DNA

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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 · 10⁹ bases with around 20,000 genes on 23 chromosomes. ^[1]

DNA was first discovered by the German biochemist Frederich Miescher in the year 1869.^[2] 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 : 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. ^[1]

1 Features of a DNA Molecule

Features of a DNA Molecule

Double Helix

consists of two polynucleotide chains, . The in DNA is composed of of a which is a beta-D-2'- deoxyribose and a purine or a pyrimidine . The four types of bases are the two double ringed purine base and and the two single pyrimidine bases and .Each nucleotide in a DNA chain is linked to another via . 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.^[3]

A C G T

Purines Pyrimidines

Complementary Bases

The two chains in a DNA are joined by hydrogen bonds between specific bases. Adenine forms base pairs with thymine and guanine with cytosine. This specific base pairing between and is known as the 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.^[4] The denatured DNA single strands have an ability to renature and form double stranded DNA again.

Grooves

In a the between C_1'-N₁ 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 and the of different width and depth. The minor groove is at the O₂ 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.^[5]^[3]

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.^[3]

1 Forms of DNA
- 1.1 A comparative representation of the three forms of DNA
- 1.2 Helical Parameters of the three forms of DNA
2 Structural Transformation between A and B DNA
3 Biological Functions
- 3.1 Replication
- 3.2 Transcription and Translation
4 See Also
5 References

Forms of DNA

See Also: Z-DNA

A comparative representation of the three forms of DNA

Sources^[6]

Synchronize the three applets showing A-, B- and Z-DNA by clicking the checkbox

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.

Parameter	A-DNA	B-DNA	Z-DNA
Helix sense	right-handed	right-handed	left-handed
Residues per turn	11	10.5	12
Axial rise [Å]	2.55	3.4	3.7
Helix pitch(°)	28	34	45
Base pair tilt(°)	20	−6	7
Rotation per residue (°)	33	36	-30
Diameter of helix [Å]	23	20	18
Glycosidic bond configuration dA,dT,dC dG	anti anti	anti anti	anti syn
Sugar pucker dA,dT,dC dG	C3'-endo C3'-endo	C2'-endo C2'-endo	C2'-endo C3'-endo
Intrastrand phosphate-phosphate distance [Å] dA,dT,dC dG	5.9 5.9	7.0 7.0	7.0 5.9
Sources:^[7]^[8]^[9]

Structural Transformation between A and B DNA

Drag the structure with the mouse to rotate

Morph Sources ^[10]

Biological Functions

Sources:^[11]

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.

References

↑ ^1.0 ^1.1 http://www.genome.gov/25520880
↑ Dahm R. Discovering DNA: Friedrich Miescher and the early years of nucleic acid research. Hum Genet. 2008 Jan;122(6):565-81. Epub 2007 Sep 28. PMID:17901982 doi:10.1007/s00439-007-0433-0
↑ ^3.0 ^3.1 ^3.2 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
↑ SantaLucia J Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1460-5. PMID:9465037
↑ Saenger, Wolfram (1984). Principles of Nucleic Acid Structure (1st ed). Springer-Verlag. pp. 398. ISBN 0-12-645750-6.
↑ http://203.129.231.23/indira/nacc/
↑ Rich A, Nordheim A, Wang AH. The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem. 1984;53:791-846. PMID:6383204 doi:http://dx.doi.org/10.1146/annurev.bi.53.070184.004043
↑ Wang AH, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, van der Marel G, Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 1979 Dec 13;282(5740):680-6. PMID:514347
↑ Sinden, Richard R (1994-01-15). DNA structure and function (1st ed.). Academic Press. pp. 398. ISBN 0-12-645750-6.
↑ Krebs WG, Gerstein M. The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res. 2000 Apr 15;28(8):1665-75. PMID:10734184
↑ Rawn,David J. "Biochemistry"(1st ed.) Harper&Row,Publishers, Inc.pp. 1024-1050. ISBN-0-06045335-4

Proteopedia Page Contributors and Editors (what is this?)

Adithya Sagar, Eran Hodis, Ala Jelani, Eric Martz, Wayne Decatur, Karsten Theis, Alexander Berchansky, Karl Oberholser, Joel L. Sussman, Ann Taylor, David Canner, Angel Herraez, Joseph M. Steinberger, Frédéric Dardel

Retrieved from "http://52.214.119.220/wiki/index.php/DNA"

@@ Line 1: / Line 1: @@
-<applet load='B-DNA.pdb' size='330'frame='true' align='right' caption='B-DNA' scene='DNA/B-dna/7' />
+<StructureSection load='B-DNA.pdb' size='540' frame='true' align='left' 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>
@@ Line 6: / Line 6: @@
 <scene name='DNA/B-dna/7'>Restore View</scene>
 == Features of a DNA Molecule ==
-<StructureSection load='B-DNA.pdb' size='540' frame='true' align='left' caption='B-DNA' scene ='User:Adithya_Sagar/Sandbox_DNA/B-dna/4'>
 === Double Helix ===
+<scene name='User:Adithya_Sagar/Sandbox_DNA/B-dna/4'>DNA</scene> consists of two polynucleotide chains, <scene name='DNA/B-dna/16'>twisted around each other to form a double helix</scene>. The <scene name='DNA/B-dna/29'>nucleotide</scene> in DNA is composed of of a <scene name='DNA/B-dna/30'>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='DNA/B-dna/22'>Adenine (A)</scene> and <scene name='DNA/B-dna/23'>Guanine (G)</scene> and the two single pyrimidine bases <scene name='DNA/B-dna/28'>Thymine (T)</scene> and <scene name='DNA/B-dna/27'>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>
-DNA consists of two polynucleotide chains, <scene name='DNA/B-dna/16'>twisted around each other to form a double helix</scene>. The <scene name='DNA/B-dna/29'>nucleotide</scene> in DNA is composed of of a <scene name='DNA/B-dna/30'>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='DNA/B-dna/22'>Adenine (A)</scene> and <scene name='DNA/B-dna/23'>Guanine (G)</scene> and the two single pyrimidine bases <scene name='DNA/B-dna/28'>Thymine (T)</scene> and <scene name='DNA/B-dna/27'>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>
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DNA