Physical Chemistry of Nucleic Acids
A, B, Z forms: Table 2.2
B form: Watson & Crick, high sodium salt of DNA (relative humidity 92%), close to cellular DNA, plane of basepair
┤helical axis, right* handed
A form: 75% sodium salt, 20 0 titls away from horizontal, right handed, maybe exist in RNA-DNA form
Z form: zigzag, poly [dG-dC], living in cells with small portion, left handed
-----------------------------
*Right handed: helix turns clockwise away from you, whether top or bottom view
Denaturation of DNA:
Denaturation of DNA = DNA melting = double strand

single strand
How to detect d-, s- strand DNA?
Hyperchromic shift: (Fig. 2.17), Tm, GC (3 H bonds)↑

Tm↑
Factors influence denaturation of DNA: heating, organic solvents
(dimethyl sulfoxide, foramide), high pH, low salt concentration, GC content of DNA (Fig. 2-18),
GC content ↑ 
DNA density ↑(Fig. 2-19)
Renaturation = annealing = reuniting the separated DNA
Factors influence renaturation
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1.
Temperature: 25 0 C below its Tm: do not promote denaturation, allow rapid diffusion of DNA, weaken transient bonding between mismatched sequences and short intrastrand base-paired regions.
Rapidly cooling (quenching ( 淬 ))

renaturation ↓
2.DNA concentration: DNA concentration↑

annealing↑
3.Renaturation time: annealing time longer

more renaturation
C
0
T: DNA concentration (C
0
) of renaturation and time (t), (M= mole / liter) /second
Fig. 2.20: DNA complex ↑ 
C
0
T 1/2 ↑
Fig. 2.21 Complexity and repetition of DNA: mouse’s DNA:
10%

short sequence repetitive, 1 million times per mouse
 highly repetitive

centromere (Fig. 2.22)
60%

single-copy

genes for proteins
30%

mid-repetitive

genes for ribosomal RNA
The role of the most of the repetitive DNAs are still unknown.
Annealing vs. hybridization:
Annealing

two strands of complemantary nucleic acid from identical origin
Hybridization

two strands of complemantary nucleic acid from different origin (DNA+RNA see Fig. 2-20, labeled DNA + unlabeled DNA)
Size of DNA: molecular weight, base pairs, length
Base pairs × 3.4 Å = length,
Å = 10 -10 m =10 -4 μm = 10nm; nm = 10 -9 m
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Base pairs × 660 (average Dalton /nucleotide pair) = molecular weight
Electron microscopy: (Fig.2.21)
Gel electrophoresis: migration distance and molecular size in base pairs (Fig.)
DNA size and Genetic Capacity (the number of genes)
How many genes are in a given DNA?
Average molecular mass of a protein = 40,000 D
Average molecular mass of an amino acid = 110 D
Average numbers of amino acid in a protein: 40,000 D/ 110 D =
364 amino acids
A gene needs 364 amino acids × 3 bp = 1092 bp
E.coli chromosome contains 4.6 × 10 6 bp/ 1092 bp = 4200 average proteins
Phages or viruses contain more information by overlapping its genes.
DNA content & C-value paradox
C-value: DNA content/haploid cell
More DNA more genes? Not really true!
Mouse and human haploid cells contain 1000 times than yeast haploid cells. But, flowering plats have more C-value, but don’t have more genes. Noncoding DNAs!
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