DNA & RNA Structure

Fig 1.9

34 Å

3.4 Å

20 Å

MinorGroove

MajorGroove

GC

CG

AT

TA

CG

GCAT

TA

TA

AT

GCCG

GC

Strands areantiparallel

Deoxyribonucleic acid (DNA)is the genetic material

-Stores genetic information in the form of a code: a linear sequence of nucleotides.

- Replicated by copying the strands using each as a template for the production of the complementary strand.

-DNA

Major groove

Minor groove

P

O

O -

C

C

O

O

3'

5'Phosphodiester

Bond

3' hydroxyl

5' phosphate

a nucleotide

This ring isdeoxyribose

A. Organic chemistry model(single stranded DNA)

C. Space filling model (double stranded DNA)

B. Ribbon model (double stranded DNA)

P

C

3'

5'

P

C

3'

5'

N1

N

O

O

HP

C

3'

5'

N1

N

N H

H

O

P

C

3'

5'

N

1N H

NH2

ON

N

N

1N

H

NH2N

N

OH

O

O

O

O

CH 3

H

H

H

H

H

T

C

G

A

3 Ways of Depicting DNA Structure

.

O

H

H

OH

H

H

H

N

N

NH2

N

N

HOCH2

2-deoxy-ADENOSINE

O

H

H

OH

H

H

H

HOCH2

N

NHN

N

O

H2N

2-deoxy-GUANOSINE

O

H

H

OH

H

H

H

HOCH2

O N

H N

O

CH3

2-deoxy-THYMIDINE

O

H

H

OH

H

H

H

HOCH2

O N

N

NH2

2-deoxy-CYTIDINE

Nucleosides (of DNA) – Precursors to Nucleotides

Nucleoside = base + sugar

Sugar = deoxyribose; 5 carbons, no OH on the 2nd (or 2’) carbon; base is attached to carbon 1

.

O

H

H

OH

H

H

H

O N

N

NH2

CH2P O

O

O -

P O

O

O -

P O- O

O

O - 1'

2'3'

4'

5'

2'-deoxycytidine 5' triphosphate

O

H

H

H

H

CH2P O

O

O -

P O

O

O -

P O- O

O

O - 1'

2'3'

4'

5'

N

N

NH2

N

N

2'-deoxyadenosine 5' triphosphate

OH H

O

H

H

OH

H

H

H

CH2P O

O

O -

P O

O

O -

P O- O

O

O - 1'

2'3'

4'

5'

N

NHN

N

O

H2N

2'-deoxyguanosine 5' triphosphate

O

H

H

OH

H

H

H

CH2P O

O

O -

P O

O

O -

P O- O

O

O - 1'

2'3'

4'

5'

O N

H N

O

CH3

thymidine 5' triphosphate

The 4 Nucleotides (precursors) of DNA

γ β α

.

RIBOSE

1

OHOCH2

H

H

OH

H

OH

H

OH23

4

5OHOCH2

H

H

OH

H

OH

H

H

1

23

4

5

2-DEOXY-RIBOSE

O N

H N

O

H

CH3

THYMINE

O N

H N

O

H

URACIL

RNA DNA

Molecular Differences between Ribonucleic Acid (RNA)& 2-deoxy-ribonucleic acid (DNA).

Ribose replaces deoxyribose; uracil replaces thymine

RNA

Before we continue some terminologyNucleotide Name Table

Purines PyrimidinesAdenine (A) Guanine (G) Cytosine (C) Thymine (T) Uracil (U)

Nucleotides in DNA deoxyadenylate deoxyguanylate deoxycytidylate deoxythymidylateor thymidylate

Nucleotides in RNA adenylate guanylate cytidylate uridylateAbbreviations

Nucleosidemonophosphates

AMP GMP CMP TMP UMP

Nucleosidediphosphates

ADP GDP CDP TDP UDP

Nucleosidetriphosphates

ATP GTP CTP TTP UTP

For deoxynucleotides add 'd' in front of the above three.

e.g., AMP is a ribonucleotide, dAMP is a deoxyribonucleotide

In DNA and RNA, nucleotides are held together by phosphodiester bonds.

Stem-loops are common elements of secondary RNA structure.

Stem loop

Stems are double-stranded regions of RNA that are A-form helices. They usually follow Watson-Crick base pairing rules (U replaces T), but other pairs occur (G – U is common).

(DNA is typically a B-form helix).

Higher Order RNA Structure

Secondary structure diagram Tertiary structure diagram

Cr.LSU rRNA intron Tetrahymena rRNA intron

What chemical forces hold (or drive) the DNA strands together?

(also applies to double-stranded regions of RNA)

1. Hydrogen bonds between bases

Also important that the purine-pyrimidine base pairs are of similar size.

2. DNA strands also held together by base stacking:Van der Waals interactions between

successive (or neighbor) base-pairs

3. Double-stranded helix structure also promoted by having phosphates on outside, interact with H2O and counter ions (K+, Mg2+, etc.)

Evidence: Compounds that interfere with Hydrogen bonds (urea, formamide) don’t separate strands by themselves, still requires heat

Double-stranded (DS) DNA statistics

(B-form)

1. Helix is right handed2. 10 base-pairs/turn3. 3.4 nm (34 angstroms)/turn4. Helix has a major groove and a minor groove.

-DNA

Major groove

Minor groove

P

O

O -

C

C

O

O

3'

5'Phosphodiester

Bond

3' hydroxyl

5' phosphate

a nucleotide

This ring isdeoxyribose

A. Organic chemistry model(single stranded DNA)

C. Space filling model (double stranded DNA)

B. Ribbon model (double stranded DNA)

P

C

3'

5'

P

C

3'

5'

N1

N

O

O

HP

C

3'

5'

N1

N

N H

H

O

P

C

3'

5'

N

1N H

NH2

ON

N

N

1N

H

NH2N

N

OH

O

O

O

O

CH 3

H

H

H

H

H

T

C

G

A

3 Ways of Depicting DNA Structure

1

0

10

Molecular Visualization:www.umass.edu/microbio/chime/

DNA Structure:

www.umass.edu/molvis/tutorials/dna/

Study Helix Stability with Melting Curves

DNA melting curve of Streptococcus DNA.

When DNA melts, the 2 strands come apart, and its absorbance in the UV region increases.

Tm= temp. at which 50% of DNA is melted.

Re-Annealing or Hybridization

Works with: • DNA - DNA• DNA - RNA• RNA - RNA

Basis of many techniques in molecular biology.

Base composition (G-C content) determines melting temperature: varies among organisms

Separation of nuclear (nuc) and mitochondrial (mt) DNA on a CsCl-ethidium bromide gradient – visualized with long-wave UV light.

G-C content also determines density of DNA (g/cc)