Purine

Pyrimidine

Adenine

Guanine

Cytosine

Uracil

Thymine

Thymine (DNA) vs.

Uracil (RNA)

Thymine has a methyl group on the 5th carbon.

Unlike proteins, nucleic acids contain no ___

Nucleic Acids vs Proteins

sulfur.

Base and Phosphate Attachments

in Ribose and Deoxyribose

1' to base via glycosidic bond

(to N9 in Purines

and N1 in Pyrimidines)

5' and 3' to phoshate

via phoshodiester bonds.

Deoxyribose

Ribose

Deoxyribose vs. Ribose

no hydroxyl at 2' in deoxyribose

Nucleoside

base + sugar

cytidine, uridine, adenosine, guanosine, thymidine

Nucleotide Abbreviations

RNA: AMP, GMP, CMP, UMP

DNA: dAMP, dGMP, dCMP, dTMP

NMP stand for nucleoside monophosphate

Rotation per residue

(base pair twist in B DNA)

36°

Height btw base pairs

in B DNA

3.4Å

Pitch of B DNA

(width of one complete turn)

repeats every 34Å

10 bases per turn

Why do major and minor grooves form?

form as consequence of fact that beta-glycosidic bonds of bases pairs are attached on the same edge. However, because helix axis passes through center of base pairs, both grooves are similar in depth.

Diameter of B DNA

20Å

Stabilizing factors of B DNA

1. base stacking

2. hydrogen bonding

3. metal ions

(DNA is a polyanion at pH 7.0)

Watson-Crick Base Pairs

Glycosidic Bond Conformations

Anti in normal A and B-DNA (base points away from sugar)

Syn found in Z form (base lies over sugar)

purines adopt syn conformation more easily than pyrimidines--esp G.

Syn glocosidic conformations

happens more often to purines--esp G: favorable interactions btw NH₂ and 5'-O-P

found in Z-DNA

why does Z DNA zig zag?

Endo-pucker

C2’ or C3’ are turned out of the sugar plane into the direction of C4'-C5' bond.

Exo-pucker

describes a shift in the opposite directio of the endo plane.

RNA sugar pucker

RNAs are A form

sugar pucker is C3' endo

don't fit into B DNAs C2' endo because of the 2'-oxygen

Why does Z DNA like

high salt conditions?

Z form is narrow and negatively charged phosphate backbones are close together. needs positive salt to stabilize the repulsion forces.

A-T pair

Carbons 3, 4 (T) go to Carbons 1, 6 (A)

C-G base pair

carbon 2,3,4 (C) bond to carbon 2,1,6 (G)

sugar puckering

markedly affects the orientation of the phosphodiester bridges and the glycosidic bond

Biological significance of propeller twist

helps maximize the stabilizing base stacking interactions

extent is sequence dependent

Deviations from ideal structure

All except twist are 0° in ideal B DNA

Deviations from Ideal Structure:

roll and tilt

roll: (goes into grooves) key property that leads to bending

tilt: (goes into backbone) also leads to bending

Shift

non-zero value of shift in A DNA

shift toward major minor grooves

base pairs closer to helix cylinder

results on hole down center

Watson crick base pairs by carbon number

A: 1, 6

T: 3, 4

C: 2, 3, 4

G: 2, 1, 6

RNA folding

RNAs are ~ 50% self-complimentary

Topoisomerase inhibitors

drug used to stop tumor growth

Nucleosome definition

RNA polymerase and nucleosome

RNA polymerase = 500 kD (14x13 nm)

Nucleosome = 300 kD (6x11 nm)

Thus, some unpacking is necessary during transcription and replication

replication complexes

vs

transcription complexes

replication complexes are bigger in size

Slippage

can cause mutations due to mismatches

or deletions

Triplet Repeat Expansion

example of diseases

CTG: Huntington's

CGG: Fragile X

also Friedrich's Ataxia

mainly neurological or muscular diseases

Oligonucleotide

short sequence of nucleotides (DNA or RNA) with 20 or fewer base pairs

Tautomers of bases

keto (C=0) & amino (NH₂)

not enol (C-OH) & imino (NH)

A and C can exist in amino or imino forms; G, T, U can exist in keto or enol forms.

Biological significance of Z DNA

provide relief from torsional stress during DNA transcription? (reservoir of energy)

Hoogsteen base-pairing for A-T

adenine goes from anti to syn

A binds to T (3,4) via 7, 6 rather than 1, 6.

Wobble pairing

G-U

U (or T) 2, 3

to

G (1, 6)

Biological significance to wobble pairing

use in translation

interaction between tRNAs and mRNAs

A-G mismatches

very common; many ways to combine H bond them together

(anti) G-A (anti)

(anti) G-A (syn)

ten possible purine pyridine

base pairs

1. and 2. Watson crick base pairs

(A-U; G-C)

3. and 4. reverse w-c base pairs

5. wobble (GT or U)

4. reverse wobble

5. A-U hoogsteen

6. A-U reverse hoogsteen

7. A-C reverse hogsteen

8. A-C reverse wobble

Wobble pairing

A-C

A-C reverse wobble

A: 1,6 ; C R: 4, 3

A (N1 + protonated)-C

A: 1, 6; C: 2, 3

Energetics of RNA Folding

extent of stabilization is sequence dep.

(stacking patterns differ)

base pairing is stabilizing

(because of stacking & H bonding)

loops, mismatches, and bulges cost energy and are destabilizing

Pseudoknots in RNAs

structure plays imp roll in life cycle of HIV and other viruses

HIV regulates protein translation via pseudoknots--polymerase can't get through

Negatively Supercoiled DNA

front strand falls from Rt->Lt

results from unwinding primary turns

Wr ~ -3

neg supercoils normally found in vivo

~ 1 neg turn per 200 bps

Topoisomerase

enzyme that cuts DNA that has formed supercoils during replication and then reconnects strands afterwards.

extremely important to DNA replication

dimensions

mm

µm

nm

mm = 10^-3meter

µm = 10^-6 meter

nm = 10^-9 meter

Nucleosome dimensions

Solenoid model

 the 30 nm fiber condenses further in loops about non-histone scaffold proteins; nucleosomes pack right handed, 6 per turn.

H1 needed to form this solenoid.

Histone modification

Histone Tails

modification sights

globular bodies of histones are localized in octamer of core particle--N-terminus tails are more flexible/accessible

H3 and H2B tails extend out

H4 tail contact H2A-H2B dimer of adjacent nucleosome

Reverse W-C

A-T

A: 1,6; T: 3, 2

G-C

G: 2, 1; C: 3, 2

Reverse Hogsteen A-T

In reversed Hoogsteen base pairs, one base is rotated 180° with respect to the other.

A (7, 6)-T (3,2)

Reverse Wobble G-T/U

G: 1, 6

T/U: 4, 3

Hogsteen Reverse

A-C

A: 7,6

C: 4, 3

DNA polymerase slippage

if mismatched pairs occur in new strand, extension occurs

if occur on template, deletion occurs

primer template misalignments:

mutational intermediates for frameshift and subsitution errors

1. slippage (in temp, del; in prim, exten)

2. miscoding->re-alignment (involves slip): (can result in deletion)

3. dislocation: slippage, incorporation, re-alignment (can result in mismatch)

Loops mismatches bulges

cost energy

are destabilizing

ΔG (kcal/mol)

hairpin loop: +7.4 - +8.9

interior loop: +0.8 - +8.4

bulge loop: +3.3 - +15.8

Lysine or Arginine

Methylation

increases bulk but does not interfere with charge

can work as activator or repressor

Methylation can inhibit acetylation and phosphorylation

Nucleotide

base + sugar + phosphate

adenylic acid, guanylic acid, cytidylic acid, thymidylic acid, uridylic acid

A DNA

11 base pairs per turn; base pair rotation: 33°

pitch: 28Å

RNA-RNA / DNA-RNA

often has runs of G's;found in reduced water environment; base planes tilt relative to axis;

hole down center

Z DNA

backbone is zigzag, not smooth; Left handed; 12 base pairs per turn; rotation -30º;

pitch 46 Å; alternating G-C; high salt, super coiled conditions; minor groove only; glycosidic bonds have both conformations: Cs are anti and Gs are syn; repeating unit is a dinucleotide; sugar pucker take A DNA and B DNA forms

Comparison of A B and Z DNA

1. handedness

2. repeating unit

3. rotation / base pair

4. base pair / turn

5. inclincation of base pair to axis

6. rise / base pair along axis

1. A: RIGHT; B: RIGHT; Z: LEFT

2. A: 1 bp; B: 1 bp; Z: 2bp.

3. A: 33º ; B: 36º; Z: - 30º.

4. A: 11; B: 10; Z: 12.

5. A: 12º; B: 0º; Z: - 7º.

6. A: 2.9 Å; B: 3.4 Å; Z: 3.8 Å.

Comparison of A B and Z DNA

7. pitch / helix turn

8. mean propeller twist

9. glycosyl angle

10. sugar pucker

11. diameter

7. A: 28 Å; B: 34 Å; Z: 46 Å.

8. A: 18°; B: 16°; Z: 0°.

9. A: anti; B: anti; Z: G: syn; C: anti

10. A: C3'-endo; B: C2'-endo; Z: C: C2' endo; G: C3' endo

11. A: 23°; B: 20°; Z: 19°.

Supercoils

aid in compacting DNA and unwinding for replication and transcription; have stored energy--when converted to unwound region, aid in replication; relieve torsional stress.

Lk can only change when DNA is cut. 

Tw + Wr = Lk

Histones

highly basic

postively charged-- charge assists in condensing DNA which is neg charged at phosphates

their amino acid sequences are highly conserved

Lysine (Lys or K)

Arginine (Arg or R)

Lysine modification

acetylation

acetylation reduces overall positive charge of a protein--loosens covalent binding to DNA

works as transcriptional activator

especially the acetylation of histone H3
and H4 tails

Serine

length of nucleic acid

E. coli

human

E. coli:

shape: Cylinder; diameter: 1.7 x 0.65µm; length: 1.3mm

Human: shape: spheroid; diamter: 6µm; length: 1.8 m

Seven possible purine-purine bps

1.A-A N1-amino sym

2.A-A N7-amino sym

3.A-A N1-am, N7-am

4.G-G N1-carbonyl sym

5.G-G N3-amino sym

6.G-G N7-N1, carb-ami

7.G-G N1-carb, N7-amino

Four possible A-G pairs

1. G-A: N1-N1, carb-amin

2. G-A: N3-amin, amin-N1

3. A-G: N7-N1, amin-carb

4. A-G: N7-amin, amin-N3

Acetylation of Lysine

Methylated form of Lysine

is the nucleosome structure present in prokaryotes?

no

true or false, RNA pseudoknots employ unused H bonding capacity of hairpin loops

true