Nucleic Acid Structures

Learning objectives

Understand the molecular structure of DNA.

Understand the molecular structure of RNA.

Understand the relationships between purines, pyrimidines, nucleosides, nucleotides, and nucleic acids.

Understand the structural differences between DNA and RNA

Nucleic acid functions DNA –genetic information storehouse

RNA message between the genome and the ribosome for the building

of proteins (messenger RNA, or mRNA), act as the catalytic moiety in a RNA-protein enzyme complex

(rRNA) serve as the translator between mRNA sequence and protein

sequence (tRNA)

RNA and DNA- recent discovery catalyze some reactions without protein involvement (ribozymes or deoxyribozymes).

DNA from

archeological

samples

Compared to modern

DNA

Evidence of DNA

stability

9000 year old “Kennewick man” skull discovered along the banks of

the Columbia River in Washington state believed to have originated

from Southeast Asia, Japan or Polynesia

SUGAR + BASE = NUCLEOSIDE

Nucleotide – monomeric unit in nucleic acid

Deoxythymidine 5’-monophosphate

Deoxyadenosine 5’-monophosphate

Deoxycytidine 5’-monophosphate

Deoxyguanosine 5’-monophosphate

N-glycosidic bond

3’,5’-phosphodiester bond

C1’-N1= Pyr

C1’-N9 = Pur

Structural features of the DNA

(secondary structure)

Double helix; 2 topographic features – major groove and minor groove

Two strands antiparallel

In aqueous environment phosphate-sugar backbone outside of the helix; purine and pyrimidine rings inside the structure

Strand stabilized by :

H-bonds between complement bases

Van der Waals and

Hydrophobic interactions between stacked bases

A B Z

Conformational varieties of the secondary

structure

Conformational varieties of the

secondary structure

B-DNA – crystallized from water; water

retained in the inner structure;

predominant form under physiological

conditions

10 base pairs/turn of helix

Right handed

Distance bet base pairs 0.34 nm

Diameter – 2.0 nm or 20 A

A-DNA

Dehydrated form of B-DNA

Right handed helix

11 base pairs/helix

Diameter = 26 A

Z-DNA

Found in short stretches of native DNA

and synthetic DNA

Left handed helix

12 base pairs/helix

Diameter = 18 A

85-90 degrees as

the melting

temperature

Tm = midpoint of each curve

At normal temp Increased tem, DNA denatures

More light is absorbed

Sample becomes more turbid

Tertiary structure of the DNA Circular (relaxed) – in E.coli; simian virus 40;

bacteriophage; certain animal species

Supercoiled DNA – extra twisting in the linear duplex; allows DNA to be more compact in the cell; regulatory role in replication Topoisomerase – change topology of the DNA

Quadruplex DNA – four stranded; in protozoan DNA; occur in G-rich regions; regulating and stabilizing telomeres and regulation of gene expression