Proteopedia - User contributions [en]

File:AdithyaSagar profile.jpg

2015-03-30T11:07:04Z

Adithya Sagar: uploaded a new version of "Image:AdithyaSagar profile.jpg"

File:AdithyaSagar profile.jpg

2015-03-30T11:03:41Z

Adithya Sagar: uploaded a new version of "Image:AdithyaSagar profile.jpg"

User:Adithya Sagar

2015-03-30T08:27:27Z

Adithya Sagar:

[[Image:AdithyaSagar_profile.jpg|thumb|right|200px]]

I graduated from the Indian Institute of Technology (IIT) with a Bachelors of Technology. I am currently pursuing my PhD from Cornell University. Previously I have been a visiting scientist in Joel Sussman Lab at Weizmann Institute of Science where I also worked on Proteopedia.

===Some of my favorites on Proteopedia===
[[Ribosome]] <br />
[[DNA]] <br />
[[Z-DNA]] <br />
[[Forms of DNA]] <br />

User:Adithya Sagar

2015-03-30T08:20:49Z

Adithya Sagar:

[[Image:AdithyaSagar_profile.jpg|thumb|right|100px]]

I graduated from the Indian Institute of Technology (IIT) with a Bachelors of Technology in 2009. I completed my Masters in Biomedical Engineering and am currently pursuing my PhD from Cornell University. Previously I have been a visiting scientist in Joel Sussman Lab at Weizmann Institute of Science and was a research associate in Briollais Lab at Mount Sinai Hospital.

Contact me at <email>asg242@cornell.edu</email>

===Some of my favorites on Proteopedia===
[[Ribosome]] <br />
[[DNA]] <br />
[[Z-DNA]] <br />
[[Forms of DNA]] <br />

User:Adithya Sagar

2013-01-24T12:30:14Z

Adithya Sagar:

[[Image:AdithyaSagar_profile.jpg|thumb|right|300px]]

I graduated from the Indian Institute of Technology (IIT) at Guwahati with a Bachelors of Technology in 2009. I completed my Masters in Biomedical Engineering and am currently pursuing my PhD from Cornell University. Previously I have been a visiting scientist in Joel Sussman Lab at Weizmann Institute of Science and was a research associate in Briollais Lab at Mount Sinai Hospital.

Contact me at <email>asg242@cornell.edu</email>

===Some of my favorites on Proteopedia===
[[Ribosome]] <br />
[[DNA]] <br />
[[Z-DNA]] <br />
[[Forms of DNA]] <br />

User:Adithya Sagar

2013-01-23T23:09:00Z

Adithya Sagar:

[[Image:AdithyaSagar_profile.jpg|thumb|right|400px]]

I graduated from the Indian Institute of Technology (IIT) at Guwahati with a Bachelors of Technology in 2009. Currently I am a graduate student at Cornell University working with Prof. William Olbricht at the Lewis Lab. I am also working as a computational biologist doing independent research in the Yu Lab at Cornell. Previously I have been a visiting scientist in Joel Sussman Lab at Weizmann Institute of Science and was a research associate in Briollais Lab at Mount Sinai Hospital.

Contact me at <email>asg242@cornell.edu</email>

===Some of my favorites on Proteopedia===
[[Ribosome]] <br />
[[DNA]] <br />
[[Z-DNA]] <br />
[[Forms of DNA]] <br />

2010-10-31T04:07:57Z

Adithya Sagar:

<applet load='B-DNA.pdb' size='330'frame='true' align='right' caption='B-DNA' scene='DNA/B-dna/7' />
'''Deoxyribonucleic acid''' or '''DNA''' is a molecule which is the carrier of genetic information in nearly all the living organisms. It contains the biological instructions for the development, survival and reproduction of organisms.
DNA is found in the nucleus of a cell where it is packaged into a compact form called a chromosome with the help of several proteins known as histones. It is also found in cell structures called mitochondria. However in case of prokaryotes DNA is not enclosed in a nucleus or a membrane but is present in the cytoplasm. The DNA in prokaryotes in generally circular and supercoiled without any histones. DNA stores genetic information as a sequence of nucleotides in special regions known as genes which are used to make proteins. The expression of genetic information into proteins is a two-stage process wherein the sequence of nucleotides in DNA is converted to a molecule called Ribonucleic acid or [[RNA]] by a process called [[transcription]]. RNA is used to make proteins by another process called [[translation]]. The human genome contains nearly 3 · 10<sup>9</sup> bases with around 20,000 genes on 23 chromosomes. <ref name='gene'>http://www.genome.gov/25520880 </ref>

DNA was first discovered by the German biochemist Frederich Miescher in the year 1869.<ref>PMID: 17901982</ref> Based on the works of Erwin Chargaff, James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin, the structure of DNA was discovered in the year 1953. The structure of DNA is a <scene name='DNA/B-dna/6'>double helix</scene>: two complementary strands of polynucleotides that run in opposite directions and are held together by hydrogen bonds between them. This structure helps the DNA replicate itself during cell division and also for a single strand to serve as template during transcription. <ref name='gene'>http://www.genome.gov/25520880 </ref>

<scene name='DNA/B-dna/7'>Restore View</scene>

== Features of a DNA Molecule ==
<applet load='B-DNA.pdb' size='540' frame='true' align='left' caption='B-DNA' scene ='User:Adithya_Sagar/Sandbox_DNA/B-dna/4'/>
=== Double Helix ===

DNA consists of two polynucleotide chains, <scene name='DNA/B-dna/10'>twisted around each other to form a double helix</scene>. The nucleotide in DNA is composed of of a <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/19'>5' phosphorylated sugar</scene> which is a beta-D-2'- deoxyribose and a purine or a pyrimidine <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/18'>base</scene>. The four types of bases are the two double ringed purine base <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/1'>Adenine (A)</scene> and <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/2'>Guanine (G)</scene> and the two single pyrimidine bases <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/6'>Thymine (T)</scene> and <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/5'>Cytosine (C)</scene>.Each nucleotide in a DNA chain is linked to another via <scene name='User:Adithya_Sagar/Workbench/Retest/B-dna/2'>3',5' phosphodiester bond</scene>. There are four nucleotides in DNA. The sugar-phosphate backbone of the DNA is very regular owing to the phosphodiester linkage whereas the ordering of bases is highly irregular.<ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref>

<scene name='DNA/B-dna/11'>Restore View</scene>
{{Template:Button Toggle NucleicDrumsColorScheme}}
{{Template:ColorKey Bases DNA}}

{{Template:Button Toggle PurinePyrimidineDrumsColorScheme}}
{{Template:ColorKey Purines Pyrimidines}}

=== Complementary Bases ===

The two chains in a DNA are joined by hydrogen bonds between specific bases. Adenine forms a base pairs with thymine and guanine with cytosine. This specific base pairing between <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/14'>Adenine-Thymine</scene> and <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/15'>Guanine-Cytosine</scene> is known as Watson-Crick base pairing. The specificity of hydrogen bonding between bases leads to complementarity in the sequence of nucleotides in the two chains. Thus in a strand of DNA the content of adenine is equal to that of thymine and the guanine content is equal to the cytosine content. In general DNA with higher GC content is more stable than the one with higher AT content owing to the stabilization due to base stacking interactions.

=== DNA denaturation and renaturation ===

A DNA double strand can be separated into two single strands by breaking the hydrogen bonds between them. This is known as DNA denaturation. Thermal energy provided by heating can be used to melt or denature DNA. Molecules with rich GC content are more stable and thus denature at higher temperatures compared to the ones with higher AT content. The melting temperature is defined as the temperature at which half the DNA strands are in double helical state and half are in random coil state.<ref>PMID: 9465037</ref> The denatured DNA single strands have an ability to renature and form double stranded DNA again.

 

 

=== Grooves ===
<applet load='B-DNA.pdb' size='330' frame='true' align='left' caption='B-DNA' scene ='DNA/Bdnasf/1' />
In a DNA double helix the <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/16'>beta-glycosyl bonds</scene> between C<sub>1'</sub>-N<sub>1</sub> branch off from one side of the base pair and do not lie opposite to each other. This results in unequally spaced sugar-phosphate backbones and gives rise to two grooves: the
<scene name='DNA/B-dna/5'>major groove</scene> and the <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/21'>minor groove</scene> of different width and depth. The minor groove is at the O<sub>2</sub> side of base pair and the major groove is on the opposite side.The floor of major groove is filled with nitrogen and oxygen atoms that project inward whereas in the minor groove they project outward. The larger size of major groove allows for the binding of DNA specific proteins.<ref name="Saenger"> Saenger, Wolfram (1984). ''Principles of Nucleic Acid Structure '' (1st ed). Springer-Verlag. pp. 398. ISBN 0-12-645750-6.</ref><ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref>

 

 

===Tautomeric forms of bases===

The hydrogen atoms on the bases move from nitrogen or oxygen atom on ring to another through shifts known as tautomeric shifts. However the hydrogens have preferred atomic locations. Based on the movement of hydrogen atoms the nitrogen atoms are in amino or imino configuration and the oxygen atoms are either in keto or enol forms. There is a preference for the amino and keto forms respectively which is very crucial for the biological functioning of DNA as it leads to the specificity in base pairing and thus complementarity of the chains.<ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref>

 

 

==Forms of DNA==
''See Also: [[Z-DNA]]''

 

 

=== A comparative representation of the three forms of DNA ===
''Sources''<ref>http://203.129.231.23/indira/nacc/</ref>
<applet load='A-DNA.pdb' name='A' size='350' frame='true' align='right' caption='A-DNA' align='left' scene='User:Adithya_Sagar/Sandbox_DNA/A-dna/1'/>
<applet load='B-DNA.pdb' name='B' size='350' frame='true' align='right' caption='B-DNA' align='left' scene='User:Adithya_Sagar/Sandbox_DNA/B-dna/3'/>
<applet load='Z-DNA.pdb' name='Z' size='350' frame='true' align='right' caption='Z-DNA' align='left' scene='User:Adithya_Sagar/Sandbox_DNA/Z-dna/1'/>

{{Clear}}
<center>
'''Synchronize the three applets showing A-, B- and Z-DNA by clicking the checkbox'''
<jmol>
<jmolCheckbox>
<target>A</target>

<scriptWhenChecked> sync jmolAppletB,jmolAppletZ </scriptWhenChecked>
<scriptWhenUnchecked> sync OFF</scriptWhenUnchecked>
<text> Synchronize</text>
</jmolCheckbox>
</jmol>
</center>

{{Clear}}

=== Helical Parameters of the three forms of DNA ===

DNA is a very flexible molecule and has the ability to exist in various forms based on the environmental conditions. Naturally occurring DNA double helices are classified into A, B and Z-types. A and B-forms of DNA are the right handed forms whereas [[Z-DNA]] is the left handed form. When hydrated the DNA generally assumes B-form. The A conformation is found when there is little water to interact with the helix and is also the conformation adopted by the RNA. The formation of Z-DNA occurs with the methylation of deoxycytosine residues and also during transcription where negative supercoiling stabilizes it.

{| class="wikitable" align= "center''
|-
!Parameter
!A-DNA
!B-DNA
!Z-DNA
|-
|Helix sense ||align="center"| right-handed ||align="center"| right-handed ||align="center"| left-handed
|-
|Residues per turn ||align="right"| 11 ||align="right"| 10.5 ||align="right"| 12
|-
|Axial rise [Å] ||align="right"| 2.55 ||align="right"| 3.4 ||align="right"| 3.7
|-
|Helix pitch(°) ||align="right"| 28 ||align="right"| 34 ||align="right"| 45
|-
|Base pair tilt(°) ||align="right"| 20 ||align="right"| −6 ||align="right"| 7
|-
|Rotation per residue (°) ||align="right"| 33||align="right"| 36||align="right"|-30
|-
|Diameter of helix [Å]||align="right"| 23||align="right"| 20||align="right"| 18
|-
|Glycosidic bond configuration<br\>dA,dT,dC<br\>dG ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>syn
|-
|Sugar pucker<br\>dA,dT,dC<br\>dG ||align="center"| <br\>C3'-endo<br\>C3'-endo ||align="center"|<br\> C2'-endo<br\>C2'-endo ||align="center"| <br\>C2'-endo<br\>C3'-endo
|-
|Intrastrand phosphate-phosphate distance [Å] <br\>dA,dT,dC<br\>dG ||align="center"| <br\>5.9<br\>5.9||align="center"| <br\>7.0<br\>7.0||align="center"| <br\>7.0<br\> 5.9
|-
|colspan="4"|''Sources:<ref name="Rich1984">PMID:6383204</ref><ref name="Rich1979">PMID: 514347</ref><ref> Sinden, Richard R (1994-01-15). ''DNA structure and function'' (1st ed.). Academic Press. pp. 398. ISBN 0-12-645750-6.</ref>
|}

== Structural Transformation between A and B DNA ==



<jmol>
<jmolApplet>
<size>660</size>
<color>white</color>
<uploadedFileContents>morph_a-b.pdb</uploadedFileContents>
<script>animation ON; animation mode PALINDROME; cartoon ON; save state ab </script> 
</jmolApplet>
</jmol>


<jmol>
<jmolButton>
<target>5</target>
<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/9/9e/Morph_a-b.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script> 
<text>Click here and activate the below options </text>
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<jmol>
<jmolRadioGroup>
<target>5</target>
<item>
<script> moveto 1.0 0 0 1 0 180.0 0.0 0.0;restore state ab; animation ON;animation mode palindrome;cartoon ON;spacefill on; spacefill 90;wireframe on;wireframe 50;zoom 180;select 9:a,4:b;hbonds ON;hbonds calculate;hbonds 0.09;select!selected; color translucent 0.9;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Base pair shift between A and B DNA"</script>
<text>Shift in Base Pair between A-B DNA</text>
</item>
<item>
<script> moveto 1.0 0 0 1 0 400.0 0.0 0.0; restore state ab;cartoon OFF;spacefill ON; spacefill 90; wireframe ON; wireframe 50;select 9:a; select!selected; color translucent 0.9; select!selected; centre selected;zoom 400;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA"</script>
<text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
</item>
<item>
<script>moveto 1.0 0 0 1 0 150.0 0.0 0.0;restore state ab;spacefill ON; spacefill 400; zoom 150; cartoon OFF;animation ON; animation mode PALINDROME;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Transition between A-B DNA spacefilling models"</script>
<text>Transition between A-B DNA spacefilling models</text>
</item>
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<jmol>
<jmolButton>
<target>5</target>
<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/9/9e/Morph_a-b.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
<text>Restore Original State </text>
</jmolButton>
</jmol>


<jmol>
<jmolApplet>
<color>white</color>
<size>660</size>
<uploadedFileContents>Morph_test.pdb</uploadedFileContents>
<script>animation ON;animation mode PALINDROME;cartoon ON; save state ab_new</script>
</jmolApplet>
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<jmol>
<jmolButton>
<target>6</target>
<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/5/50/Morph_test.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
<text>Click here and activate options below </text>
</jmolButton>
</jmol>

<jmol>
<jmolRadioGroup>
<target>6</target>
<item>
<script> moveto 1.0 0 0 1 0 180.0 0.0 0.0;restore state ab; animation ON;animation mode palindrome;cartoon ON;spacefill on; spacefill 90;wireframe on;wireframe 50;zoom 180;select 9:a,4:b;hbonds ON;hbonds calculate;hbonds 0.09;select!selected; color translucent 0.9;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Shift in Base Pair between A-B DNA"</script>
<text>Shift in Base Pair between A-B DNA</text>
</item>
<item>
<script> moveto 1.0 0 0 1 0 400.0 0.0 0.0; restore state ab;cartoon OFF;spacefill ON; spacefill 90; wireframe ON; wireframe 50;select 9:a; select!selected; color translucent 0.9; select!selected; centre selected;zoom 400;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA"</script>
<text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
</item>
<item>
<script>moveto 1.0 0 0 1 0 150.0 0.0 0.0;restore state ab;spacefill ON; spacefill 400; zoom 150; cartoon OFF;animation ON; animation mode PALINDROME;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Transition between A-B DNA spacefilling models"</script>
<text>Transition between A-B DNA spacefilling models</text>
</item>
</jmolRadioGroup>
</jmol>

<jmol>
<jmolButton>
<target>6</target>
<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/5/50/Morph_test.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
<text>Restore Original State </text>
</jmolButton>
</jmol>

''Morph Sources'' <ref>PMID: 10734184</ref>



== Biological Functions ==
''Sources:''<ref name='Rawn' > Rawn,David J. "Biochemistry"(1st ed.) Harper&Row,Publishers, Inc.pp. 1024-1050. ISBN-0-06045335-4</ref>

=== Replication===
DNA undergoes what is known as semi conservative mode of replication wherein the daughter DNA contains one DNA strand of the parent. The replication proceeds through the unwinding of double helix followed by synthesis primers from where the replication begins. An enzyme DNA polymerase synthesizes complementary strands to each parent strand from 5'-3' direction.

===Transcription and Translation===
The expression of genes into proteins and is a process involving two stages called transcription and translation. In the transcription stage a strand of DNA molecule serves as a template for the synthesis of an RNA molecule called messenger RNA. This messenger RNA is then translated into proteins on ribosomes.

== See Also ==
*[[DNA Replication, Repair, and Recombination]] - Articles in Proteopedia concerning DNA Replication, Repair, and/or Recombination
*[[DNA Replication,Transcription and Translation]]
*[[Z-DNA]]
*[[1ehz|Transfer ribonucleic acid (tRNA)]]
* For additional information, see: [[Nucleic Acids]]

== References==
<references/>

DNA

2010-10-31T04:05:30Z

Adithya Sagar:

<applet load='B-DNA.pdb' size='330'frame='true' align='right' caption='B-DNA' scene='DNA/B-dna/7' />
'''Deoxyribonucleic acid''' or '''DNA''' is a molecule which is the carrier of genetic information in nearly all the living organisms. It contains the biological instructions for the development, survival and reproduction of organisms.
DNA is found in the nucleus of a cell where it is packaged into a compact form called a chromosome with the help of several proteins known as histones. It is also found in cell structures called mitochondria. However in case of prokaryotes DNA is not enclosed in a nucleus or a membrane but is present in the cytoplasm. The DNA in prokaryotes in generally circular and supercoiled without any histones. DNA stores genetic information as a sequence of nucleotides in special regions known as genes which are used to make proteins. The expression of genetic information into proteins is a two-stage process wherein the sequence of nucleotides in DNA is converted to a molecule called Ribonucleic acid or [[RNA]] by a process called [[transcription]]. RNA is used to make proteins by another process called [[translation]]. The human genome contains nearly 3 · 10<sup>9</sup> bases with around 20,000 genes on 23 chromosomes. <ref name='gene'>http://www.genome.gov/25520880 </ref>

DNA was first discovered by the German biochemist Frederich Miescher in the year 1869.<ref>PMID: 17901982</ref> Based on the works of Erwin Chargaff, James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin, the structure of DNA was discovered in the year 1953. The structure of DNA is a <scene name='DNA/B-dna/6'>double helix</scene>: two complementary strands of polynucleotides that run in opposite directions and are held together by hydrogen bonds between them. This structure helps the DNA replicate itself during cell division and also for a single strand to serve as template during transcription. <ref name='gene'>http://www.genome.gov/25520880 </ref>

<scene name='DNA/B-dna/7'>Restore View</scene>

== Features of a DNA Molecule ==
<applet load='B-DNA.pdb' size='540' frame='true' align='left' caption='B-DNA' scene ='User:Adithya_Sagar/Sandbox_DNA/B-dna/4'/>
=== Double Helix ===

DNA consists of two polynucleotide chains, <scene name='DNA/B-dna/9'>twisted around each other to form a double helix</scene>. The nucleotide in DNA is composed of of a <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/19'>5' phosphorylated sugar</scene> which is a beta-D-2'- deoxyribose and a purine or a pyrimidine <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/18'>base</scene>. The four types of bases are the two double ringed purine base <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/1'>Adenine (A)</scene> and <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/2'>Guanine (G)</scene> and the two single pyrimidine bases <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/6'>Thymine (T)</scene> and <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/5'>Cytosine (C)</scene>.Each nucleotide in a DNA chain is linked to another via <scene name='User:Adithya_Sagar/Workbench/Retest/B-dna/2'>3',5' phosphodiester bond</scene>. There are four nucleotides in DNA. The sugar-phosphate backbone of the DNA is very regular owing to the phosphodiester linkage whereas the ordering of bases is highly irregular.<ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref>

<scene name='DNA/B-dna/10'>Restore View</scene>
{{Template:Button Toggle NucleicDrumsColorScheme}}
{{Template:ColorKey Bases DNA}}

{{Template:Button Toggle PurinePyrimidineDrumsColorScheme}}
{{Template:ColorKey Purines Pyrimidines}}

=== Complementary Bases ===

The two chains in a DNA are joined by hydrogen bonds between specific bases. Adenine forms a base pairs with thymine and guanine with cytosine. This specific base pairing between <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/14'>Adenine-Thymine</scene> and <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/15'>Guanine-Cytosine</scene> is known as Watson-Crick base pairing. The specificity of hydrogen bonding between bases leads to complementarity in the sequence of nucleotides in the two chains. Thus in a strand of DNA the content of adenine is equal to that of thymine and the guanine content is equal to the cytosine content. In general DNA with higher GC content is more stable than the one with higher AT content owing to the stabilization due to base stacking interactions.

=== DNA denaturation and renaturation ===

A DNA double strand can be separated into two single strands by breaking the hydrogen bonds between them. This is known as DNA denaturation. Thermal energy provided by heating can be used to melt or denature DNA. Molecules with rich GC content are more stable and thus denature at higher temperatures compared to the ones with higher AT content. The melting temperature is defined as the temperature at which half the DNA strands are in double helical state and half are in random coil state.<ref>PMID: 9465037</ref> The denatured DNA single strands have an ability to renature and form double stranded DNA again.

 

 

=== Grooves ===
<applet load='B-DNA.pdb' size='330' frame='true' align='left' caption='B-DNA' scene ='DNA/Bdnasf/1' />
In a DNA double helix the <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/16'>beta-glycosyl bonds</scene> between C<sub>1'</sub>-N<sub>1</sub> branch off from one side of the base pair and do not lie opposite to each other. This results in unequally spaced sugar-phosphate backbones and gives rise to two grooves: the
<scene name='DNA/B-dna/5'>major groove</scene> and the <scene name='User:Adithya_Sagar/Workbench_newDNA/B-dna/21'>minor groove</scene> of different width and depth. The minor groove is at the O<sub>2</sub> side of base pair and the major groove is on the opposite side.The floor of major groove is filled with nitrogen and oxygen atoms that project inward whereas in the minor groove they project outward. The larger size of major groove allows for the binding of DNA specific proteins.<ref name="Saenger"> Saenger, Wolfram (1984). ''Principles of Nucleic Acid Structure '' (1st ed). Springer-Verlag. pp. 398. ISBN 0-12-645750-6.</ref><ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref>

 

 

===Tautomeric forms of bases===

The hydrogen atoms on the bases move from nitrogen or oxygen atom on ring to another through shifts known as tautomeric shifts. However the hydrogens have preferred atomic locations. Based on the movement of hydrogen atoms the nitrogen atoms are in amino or imino configuration and the oxygen atoms are either in keto or enol forms. There is a preference for the amino and keto forms respectively which is very crucial for the biological functioning of DNA as it leads to the specificity in base pairing and thus complementarity of the chains.<ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref>

 

 

==Forms of DNA==
''See Also: [[Z-DNA]]''

 

 

=== A comparative representation of the three forms of DNA ===
''Sources''<ref>http://203.129.231.23/indira/nacc/</ref>
<applet load='A-DNA.pdb' name='A' size='350' frame='true' align='right' caption='A-DNA' align='left' scene='User:Adithya_Sagar/Sandbox_DNA/A-dna/1'/>
<applet load='B-DNA.pdb' name='B' size='350' frame='true' align='right' caption='B-DNA' align='left' scene='User:Adithya_Sagar/Sandbox_DNA/B-dna/3'/>
<applet load='Z-DNA.pdb' name='Z' size='350' frame='true' align='right' caption='Z-DNA' align='left' scene='User:Adithya_Sagar/Sandbox_DNA/Z-dna/1'/>

{{Clear}}
<center>
'''Synchronize the three applets showing A-, B- and Z-DNA by clicking the checkbox'''
<jmol>
<jmolCheckbox>
<target>A</target>

<scriptWhenChecked> sync jmolAppletB,jmolAppletZ </scriptWhenChecked>
<scriptWhenUnchecked> sync OFF</scriptWhenUnchecked>
<text> Synchronize</text>
</jmolCheckbox>
</jmol>
</center>

{{Clear}}

=== Helical Parameters of the three forms of DNA ===

DNA is a very flexible molecule and has the ability to exist in various forms based on the environmental conditions. Naturally occurring DNA double helices are classified into A, B and Z-types. A and B-forms of DNA are the right handed forms whereas [[Z-DNA]] is the left handed form. When hydrated the DNA generally assumes B-form. The A conformation is found when there is little water to interact with the helix and is also the conformation adopted by the RNA. The formation of Z-DNA occurs with the methylation of deoxycytosine residues and also during transcription where negative supercoiling stabilizes it.

{| class="wikitable" align= "center''
|-
!Parameter
!A-DNA
!B-DNA
!Z-DNA
|-
|Helix sense ||align="center"| right-handed ||align="center"| right-handed ||align="center"| left-handed
|-
|Residues per turn ||align="right"| 11 ||align="right"| 10.5 ||align="right"| 12
|-
|Axial rise [Å] ||align="right"| 2.55 ||align="right"| 3.4 ||align="right"| 3.7
|-
|Helix pitch(°) ||align="right"| 28 ||align="right"| 34 ||align="right"| 45
|-
|Base pair tilt(°) ||align="right"| 20 ||align="right"| −6 ||align="right"| 7
|-
|Rotation per residue (°) ||align="right"| 33||align="right"| 36||align="right"|-30
|-
|Diameter of helix [Å]||align="right"| 23||align="right"| 20||align="right"| 18
|-
|Glycosidic bond configuration<br\>dA,dT,dC<br\>dG ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>syn
|-
|Sugar pucker<br\>dA,dT,dC<br\>dG ||align="center"| <br\>C3'-endo<br\>C3'-endo ||align="center"|<br\> C2'-endo<br\>C2'-endo ||align="center"| <br\>C2'-endo<br\>C3'-endo
|-
|Intrastrand phosphate-phosphate distance [Å] <br\>dA,dT,dC<br\>dG ||align="center"| <br\>5.9<br\>5.9||align="center"| <br\>7.0<br\>7.0||align="center"| <br\>7.0<br\> 5.9
|-
|colspan="4"|''Sources:<ref name="Rich1984">PMID:6383204</ref><ref name="Rich1979">PMID: 514347</ref><ref> Sinden, Richard R (1994-01-15). ''DNA structure and function'' (1st ed.). Academic Press. pp. 398. ISBN 0-12-645750-6.</ref>
|}

== Structural Transformation between A and B DNA ==



<jmol>
<jmolApplet>
<size>660</size>
<color>white</color>
<uploadedFileContents>morph_a-b.pdb</uploadedFileContents>
<script>animation ON; animation mode PALINDROME; cartoon ON; save state ab </script> 
</jmolApplet>
</jmol>


<jmol>
<jmolButton>
<target>5</target>
<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/9/9e/Morph_a-b.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script> 
<text>Click here and activate the below options </text>
</jmolButton>
</jmol>


<jmol>
<jmolRadioGroup>
<target>5</target>
<item>
<script> moveto 1.0 0 0 1 0 180.0 0.0 0.0;restore state ab; animation ON;animation mode palindrome;cartoon ON;spacefill on; spacefill 90;wireframe on;wireframe 50;zoom 180;select 9:a,4:b;hbonds ON;hbonds calculate;hbonds 0.09;select!selected; color translucent 0.9;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Base pair shift between A and B DNA"</script>
<text>Shift in Base Pair between A-B DNA</text>
</item>
<item>
<script> moveto 1.0 0 0 1 0 400.0 0.0 0.0; restore state ab;cartoon OFF;spacefill ON; spacefill 90; wireframe ON; wireframe 50;select 9:a; select!selected; color translucent 0.9; select!selected; centre selected;zoom 400;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA"</script>
<text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
</item>
<item>
<script>moveto 1.0 0 0 1 0 150.0 0.0 0.0;restore state ab;spacefill ON; spacefill 400; zoom 150; cartoon OFF;animation ON; animation mode PALINDROME;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Transition between A-B DNA spacefilling models"</script>
<text>Transition between A-B DNA spacefilling models</text>
</item>
</jmolRadioGroup>
</jmol>


<jmol>
<jmolButton>
<target>5</target>
<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/9/9e/Morph_a-b.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
<text>Restore Original State </text>
</jmolButton>
</jmol>


<jmol>
<jmolApplet>
<color>white</color>
<size>660</size>
<uploadedFileContents>Morph_test.pdb</uploadedFileContents>
<script>animation ON;animation mode PALINDROME;cartoon ON; save state ab_new</script>
</jmolApplet>
</jmol>

<jmol>
<jmolButton>
<target>6</target>
<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/5/50/Morph_test.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
<text>Click here and activate options below </text>
</jmolButton>
</jmol>

<jmol>
<jmolRadioGroup>
<target>6</target>
<item>
<script> moveto 1.0 0 0 1 0 180.0 0.0 0.0;restore state ab; animation ON;animation mode palindrome;cartoon ON;spacefill on; spacefill 90;wireframe on;wireframe 50;zoom 180;select 9:a,4:b;hbonds ON;hbonds calculate;hbonds 0.09;select!selected; color translucent 0.9;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Shift in Base Pair between A-B DNA"</script>
<text>Shift in Base Pair between A-B DNA</text>
</item>
<item>
<script> moveto 1.0 0 0 1 0 400.0 0.0 0.0; restore state ab;cartoon OFF;spacefill ON; spacefill 90; wireframe ON; wireframe 50;select 9:a; select!selected; color translucent 0.9; select!selected; centre selected;zoom 400;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA"</script>
<text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
</item>
<item>
<script>moveto 1.0 0 0 1 0 150.0 0.0 0.0;restore state ab;spacefill ON; spacefill 400; zoom 150; cartoon OFF;animation ON; animation mode PALINDROME;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Transition between A-B DNA spacefilling models"</script>
<text>Transition between A-B DNA spacefilling models</text>
</item>
</jmolRadioGroup>
</jmol>

<jmol>
<jmolButton>
<target>6</target>
<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/5/50/Morph_test.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
<text>Restore Original State </text>
</jmolButton>
</jmol>

''Morph Sources'' <ref>PMID: 10734184</ref>



== Biological Functions ==
''Sources:''<ref name='Rawn' > Rawn,David J. "Biochemistry"(1st ed.) Harper&Row,Publishers, Inc.pp. 1024-1050. ISBN-0-06045335-4</ref>

=== Replication===
DNA undergoes what is known as semi conservative mode of replication wherein the daughter DNA contains one DNA strand of the parent. The replication proceeds through the unwinding of double helix followed by synthesis primers from where the replication begins. An enzyme DNA polymerase synthesizes complementary strands to each parent strand from 5'-3' direction.

===Transcription and Translation===
The expression of genes into proteins and is a process involving two stages called transcription and translation. In the transcription stage a strand of DNA molecule serves as a template for the synthesis of an RNA molecule called messenger RNA. This messenger RNA is then translated into proteins on ribosomes.

== See Also ==
*[[DNA Replication, Repair, and Recombination]] - Articles in Proteopedia concerning DNA Replication, Repair, and/or Recombination
*[[DNA Replication,Transcription and Translation]]
*[[Z-DNA]]
*[[1ehz|Transfer ribonucleic acid (tRNA)]]
* For additional information, see: [[Nucleic Acids]]

== References==
<references/>