1- B DNA -- Genome2- Double helix -- Relaxed form3- Antiparallel -- Super coil4- Major groove -- Histone like proteins5- Minor groove -- Nucleosome6- Sugar puckering -- Nucleosome core7- C2 endo --Chromatin8- C3 Exo -- Linker9- Syn, Anti -- Sscaffold--Right handed -- Solenoid10- A DNA, C3 endo position --Melting point 11- Z DNA-- Left handed, G and A in syn position-- G and (A) in C3 endo position-- Base stacking--Hydrogen bond -- Phosphate position-- Hoogsteen Base pair-- Triple stranded helix

Hypochromism. (A) Single-stranded DNA absorbs light more effectively than does double-helical DNA. (B) The absorbance of a DNA solution at a wavelength of 260 nm increases when the double helix is melted into single strands.

Step Melting ΔG/Kcal mol-1

T A -0.12

T G or C A -0.78

C G -1.44

A G or C T -1.29

A A or T T -1.04

A T -1.27

G A or T C -1.66

C C or G G -1.97

A C or G T -2.04

G C -2.70

Direction of helix rotation

Right handed Right handed Left handed

Residue per helical turn

11 10 12

Pitch (length) of the helix

28.2 Å 34 Å 44.4 Å

Base pair tilt 20° -1° 7°

Rotation per residue 32.7° 34.3° -30°

Diameter of helix 23 Å 20 Å 18 Å

Configuration dA, dT, dC

anti anti anti

of glycosidic bond dG anti anti syn

Sugar Pucker dA, dT, dC

C3' endo C2' endo C2' endo

dG C3' endo C2' endo C3' endo

Topology of major groove

Narrow, deep Wide, deep Flat

Topology of minor groove

Broad, shallow Narrow, shallow Narrow, deep

Major- and Minor-Groove Sides. Because the two glycosidic bonds are not diametrically opposite each other, each base pair has a larger side that defines the major groove and a smaller side that defines the minor groove.

The grooves are lined by potential hydrogen-bond donors (blue) and acceptors (red).

Propeller Twist. The bases of a DNA base pair are often not precisely coplanar. They are twisted with respect to each other, like the blades of a propeller.

Axial View of DNA. Base pairs are stacked nearly one on top of another in the double helix

Step Stacking ΔG/kcal mol-1

T A -0.19

T G or C A -0.55

C G -0.91

A G or C T -1.06

A A or T T -1.11

A T -1.34

G A or T C -1.43

C C or G G -1.44

A C or G T -1.81

G C -2.17

Histonea Molecular weight

Number of amino acids Percentage Lysine + Arginine

H1 22,500 244 30.8

H2A 13,960 129 20.2

H2B 13,774 125 22.4

H3 15,273 135 22.9

H4 11,236 102 24.5

a Data are for rabbit (H1) and bovine histones.

Structure of Histone Acetyltransferase.      The amino-terminal tail of histone H3 extends into a pocket in which a lysine side chain can accept an acetyl group from acetyl CoA bound in an adjacent site

Histone modificationsHistone proteins can undergo various types of modification, the best studied of these being histone acetylation. – the attachment of acetyl groups to lysine amino acids in the N-terminal regions of each of the core molecules. These N termini form tails that protrude from the nucleosome core octamer and their acetylation reduces the affinity of the histones for DNA and possibly also reduces the interaction between individual nucleosomes that leads to formation of the 30 nm chromatin fiber Histone acetyltransferases (HATs) – the enzymes that add acetyl groups to histones. Histone acetylation plays a prominent role in regulating genome expression. The tails of the core histones also have attachment sites for methyl and phosphate groups and for the common (‘ubiquitous') protein called ubiquitin. Ubiquitination of histone H2B is part of the general role that ubiquitin plays in control of the cell cycle.Phosphorylation of histone H3 and of the linker histone has been associated with formation of metaphase chromosomesMethylation of a pair of lysine amino acids at the fourth and ninth positions from the N-terminus of histone H3. Methylation of lysine-9 forms a binding site for the HP1 protein which induces chromatin packaging and silences gene expression

Methylation of lysine-4 has the opposite effect and promotes an open chromatin structure Lysine-4 methylation is closely correlated with acetylation of histone H3 Two types of modification may work hand in hand to activate regions of chromatin. Remodeling is induced by an energy-dependent process that weakens the contact between the nucleosome and the DNA with which it is associated. Three distinct types of change can occur Remodeling, in the strict sense, involves a change in the structure of the nucleosome, but no change in its position.

Sliding, or cis-displacement, physically moves the nucleosome along the DNA

Transfer, or trans-displacement, results in the nucleosome being transferred to a second DNA molecule the proteins responsible for nucleosome remodeling work together in large complexes. One of these is Swi/Snf, made up of at least 11 proteins, which is present in many eukaryotes

Direct methylation of DNA also has a silencing effect Silencing can be implemented is by removing acetyl groups from histone tails This is the role of the histone deacetylases (HDACs). HDACs are contained in multiprotein complexes. One of these is the mammalian Sin3 complex, which comprises at least seven proteins, including HDAC1 and HDAC2 along with others that do not have deacetylase activity but which provide ancillary functions essential to the processBoth Sin3 and NuRD contain proteins that bind to methylated DNA.