Molecular Biology

CHM6640/7640

Lecture #2

“Structure of DNA and RNA”

Presented by Joanna Klapacz

For Dr. Ashok S. Bhagwat

Thursday January 10, 2008

Nucleic Acids:

• 2 major types: DNA and RNA

• Molecular repositories of genetic information in cells

• Variety of other roles in cellular metabolism:

• energy currency of metabolic transactions

• messengers in signaling pathways

• components of enzyme cofactors

1. Nucleotides are the building blocks/polymers of nucleic acids.

2. Nucleotides are composed of three parts:

• Nitrogen containing base

• Pentose sugar moiety

• Phosphate group

3. Nucleoside is composed of base + sugar.

Solution Confirmations of Ribose Sugar Moiety

1’

2’3’

4’

5’

1’

2’

3’

4’

5’

Remember the numbering!

D-ribose

Ribonucleotide

Found in Ribonucleic Acids (RNA)

DeoxyribonucleotideFound in Deoxyribonucleic Acids (DNA)

H D-deoxyribose

Remember the numbering!

Two Parent Nitrogenous Bases

Bases Found in Nucleic Acids

Nucleotides in RNA

Nucleotides in DNA

or TTP

Nucleoside can have more than one phosphate groups

Rotation Between Seven Bonds is

Observed in Nucleic Acids

GLYCOSYL BOND

C1’C1’

Conformation of Purines with Respect to Attached Sugar

Only the anti- configuration is found in DNA

or 2’-H

Default

or 2’-H

Structures of Adenosine Monophosphates

Found in DNA and RNA: Found in RNA only:

RNA is Chemically Less Stable

pH >11

Naturally occurring base modifications in nucleic acids

Practice drawing:

8-oxoguanosine

2,6-diaminopurine

etc etc

Covalent backbones of

nucleic acids consist of

alternating phosphate

and sugar residues.

DNA RNA

Schematic Representation of DNA Sequence

Hydrogen –Bonding of Base Pairs

O

HN C

OH

N C

keto enol

NH

HN C

NH2

N Camino imino

>10,000 : 1

Keto and Amino Groups in Bases Can Undergo Rearrangements.

Resonance Structure of Bases

Keto- and Amino groups in bases can undergo rearrangements.

Predominant Forms

Could Lead to Base Mispairing

Chemical Properties of Nucleic Acids

If pH is <4 or >10 in solution, the base pairs are disrupted because of protonation/deprotonation of keto and amino groups.

Site Affected pKa

Adenylate N1 3.9Guanylate N1 10.0Cytidylate N3 4.5Thymidylate N3 10.5Adenylate N7 2.4Guanylate N7 2.4

B-Form DNA

• Defined by Watson-Crick base pairing.• Most stable structure of DNA under physiological conditions.

Schematic Representation of DNA

(b) Stick Model

(c) Space-Filling Model

Comparison of A and B Form DNA

dsRNA or

DNA:RNAdouble-stranded

(ds) DNA

Specialized Structure in Nucleic Acids

: read identically either forwards or backwards

Regions of DNA with inverted repeats that are self-complementary.

Hairpin Structures Formed in DNA and RNA from a Single Nucleic Acid Strand

Cruciform Structures Formed in DNA and RNA from both Strands of Nucleic Acids

RNA Can Adopt Complex Structures

Transfer-RNA (tRNA)

Tertiary (3D) Structure Secondary Structure

tRNA Contains Modified Bases

1-Methyladenine

1

DNA Damaging Agents

Hoeijmakers. Nature. 2001. 411:366-74.

DISEASE

CELL DEATH

Mutation

Cell cycle arrest

DNA REPAIR

Certain chronic or metabolic diseases

CH3

Alkylating Agents Occur Ubiquitously

and Cause DNA Damage

Endogenous

Environmental

Man-made

Alkylating Agents

Bi-functional/Cross-Linking

SN1 Alkylating Agent

SN2 Agent

SN1 Alkylating Agents

* Alkylating Agents used clinically as chemotherapeutics

Model

Mono-functional

Bi-functional

Wyatt and Pittman. 2006. Chem. Res. Toxicol. 19:1580-94

DNA Methylating Agents Induce More than a Dozen Different Lesions in DNA

Other targets• phosphotriesters• deoxyribose

Filled Arrows: SN1Empty Arrows: SN1 and SN2

O6-methylguanine is Mutagenic

Cytosine Guanine

N

N

N HH

OdR

N

N N

N

dR

O

H

NHH

Thymine O6-methylguanine

N

N

O

OCH3

dR

H

N

N N

N

dR

O

NHH

CH3

3-methyladenine is a Toxic Lesion that Inhibits DNA Polymerases

3meA also rapidly depurinates

7-methyl Adduct Causes Rapid Base Loss

H

OH

Abasic (AP) site in DNA

Free Base +