汪世华分子生物学 2

*The writhing number is the number of
times a duplex axis crosses over itself in space.
Most natural • DNA is negatively supercoiled, that is the DNA is deformed in the direction of unwinding of the double helix.
the major importance of the A-form is that it is the helix formed by RNA, and by DNA-RNA hybrids.
Notes
Z-DNA is stable in synthetic double stranded DNA consisting purely of alternating pyrimidine-purine sequence. activation of at least one gene requires that a regulatory sequence switch to the Z-DNA form.
double-stranded DNA sample can be used to assess its purity. For pure DNA, the value is 1.8. Values above 1.8 suggest RNA contamination and those below 1.8 suggest protein contamination.
H2A, H2B, H3, H4, and a further family, H1, which has some different properties, and a distinct role.
2.2.3 Telomere
A telomere is a region of repetitive nucleotide sequences at the end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes.
Tm
The midpoint of the temperature range over which the strands of DNA separate is called the melting temperature (Tm). Marmur-Doty empirical formula: Tm=69.3+0.41 (G+C) % Or Tm=4(G+C)＋2(A+T)
2.2.2 Histone
*The major protein components of
chromatin are the histones; small, basic (positively charged) proteins which bind tightly to DNA.
*There are four families of core histone,
2.2.1 Nucleosomes
The nucleosome core is the basic unit of chromosome structure, consisting of a protein octamer containing two each of the core histones, with 146 bp of DNA wrapped 1.8 times in a left-handed fashion around it.
Linking number
*The linking number is the number of times the
two strands of a closed DNA duplex cross over each other. The linking number is always an integer, but may be positive or negative depending on the orientation of the two curves.
The stability of a nucleic acid helix
stacked base pairs
H-bonds Charge interactions
Denaturation and Renature
The process of strand separation is called denaturation or melting.
Hyperchromicity : The UV absorption is increased when the two single DNA strands are being separated.
UV absorption
*Nucleic acids absorb UV light due to the
Chapter 2
DNA and Chromosome
2.1 DNA structure
Primary structure
(Nucleotide residue sequence) Secondary structure (DNA double helix) Advance structure (DNA supercoiling)
△ Lk = △ Tw + △ Wr
Twisting number & Writhe
*The twisting number of a DNA is the
number of base pairs divided by the number of base pairs per turn of the double helix.
DNA through the break, and resealing the
DNA.
Topoisomerases Type I Type II
Break LK one strand ± 1 both strands ± 2
Energy +
2.2 Chromosome
Eukaryotic chromosomes each contain a long linear DNA molecule, which must be packaged into the nucleus. The name chromatin is given to the highly ordered DNA– protein complex which makes up the eukaryotic chromosomes.
•
2.1.3 Advance structure
•
DNA supercoiling is the coiling of the DNA axis upon itself, caused by a change in the linking number from Lk°, the value for a relaxed closed ci Variety of DNA
Structure
Notes
DNA can be induced to form an alternative helix, known as the A-form, under conditions of low humidity.
Notes A telomere consists of up to hundreds of copies of a short repeated sequence (5’-TTAGGG-3’ in humans), which is synthesized by the enzyme telomerase. The telomeric DNA forms a special secondary structure, the function of which is to protect the ends of the chromosome proper from degradation.
Northern blotting involves the use of electrophoresis to separate RNA samples by size and detection with a hybridization probe complementary to part of or the entire target sequence.
Topoisomerases
*A DNA topoisomerase is an enzyme that
changes the number of times the two strands
in a closed DNA molecule cross each other.
*It does this by cutting the DNA, passing
2.1.1 Primary structure
the nucleotide residue sequence of
the polynucleotide chain；
3’,5’-phosphodiester bond; write as 5’ →3’；(replication)
2.1.2 Secondary structure
Renaturation
The ability of the two separated complementary strands to reform into a double helix is called renaturation （Annealing）.