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By Levi Clancy for Student Reader on

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DNA is not really two parallel lines, as we diagram it, is not straight, but is quite flexible. The lengths of the H-bonds in double-stranded DNA do not change very much when the DNA is bent and unwound slightly, or overwound slightly (not shown).



2'-deoxyribose (a sugar) bound to base


2'-deoxyribose bound to a base and Pi


joined by phosphodiester linkages.

Base-sugar bond is glycosidic.

Phosphate-sugar bond is a phosphoester.

Nucleotides form chains. Two chains bind to form DNA. Hence, DNA is 2 double-helical polynucleotide chains. DNA is negatively charged, stable at low pH (H+ neutralize), moderate in saline but Cl- counteracts Na+, high pH is bad. High ph/heat reversibly denatures DNA. Denaturation is separation of strands. Hybridization is when complementary strands of DNA or RNA reassociate (anneal). Unpaired loops can form within hybrids. A:T & G:C, which are DNA's only basepairs, interact via hydrogen bonding. G:C has 3 hydrogen bonds, while A:T has 2 hydrogen bonds. High G:C levels increase DNA stability. Glycine, tyrosine and serine are rare in alpha-helices; proline disrupts them. Aromatic rings are planar and can get into the major groove. Chromatid holds chromosomes together. Chromatin is highly compacted DNA-wrapped histone. Nucleosomes, solanoids, chromatin. When a base points away from alpha-helix (base flipping), it can fit inside an active site. DNA is degenerate because more than one codon can encode the same amino acid.


Major Groove

A:T bp edge displays in this order: 2 Hydrogen-bond acceptors; Hydrogen-bond donor; bulky hydrophobic surface.

Minor Groove

Less rich in chemical information, no distinguishing between G:C & C:G or A:T & T:A.

A: 11 bp/turn, relative to B major groove narrower/deeper & minor groove broader/shalower, low humidity.

B: most common, 10.5 bp/turn.

Z: left-handed zig-zag shape.

Link, Twist and Writhe

Link:     Always an integer.

Twist:   # of times alpha-helix backbones overlap.

Writhe: # of times alpha-helix overlaps itself.

Link = Twist + Writhe

Twists = ( Total Base Pairs ) / ( Base Pairs Per Turn)

Strain causes DNA supercoiling. Negative supercoils are underwound (more bp per turn); positive supercoils are overwound (less bp per turn). Helicase (an enzyme) unwinds DNA. Chromosomal DNA might be tethered by protein. DNA wraps around histone in a left-handed form. Plectonemic left-handed is positive. Topoisomerae reduced linking number by unwinding DNA. Writhe comes in two forms: interwound, plectonemic. With two helices, twist is writhe.

Why Nucleoside Triphosphates?

Why do cells prefer to synthesize nucleic acids from nucleoside triphosphates rather than diphosphates? If nucleoside diphosphates were used, phosphate rather than pyrophosphate would be liberated as the backbone phospho-diester linkages were made. These phospho-diester linkages are not stable in the presence of significant quantities of phosphate, because they are formed without a significant release in free energy. Therefore, the biosynthetic reaction would be easily reversible. By using nucleoside triphosphates, the liberation of pyrophosphate and its rapid breakdown into two phosphates disconnects the liberation of phosphate from the nucleic acid biosynthesis reaction, preventing the possibility of reversing the biosynthesis reaction.

DNA in Viruses, Prokaryotes and Eukaryotes

OrganismNucleic AcidChromosomeSize and # of Genes


ss or ds RNA or DNA

Linear or Circular

103nt & 25 genes



Haploid plasmid

106nt & 103 genes



Multiple linear xsms
haploid or diploid
some organelles have plasmid xsms

108nt & 104 genes

Plasmids are circular and prokaryotic. They replicate independently of the host chromosome. They are covalently close, circular ccDNA. Therefore, they dislike twisting because it strains sugar-phosphate backbone.