slide1 n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
Nucleic Acids Structures PowerPoint Presentation
Download Presentation
Nucleic Acids Structures

Loading in 2 Seconds...

play fullscreen
1 / 38

Nucleic Acids Structures - PowerPoint PPT Presentation


  • 81 Views
  • Uploaded on

Nucleic Acids Structures. 1-Discovery of DNA structure. 2- A, B and Z conformations of dsDNA/dsRNA. 3- DNA tertiary Structures Nucleosome , G- quadruplex. 4- Secondary and tertiary Structure of RNA. 5- Principles of DNA Recognition by sequence-specific DNA binding proteins .

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Nucleic Acids Structures' - dragon


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
slide1

Nucleic Acids Structures

1-Discovery of DNA structure

2- A, B and Z conformations of

dsDNA/dsRNA

3- DNA tertiary Structures

Nucleosome, G-quadruplex

4- Secondary and tertiary Structure of RNA

5- Principles of DNA Recognition by

sequence-specific DNA binding proteins

  • • Not treated:
  • DNA topology
  • DNA Sequencing

6- Principles of Nucleic Acids

Denaturation

slide2

Polymeric

Structure

Of Nucleic

Acids

• Links 3’-O of preceding

nucleotide to 5’ of next

nucleotide

->5’-3’

polarity

• 1 negative charge per residue

slide3

Rosalind Franklin

(1950 or 1951)

Chargaff. 1950: “It is, however, noteworthy

-whether this is more than accidental,

cannot yet be said-that in all deoxypentose

nucleic acids examined thus far the molar

ratios of total purines to total pyrimidines,

and also of adenine to thymine and of

guanine to cytosine, were not far from 1”.

Watson and Crick (1953)

Watson and Crick (1953): “It has not

escaped our notice that the specific

pairing we have postulated immediately

suggests a possible copying mechanism

for the genetic material”.

slide4

Information that Watson and Crick used to propose the double helix model:

1) R. Franklin DNA fibers

X-ray diffraction data

2) bases are in the keto conformation

Maltese Cross

Indicates an

Helical pattern

Spacing

between

Phosphates

= 3.4A

enol

Helical Pitch

= 34A

keto

Bragg’s Law: 2dsinQ = nl

used to interpret X-ray diffraction pictures

4) Density measurements:

~2 polymers/helix

3) Chargaff’s rules:

(G+C)/(A+T) can vary

But (G+A)/(C+T) = G/C = A/T =1

5) C2’ endo sugar pucker

conformation

slide5

Bragg's Law

= repeated atomic features

in the crystal or fiber

Bragg’s law indicates an inverse relationship between diffraction

angle and actual distances between repeated features in crystal/fiber

slide6

The original model for DNA structure

Watson and Crick (1953)

Nature 171, 964-967

  • Essential features of the model that
  • proved correct:
  • Antiparallel

right-handed

double helix

  • 2) Strands are linked by
  • complementary sets of
  • donors and acceptor groups
  • on bases

Helical

Pitch

= 34 A

(10 residues/turn)

Rise/

residue

= 3.4 A

slide8

A comparison of

the Watson-Crick

model (1953)

and of the first

B-DNA

structure solved (1980)

The Dickerson

Dodecamer

X-ray structure

(CGCGAATTCGCG)

PDB ID:

1BNA

Watson-Crick

Model

slide9

DNA Double Helix

Definitions

Bases Orientation

slide10

Base pairs seen

from above the helix

(helical projection)

Helical Axis

Major Groove

>180°

H

O

H

N

N7

N1

H

N3

N9

N1

N3

O

H

N

dR

dR

H

Minor Groove

<180°

Pseudo

Dyad Axis

slide11

H

H

N

O

CH3

N7

A

T

N1

H

N3

N9

N1

N3

O

dR

dR

H

O

H

CH3

N

N7

T

A

N1

H

N3

N9

N1

N3

dR

O

dR

dR

dR

O

CH3

H

T

O

H

H

N

N3

O

G

N7

N7

N1

G

C

O

N3

H

N1

N1

H

N9

N9

N1

N3

N3

O

N

H

H

N

dR

dR

H

H

H

H

O

O

H

H

N

N

G

G

C

C

N7

N7

N1

N1

H

H

N3

N3

N9

N9

N1

N1

N3

N3

O

O

H

H

N

N

dR

dR

dR

dR

H

H

Isostericity of Watson-Crick Base Pairs

(and non isostericity of non WC base pairs)

Example of a G-T non WC base pair

slide12

B

A vs B DNA

H20

A

B

PDB ID:

1BNA

Ethanol

A

PDB ID = 115D

slide13

Sugar Pucker

Planar

C3’endo

C2’endo

Exact values need not to be remembered…

helical projection

Major differences :

- A DNA is shorter than B DNA: 1 helix turn is 28.6A vs 34 A

for B DNA. This is due to the 3’ endo sugar pucker in A

- The Bases of A-DNA are shifted away from the helical axis.

This results in a deep major groove and in a shallow

minor groove. There is a 6 A hole in a helical projection.

A

B

slide14

Sugar puckering: C2’ endo or C3’ endo

dsRNA or A-DNA :

C3’ endo

B-DNA: C2’ endo

Distance between Consecutive Phosphates:

5.9 Å

7 Å

slide15

Base tilting in A-DNA

B-DNA

A-DNA

Base pairs are more tilted in A-DNA.

slide16

H20 is essential

in the transition

A <--> B DNA

H20

A

B

A water spine (green dots)

has been proposed to exist

in the minor groove of B-DNA

that would stabilize the B-form

This concept is controversial

and will not be detailed further

slide17

Z-DNA

Left handed Helix

Occurs in DNA

sequences with

stretches of

consecutive

G-C base pairs

jagged backbone

G nucleotides:

Switch

C2’endo -> C3’ endo

anti -> Syn

Requires high salt

in vitro

PDB ID:

1DCG

C nucleotides:

No change

www.mun.ca/biology/scarr/A_B_Z_DNA.html

slide18

Nucleotides flipping and grooves in Z-DNA

Z-DNA

Major

Minor

Major

Minor

B-DNA

Note: this simplified diagram only summarizes the conformation

changes during the B->Z transition – it does not accurately shows the Z structure

slide19

Glycosidic bond Anti /Syn conformations

Anti and Syn conformations are defined based on the torsion angle of the glycosidic bond

The sequence of atoms chosen to define the torsion angle to define anti/syn conformation is: O4'-C1'-N9-C4 for purines - O4'-C1'-N1-C2 for pyrimidines.

Anti C/T:

C1’-O4’ and N1-C2 are

pointing away from

each other

Syn A/G:

C1’-O4’ and N9-C4 are

pointing in same direction

Anti A/G:

C1’-O4’ and N9-C4

are pointing away

from each other

4

4

2

9

9

1

4'

4'

4'

1'

1'

1'

slide20

Anti /Syn conformations in pseudo-3D

9

4

4'

4

4'

9

1'

1'

Syn- A

4

9

4'

4'

4

9

1'

1'

Anti A/G:

C1’-O4’ and N9-C4 are pointing

away from each other

Syn A/G:

C1’-O4’ and N9-C4 are

pointing in same direction

slide21

B

Z

A

ABZ-DNAs

B

Z

Backbone

Profiles

Helical

Projections

slide22

Z

A

B

www.mun.ca/biology/scarr/A_B_Z_DNA.html

slide23

Why Study DNA Structure ?

• Structure and Sequence Recognition by DNA binding

proteins

• Some non B-DNA structures are biologically relevant

- dehydrated living forms

- dsRNA is A form (see PDB: 2KYD)

- DNA/RNA duplex (replication, transcription) is A form

- Z-DNA might be associated with promoter elements,

regulatory sequences

• There are conformations other than A/B/Z

e.g.: conformations intermediate between A and B

Also Tertiary conformation of DNA

slide24

Double-Stranded DNA is wrapped around nucleosomes in eukaryotic cells

Binding of histones to DNA through electrostatic interactions:

Histones are + charged, DNA is - charged

Consequences for:

DNA Replication,

DNA Repair

Transcription

http://www.bio.miami.edu/dana/104/nucleosome.jpg

slide25

Double-Stranded DNA is wrapped around nucleosomes in eukaryotic cells

PDB ID:

1AOI

http://www.chem.ucsb.edu/~molvisual/dna_biochem.html

slide26

Example of intrinsic

DNA Tertiary Structure

G-quadruplex structures

in telomeric DNA:

case of (T2G4) repeats

Na+

PDB ID:

156D

slide27

Secondary and Tertiary Structure of RNA

Single strandedness nature of RNA makes it able to

“fold” on itself and base-pair with complementary segments

within the same molecule

slide29

Secondary and Tertiary Structure of RNA:

See other examples

in the RNA Processing

and Translation Chapters

Secondary Structure of the

M1 RNA, a component of RNase P

(see RNA processing chapter)

Two major observations:

1-Abundance of

G:U base pairs

2-Pseudoknot:

long range

base-pairing

“A” form tolerates

the geometry of G:U base pairs

slide30

Can you read ?

(the sequence of this DNA)

slide32

Recognition of Specific sequences

by DNA-binding proteins

Distribution of H-bonds

Donors (D) Acceptors (A)

and Hydrophobic groups (H)

H

Major

groove

H

N

O

CH3

D

N7

A

A

H

A

T

N1

H

N3

N9

Minor

groove

N1

A

A

N3

O

dR

dR

Major

groove

H

D

O

H

CH3

N

H

A

A

N7

Minor

groove

T

A

N1

H

N3

N9

A

A

N1

N3

O

dR

dR

Conclusion: DNA binding proteins can differentiate

A-T base pairs from T-A base pairs if they bind

from the major groove side, but not from the minor groove side

slide33

Patterns of H-bonds

Donors (D), Acceptors (A),

and Hydrophobic groups (H)

available for recognition

Recognition of Specific sequences

by DNA-binding proteins

C

H

G

O

H

N

D

N7

Major

groove

A

A

N3

H

N1

N9

N1

Minor

groove

N3

A

O

N

H

A

dR

dR

D

H

H

Major

groove

D

O

H

N

G

A

C

A

N7

N1

H

N3

N9

Minor

groove

A

N1

N3

A

O

H

N

D

dR

dR

H

Conclusion: DNA binding proteins can differentiate

G-C base pairs from C-G base pairs if they bind

from the major groove side, but not from the minor groove side

slide34

DS DNA (Helix)

What influences the equilibrium ?

(important because DNA is “opened”

during replication and transcription)

In favor of double-stranded DNA

- Hydrogen bonds between strands (minor)

- Base stacking Interactions (major)

In favor of single-stranded DNA

- Electrostatic Repulsion between strands

- Entropic considerations:

Increased entropy for ssDNAvsdsDNA

2 SS DNAs (“random coils”)

slide35

Experimental Studies of DNA denaturation

Relative

Absorbance

Hyperchromic Effect:

SS DNA > native DNA

DNA

molecule

Denatured DNA

Native

DNA

240

180

200

220

260

280

Wavelength (nm)

UV spectroscopic analysis of

SS (denatured) vs DS

(native) DNA

“melting curves” for two different

DNA molecules (red and blue) show different “melting points” =

2 different Tms

slide36

DNA melting is a cooperative process:

this explains the sigmoid denaturation curves

Increasing Conformational Entropy

Increasing

Entropy

( 1 -> 2 molecules)

slide38

The Tm of a DNA molecule is a linear function

of its G-C content/this is not because of higher energy

of 3 H-bonds (GC) vs 2 (AT)

Effect of G-C content on

Stability is due to higher

stacking of G-C base

pairs compared to AT base pairs

DG BP≅ contribution of stacking

to the stability of base pair

Yakovchuk P et al.

Nucl. Acids Res. 2006;

34:564-574