compact or "package" DNA to carry it within them. This is one of the functions of the chromosomes, which contain spool-like proteins known as histones, around which DNA winds. ===Different helix geometries=== The DNA helix can assume one of three slightly different geometries, of which the "B" form described by James D. Watson and Francis Crick is believed to predominate in cells. It is 2 nanometres wide and extends 3.4 nanometres per 10 Base pair of sequence. This is also the approximate length of sequence in which the double helix makes one complete turn about its axis. This frequency of twist (known as the helical ''pitch'') depends largely on stacking forces that each base exerts on its neighbors in the chain. ====Supercoiled DNA==== The B form of the DNA helix twists 360° per 10.6 bp in the absence of strain. But many molecular biological processes can induce strain. A DNA segment with excess or insufficient helical twisting is referred to, respectively, as positively or negatively "supercoil". DNA ''in vivo'' is typically negatively supercoiled, which facilitates the unwinding of the double-helix required for transcription. ====Conditions for formation of A and Z helices==== The two other known double-helical forms of DNA, called A and Z-DNA, differ modestly in their geometry and dimensions. The A form appears likely to occur only in dehydrated samples of DNA, such as those used in crystallography experiments, and possibly in hybrid pairings of DNA and RNA strands. Segments of DNA that cells have methylation for regulatory purposes may adopt the Z geometry, in which the strands turn about the helical axis like a mirror image of the B form. ====Table of comparison of the properties of different helical forms==== {| border="0" align="center" style="border: 1px solid #999; background-color:#FFFFFF" |-align="center" bgcolor="#CCCCCC" !Geometry attribute !A-form !B-form !Z-form |- |Helix sense ||align="center"| right-handed ||align="center"| right-handed ||align="center"| left-handed |--bgcolor="#EFEFEF" |Repeating unit ||align="right"| 1 bp ||align="right"| 1 bp ||align="right"| 2 bp |----- |Rotation/bp ||align="right"| 33.6° ||align="right"| 35.9° ||align="right"| 60°/2 |--bgcolor="#EFEFEF" |Mean bp/turn ||align="right"| 10.7 ||align="right"| 10.0 ||align="right"| 12 |----- |Inclination of bp to axis ||align="right"| +19° ||align="right"| -1.2° ||align="right"| -9° |--bgcolor="#EFEFEF" |Rise/bp along axis ||align="right"| 0.23 nm ||align="right"| 0.332 nm ||align="right"| 0.38 nm |----- |Pitch/turn of helix ||align="right"| 2.46 nm ||align="right"| 3.32 nm ||align="right"| 4.56 nm |--bgcolor="#EFEFEF" |Mean propeller twist ||align="right"| +18° ||align="right"| +16° ||align="right"| 0° |----- |Glycosyl angle ||align="center"| anti ||align="center"| anti ||align="center"| C: anti,
G: syn |--bgcolor="#EFEFEF" |Sugar pucker ||align="center"| C3'-endo ||align="center"| C2'-endo ||align="center"| C: C2'-endo,
G: C2'-exo |----- |Diameter ||align="right"| 260 nm ||align="right"| 200 nm ||align="right"| 180 nm |--bgcolor="#EFEFEF" |} ===Non-helical forms=== Other, including non-helical, forms of DNA have been described, for example a side-by-side (SBS) configuration. Indeed, it is far from certain that the B-form double helix is the dominant form in living cells.
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Mechanical properties of DNA
The Mechanical properties of DNA are closly related to its molecular structure and the reletive weekness of the hydrogen bonds that hold strands of DNA together compared to the strength of the bonds within each strand. ===Strands association and dissociation=== The hydrogen bonds between the strands of the double helix are weak enough that they can be easily separated by enzymes. Enzymes known as helicases unwind the strands to facilitate the advance of sequence-reading enzymes such as DNA polymerase. The unwinding requires that helicases chemically cleave the phosphate backbone of one of the strands so that it can swivel around the other. The strands can also be separated by gentle heating, as used in PCR, provided they have fewer than about 10,000 base pairs (10 kilobase pairs, or 10 kbp). The intertwining of the DNA strands makes long segments difficult to separate. ===Circular DNA=== When the ends of a piece of double-helical DNA are joined so that it forms a circle, as in plasmid DNA, the strands are knot theory knotted. This means they cannot be separated by gentle heating or by any process that does not involve breaking a strand. The task of unknotting topologically linked strands of DNA falls to enzymes known as topoisomerases. Some of these enzymes unknot circular DNA by cleaving two strands so that another double-stranded segment can pass through. Unknotting is required for the replication of circular DNA as well as for various types of recombination in linear DNA. ===Great length versus tiny breadth=== The narrow breadth of the double helix makes it impossible to detect by conventional transmission electron microscope, except by heavy staining. At the same time, the DNA found in many cells can be macroscopic in length -- approximately 5 centimetres long for strands in a human chromosome. Consequently, cells must compact or "package" DNA to carry it within them. This is one of the functions of the chromosomes, which contain spool-like proteins known as histones, around which DNA winds. ===Different helix geometries=== The DNA helix can assume one of three slightly different geometries, of which the "B" form described by James D. Watson and Francis Crick is believed to predominate in cells. It is 2 nanometres wide and extends 3.4 nanometres per 10 Base pair of sequence. This is also the approximate length of sequence in which the double helix makes one complete turn about its axis. This frequency of twist (known as the helical ''pitch'') depends largely on stacking forces that each base exerts on its neighbors in the chain. ====Supercoiled DNA==== The B form of the DNA helix twists 360° per 10.6 bp in the absence of strain. But many molecular biological processes can induce strain. A DNA segment with excess or insufficient helical twisting is referred to, respectively, as positively or negatively "supercoil". DNA ''in vivo'' is typically negatively supercoiled, which facilitates the unwinding of the double-helix required for transcription. ====Conditions for formation of A and Z helices==== The two other known double-helical forms of DNA, called A and Z-DNA, differ modestly in their geometry and dimensions. The A form appears likely to occur only in dehydrated samples of DNA, such as those used in crystallography experiments, and possibly in hybrid pairings of DNA and RNA strands. Segments of DNA that cells have methylation for regulatory purposes may adopt the Z geometry, in which the strands turn about the helical axis like a mirror image of the B form. ====Table of comparison of the properties of different helical forms==== {| border="0" align="center" style="border: 1px solid #999; background-color:#FFFFFF" |-align="center" bgcolor="#CCCCCC" !Geometry attribute !A-form !B-form !Z-form |- |Helix sense ||align="center"| right-handed ||align="center"| right-handed ||align="center"| left-handed |--bgcolor="#EFEFEF" |Repeating unit ||align="right"| 1 bp ||align="right"| 1 bp ||align="right"| 2 bp |----- |Rotation/bp ||align="right"| 33.6° ||align="right"| 35.9° ||align="right"| 60°/2 |--bgcolor="#EFEFEF" |Mean bp/turn ||align="right"| 10.7 ||align="right"| 10.0 ||align="right"| 12 |----- |Inclination of bp to axis ||align="right"| +19° ||align="right"| -1.2° ||align="right"| -9° |--bgcolor="#EFEFEF" |Rise/bp along axis ||align="right"| 0.23 nm ||align="right"| 0.332 nm ||align="right"| 0.38 nm |----- |Pitch/turn of helix ||align="right"| 2.46 nm ||align="right"| 3.32 nm ||align="right"| 4.56 nm |--bgcolor="#EFEFEF" |Mean propeller twist ||align="right"| +18° ||align="right"| +16° ||align="right"| 0° |----- |Glycosyl angle ||align="center"| anti ||align="center"| anti ||align="center"| C: anti,
G: syn |--bgcolor="#EFEFEF" |Sugar pucker ||align="center"| C3'-endo ||align="center"| C2'-endo ||align="center"| C: C2'-endo,
G: C2'-exo |----- |Diameter ||align="right"| 260 nm ||align="right"| 200 nm ||align="right"| 180 nm |--bgcolor="#EFEFEF" |} ===Non-helical forms=== Other, including non-helical, forms of DNA have been described, for example a side-by-side (SBS) configuration. Indeed, it is far from certain that the B-form double helix is the dominant form in living cells.
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