Nucleic Acid Structure

• Objectives:

To know and identify the structure, roles and classifications of

• bases• sugars• nucleosides• nucleotides• DNAs• RNAs

Bases

Nucleic Acids / Bases/Structure

Pyrimidine

Imidazole

By the attachment of differentBy the attachment of different

groups to the rings, different typesgroups to the rings, different types

of Py and Pu are generated.of Py and Pu are generated.

Structures of the nitrogenous bases in DNA and RNA

NA / Bases/ Classification

• Purine Bases (pu): Purine Bases (pu): • Major : (A)&(G)Major : (A)&(G)• Minor: Inosine(I) & Minor: Inosine(I) & methyl guanine(7mG) methyl guanine(7mG) • Unnatural : Unnatural :

MercaptopurineMercaptopurine,,

Allopurinol & Allopurinol &

8-Azaguanine 8-Azaguanine

• Pyrimidines (py): Pyrimidines (py):

• Major : (T), (C) & (U) Major : (T), (C) & (U)

•Minor: DHU , 5mC & 5hmCMinor: DHU , 5mC & 5hmC

•Unnatural: Fluorouracil (5FU) & Unnatural: Fluorouracil (5FU) & 6-aza cytosine( AZC) 6-aza cytosine( AZC)

NA / Bases/ Classification/ Py

NA / Bases/ Isomerism/ Tautomerism

Diffinition:Diffinition: is a kind is a kind of isomerism between of isomerism between amine-imine or keto amine-imine or keto (oxo)- enol groups.(oxo)- enol groups.

Types:Types: Lactam( Keto, Amine) Lactam( Keto, Amine) Lactyme (Enol, Imine)Lactyme (Enol, Imine)

Properties:Properties: They They have different have different hydrogen bonding hydrogen bonding patternspatterns

Physiologic Types:Physiologic Types: amino and oxo forms amino and oxo forms

Sugars

Nucleic Acids / Sugars

D-family

Aldo pentose

Furanose

β-Anomer

Ribose or deoxy Ribose

Numbered by Prime

Isomerism ( 2’ endo in DNA , 3’ endo in RNA)

Structures of deoxyribose and ribose in DNA and RNA

Nucleosides

Nucleic Acids / Nucleosides

Structure :

Isomerism :

Nomenclature:

Roles :

Classification:

• β-N-glycosidic linkage of a base and a

pentose (1‘ to 9 in PU and 1‘ to

1 in PY).

• syn or anti conformation

• Name of the base + suffix sine for Pus(adenosine & guanosine)

• dine for PYs (uridine & thymidine)

• They are major part of nucleosides.

• Synthetic forms are used as drugs (Cytarabin)

Major:: Cytidine & deoxy cytidine.

• There are 8 major nucleotides.

Minor : ribothymidine (rT) & psudouracil (ΨU).

Unnatural : Cytarabin.

Nucleotides

Building block

Coenzymes (NAD, FAD & Co-A)

Group transfer

Energy carrier ( ATP & GTP)

Regulatory roles: Drugs

• in lipid synthesis( CDP-acylglycerol)in lipid synthesis( CDP-acylglycerol)• in sugar synthesis( UDP-glucose)in sugar synthesis( UDP-glucose)• in protein synthesis(tRNA)in protein synthesis(tRNA)• methyl donor as methyl donor as SAM SAM

(S-adenosylmethionine)(S-adenosylmethionine)

NA/ Nucleosides/ Biomedical importance

•Second messenger for hormones (cAMP or GMP)•Allosteric regulator of many enzymes (ATP & AMP in metabolic pathways)

• Synthetic pu & py analogs that contain

• Halogens, thiols or additional nitrogen are

• employed in:• treatment of gout or Hyperuricemia• (Allopurinol)• Chemotherapy of cancer ( cytarabin)• AIDS treatment ( azathioprine)• Immunosuppression responses

during organ • transplantation ( azathioprine)

Nucleic Acids / Nucleotides

Structure:Isomerism:Nomenclature:Roles:Classification:

• Nucleoside+ Phosphate group(s

=phospho ester of nucleosides• In most cases the phosphate

group is linked to the 5’ carbon.• They may have 1, 2,or 3

phosphate groups.They may have syn or anti conformation They may have syn or anti conformation

with with predominate anti conformerpredominate anti conformer..

1-Name of the nucleoside1-Name of the nucleoside

+ the number of phosphate group.+ the number of phosphate group.

2-Name of their corresponding acid2-Name of their corresponding acid

such as thymidylic or guanylic acid.such as thymidylic or guanylic acid.

• Building block• Coenzymes (NAD, FAD & Co-A)• Group transfer• Energy carrier ( ATP & GTP)• Regulatory roles: • Drugs

MajorMajor:: CMP, dCMP, CDP, CTPCMP, dCMP, CDP, CTP

There are 24 major nucleotidesThere are 24 major nucleotides

MinorMinor : : cAMP, cGMPcAMP, cGMP

UnnaturalUnnatural : : Cytarabin Cytarabin

Nucleic Acid:1-DNA2-RNA

Nucleic Acids /DNA/ Structure• Objectives To know and identify different levels of

DNA organization

1- Primary structure

2-Secondary structure

Different geometry of

base pairs & base steps

3- Higher order of DNA structure

in prokaryotes

in Eukaryotes

2’-deoxyribose sugars

Phosphodiester linkages

Directional chain (5’ to 3’)

4 Bases

purines: adenine & guanine

pyrimidines: cytosine & thymine

DNA is a polymer of2’-deoxyribonucleotides

GCTAp

5’ end

3’ end

C

G

T

A

HO-CH2

O

H2N-C

C

C

HN

N

N

CH

C

O

N

O

O

O P O CH2

O

O

C

N

N

CHC

CH

NH2

NH2

C

CN

N

N

CH

C

NHC

O

O

O P O CH2

O

O-PO32

O

O

O P O CH2

O

N

CC

O

HN

CHCO

CH3

1’

2’3’

4’

5’

3’

DNA / Different ways to show primary structure

5’ 3’

Primary structure is a huge linear polymer of dNTPs that are joined to each other by 5’-3’ PDE bonds.

Different bonds and interactions in

• Covalent:

PDE bonds in the backbone

• Hydrogen: between complementary bases

• Hydrophobic (van der Waals)

between the stacked adjacent base pairs.

Secondary structure of DNA / Different ways to show it

5’ 3’

3’ 5’

Secondary structure is formed by base pairing between two complementary strands. It may be B, A or Z form.

DNA / Different secondary structures

• B (duplex)

• A (duplex)

• Z (duplex)

B-form DNA consists of a right-handed double helix with antiparallel strands

34 Å (10 bp) per turn

major groove

minor groovemajor groove

minor

3.4 Å per bp

These dimensions are for DNA fibers. In solution, there are ~10.5 base-pairs per turn.

5’ 3’

5’3’

Summary of the main structural features of B-form DNA

•Right-handed helix

•Two antiparallel strands held together by Watson-

Crick hydrogen bonds

•Pitch (repeat length) = 34 Å (3.4 nm)

•36o rotation between residues

•Helix diameter of 20 Å (2.0 nm)

•Wide major groove, narrow minor groove

•Chargaff’s Rules: A = T; G = C

•Charged phosphates

•Bases in anti configuration

•The strands separate at high temperatures

dsDNA

ssDNAnucleotides

dA

dC

dG

dU

The absorbance of double-stranded DNA (dsDNA) at 260 nm is less than that of either single-stranded DNA (ssDNA) or the free bases. This is called “hypochromism.”

Double-stranded and single-stranded DNA differ in their optical absorption at 260 nm

100

80

60

40

20

0

% D

enat

ured

110100908070Temperature /

oC

40 50 70% GC60

The temperature at which this “denaturation” or “melting” occurs depends on the pH and salt concentration, and increases with the GC content of the DNA. (The curves drawn here are schematic.)

2nd structure of DNA/ A- DNAG enerated by dehydration of B-DNA

It is more compact than B-DNA

Has 2 grooves

Has 11bp/turn

Is right handed

Has a pitch per turn of helix 28 Ao

Side and top view of A -DNA in

ball-and-stick and space filling representation

2nd structure of DNA/ Z- DNA

• Alternative G -C sequences form this zigzag

form DNA

• Is more narrower than B-DNA

• Has one groove

• Has 12 bp/turn

• Is left handed

• The stacked bases are almost perpendicular

• Has a pitch per turn of helix 45.6 Ao

PDB

Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.

A possible nucleosome structure

Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.

Fig. 2.26 Nucleosomes connected together by linker DNA and H1 histone to produce

the “beads-on-a-string” extended form of chromatin

Packaging of nucleosomes into the 30-nm chromatin fiber

Model for the organization of 30-nm chromatin fiber into looped domains

that are anchored to a nonhistone protein chromosome scaffold

The many different orders of chromatin packing that give rise to the highly

condensed metaphase chromosome

Histon likes proteins

HU (heat unstable)

H-NS(Histon like Nucleotide Structuring)

RNAs

tRNA

mRNA

rRNA

hnRNA(hetererogenous nuclear RNA)

SnRNA (Snurps)

RNA• Objectives:

To know and identify: Primary, secondary and Tertiary

structure of RNA.Structure and function of tRNA. Structure and function of rRNA. Structure and function of mRNA.

RNA is a polymer of ribonucleotides

ribose sugars

Phosphodiester linkages

Directional chain (5’ to 3’)

4 Bases

purines: adenine & guanine

pyrimidines: cytosine & uracil

GCUAC

G

U

A

5’ end

3’ end

1’

2’3’

4’

5’

3’

OH

HO-CH2

O

H2N-C

C

C

HN

N

N

CH

C

O

N

O

O

O P O CH2

O

O

C

N

N

CHC

CH

NH2

OH

O

O

O P O CH2

O

N

CHC

O

HN

CHCO

OH

NH2

C

CN

N

N

CH

C

NHC

O

O

O P O CH2

O

O-PO32

OH

tRNA Structure 5’’ 3’

DNA / General facts

Particular region bound to protein clearly depart from the standard conformation

• Has specific groove (s)• It is flexible about its long axis it

• It may be linear or circular

d. The bases of the two strands are held together by hydrogen bonds between complementary bases (two for A-T pairs and three for G-C pairs). Individual H-bonds are relatively weak and so the strands can be separated (by heating, for example). Complementary base pairing means that the sequence of one strand dictates the sequence of the other strand.

Palindromic* sequences (inverted repeats) in DNA or RNA can form hairpin or cruciform structures

inverted repeats in an antiparallel double helix

3’

5’

5’

3’

T G C G A T A C T C A T C G C A

A C G C T A T G A G T A G C G T

hairpin

C

A C

T

3’5’

TAGCGT

ATCGCA

T

G AG

C

A C

T

cruciform

3’5’

5’3’

TAGCGT

ATCGCA

TGCGAT

ACGCTA

Mirror repeats cannot form these structures.

*A palindrome reads the same in either direction (“Radar,” “Madam, I’m Adam”).

DNA / General facts• Its structure was discovered in 1953 by Watson

and Crick• It is a polyester compound• Has acidic character

It is a polymer in which the monomers (nucleotides)are joined by PDE bonds between5’ and 3’ carbon atoms of two successive nucleotides.

Because of the phosphate

moiety, they have acidic

character (negatively charged).

• Has polarity

• It is double helix

DNA / General facts

DNA has end-to-end

chemical Orientation

(3’ and 5’ ends) and

by convention it

is written in the

5’ 3’ direction

• The two strand are:

1- in opposite polarities

2- stabled by different bonds:

-Hydrophobic bond

-H bond

RNA is easily hydrolyzed under alkaline conditions

The reaction proceeds through a 2’,3’-cyclic monophosphate intermediate. Enzymatic hydrolysis of RNA by RNase proceeds through a similar intermediate. Because DNA lacks the 2’-OH group, it is stable under alkaline conditions.

.

...

O P O-CH2

O

OO

N

OHO

O P O CH2

OO

N

OHO

O P O

O

...

OH

ON

OHO

O P O

O

...

HOCH2

O

.

...

O P O-CH2

O

O

N

OO

POO

H+

.

...

O P O-CH2

O

OO

N

OHO

O P OH

O

mixture of 2’- and 3’- monophosphate derivatives

H2O

shortened RNA

RNA

What about DNA grooves

• They are generated because of the angle of base pairs

• They are important for the interaction with proteins

2nd structure of DNA/ B- DNA• Is the abundant form• Has 2 groooves• Has 10 (10.5) bp/ turn• Is right handed• Has a pitch per turn of helix 34 Ao

Side and top view of B-DNA in ball-and-stick and space filling representation

The helix tilted 32˚ from the viewer to show minor (m) and major (M) grooves.