Chapter 3

Structures and Functions of Nucleic Acids

Nucleic acid

A biopolymer composed of nucleotides linked in a linear sequential order through 3’,5’ phosphodiester bonds

Classification of nucleic acid

• Ribonucleic acid (RNA) is composed of ribonucleotides.– in nuclei and cytoplasm – participate in the gene expression

• Deoxyribonucleic acid (DNA) is composed of deoxyribonucleotides.– 90% in nuclei and the rest in mitochon

dria – store and carry genetic information; d

etermine the genotype of cells

Interesting history

• 1944: proved DNA is genetic materials (Avery et al.)• 1953: discovered DNA double helix (Watson and Cri

ck)• 1968: decoded the genetic codes (Nirenberg)• 1975: discovered reverse transcriptase (Temin and

Baltimore)• 1981: invented DNA sequencing method (Gilbert and

Sanger)• 1985: invented PCR technique (Mullis)• 1987: launched the human genome project • 1994: HGP in China• 2001: accomplished the draft map of human genome

Section 1

Chemical Components of Nucleic Acids

nucleic acid nucleotidesphosphate

nucleosides

pentose

bases

§ 1.1 Molecular Constituents

Nucleic acid can be hydrolyzed into nucleotides by nucleases. The hydrolyzed nucleic acid has equal quantity of base, pentose and phosphate.

N

N

NH

N1

23

4

567

89

N

N

NH

N

NH2

Adenine (A)

N

NH

NH

N

NH2

O

Guanine (G)

Base: Purine

N

NH1

32

45

6

Base: Pyrimidine

Cytosine (C)

N

NH

NH2

O

Uracil (U)NH

NH

O

O

Thymine (T)

NH

NH

O

O

CH3

Pentose

1´

2´3´4´

5´OH

O

CH2OH

OH OH

-D-ribose

OHO

CH2OH

OH

-D-2-deoxyribose

Ribonucleoside

OHO

CH2

OHOH

N

N

NH2

O

1´

1

Purine N-9 or pyrimidine N-1 is connected to pentose (or deoxypentose) C-1’ through a glycosidic bond.

glycosidic bond

P

O

O

OH

OHO

CH2

OHOH

N

N

NH2

O

A nucleoside (or deoxynucleoside) and a phosphoric acid are linked together through the 5’-phosphoester bond.

Ribonucleotide

phosphoester bond

base nucleoside nucleotide

guanine guanosine guanosine monophosphate

(GMP)

cytosine cytidine cytidine monophosphate

(CMP)

adenine adenosine adenosine monophosphate

(AMP)

uracil uridine uridine monophosphate

(UMP)

(NMP)

Nomenclature

base nucleoside nucleotideguanine deoxyguanosine deoxyguanosine monophosphate

(dGMP)

cytosine deoxycytidine deoxycytidine monophosphate

(dCMP)

adenine deoxyadenosine deoxyadenosine monophosphate

(dAMP)

thymine deoxythymidine deoxythymidine monophosphate

(dTMP)

(dNMP)

Nomenclature

Nucleic acid

base ribose

DNA A、 G、 C、 T deoxyribose

RNA A、 G、 C、 U ribose

Composition of DNA and RNA

Nucleic acid derivatives

Multiple phosphate nucleotides adenosine monophosphate (AMP)adenosine diphosphate (ADP)adenosine triphosphate (ATP)

NO

CH2O

OHOH

N

NN

NH2

P

O

OH

OH

AMPAMP

NO

CH2O

OHOH

N

NN

NH2

P

O

OH

OP

O

OH

OH

ADPADP

NO

CH2O

OHOH

N

NN

NH2

P

O

OH

OP

O

OH

OP

O

OH

OH

ATPATP

Cyclic ribonucleotide: 3’,5’-cAMP, 3’,5’-cGMP, used in signal transduction

NO

CH2O

OHO

N

NN

NH2

PO

OH

cAMPcAMP

Nucleic acid derivatives

Biologically active systems containing ribonucleotide: NAD+, NADP+, CoA-SH

Nucleic acid derivatives

The -P atom of the triphosphate group of a dNTP attacks the C-3’ OH group of a nucleotide or an existing DNA chain, and forms a 3’-phosphoester bond.

Phosphoester bond formation

Nucleic acid chain extension

A nucleic acid chain, having a phosphate group at 5’ end and a -OH group at 3’ end, can only be extended from the 3’ end.

Phosphodiester bonds

Alternative phosphodiester bonds and pentoses constitute the 5’-3’ backbone of nucleic acids.

Section 2

Structures and Functions of Nucleic Acids

§ 2.1 Primary Structure

• The primary structure of DNA and RNA is defined as the nucleotide sequence in the 5’ – 3’ direction.

• Since the difference among nucleotides is the bases, the primary structure of DNA and RNA is actually the base sequence.

• The nucleotide chain can be as long as thousands and even more, so that the base sequence variations create phenomenal genetic information.

P P

A

P

C

P

C

P

T

P

G

OH

C

P

T

P

A

P

A

5' 3'

pApCpTpGpCpTpApApC-OH 3'

5' ACTGCTAAC 3'

5'

§ 2.2 Secondary structure

The secondary structure is defined as the relative spatial position of all the atoms of nucleotide residues.

§ 2.2.a Chargaff’s rules

• The base composition of DNA generally varies from one species to another.

• DNA isolated from different tissues of the same species have the same base composition.

• The base composition of DNA in a given species does not change with its age, nutritional state, and environmental variations.

• The molarity of A equals to that of T, and the molarity of G is equal to that of C.

Molarity of bases

  A G C T A/T G/C G+C Pu/Py

E. coli 26.0 24.9 25.2 23.9 1.09 0.99 50.1 1.04

Tuberculosis

15.1 34.9 35.4 14.6 1.03 0.99 70.3 1.00

Yeast 31.7 18.3 17.4 32.6 0.97 1.05 35.7 1.00

Cow 29.0 21.2 21.2 28.7 1.01 1.00 42.4 1.01

Pig 29.8 20.7 20.7 29.1 1.02 1.00 41.4 1.01

Human 30.4 19.9 19.9 30.1 1.01 1.00 39.8 1.01

Historic X-ray diffraction picture

Building a milestone of life

James Watson and Francis Crick proposed a double helix model of DNA in 1953.

It symbolized the new era of modern biology.

• Two DNA strands coil together around the same axis to form a right-handed double helix (also called duplex).

• The two strands run in opposite directions, i.e., antiparallel.

• There are 10 base pairs or 3.4nm per turn and the diameter of the helix is 2.0nm.

§ 2.2.b Double helix of DNA

Antiparallel

The hydrophilic backbone is on the outside of the duplex, and the bases lie in the inner portion of the duplex.

Backbone and bases

• The two strands of DNA are stabilized by the base interactions.

• The bases on one strand are paired with the complementary bases on another strand through H-bonds, namely G≡C and A=T.

• The paired bases are nearly planar and perpendicular to helical axis.

• Two adjacent base pairs have base-stacking interactions to further enhance the stability of the duplex.

Base interactions

Watson-Crick base pair

Watson-Crick base pair

Base-stacking interaction

Major and minor grooves

Groove binding

Small molecules like drugs bind in the minor groove, whereas particular protein motifs can interact with the major grooves.

§ 2.2.c Polymorphisms of DNA

• DNA can resume different forms depending upon their chemical microenvironment, such as ionic strength and relative humidity.

• B-form DNA is the predominant structure in the aqueous environment of the cells.

• A-form and Z-form are also native structures found in biological systems.

Feature A-DNA B-DNA Z-DNA

Helix rotation Right-handed Right-handed Left-handed

Base pair per turn 11 10 12

Pitch 2.46nm 3.4nm 4.56nm

Helical diameter 2.55nm 2.0nm 1.84nm

Rise per base pair 0.26nm 0.34nm 0.37nm

Glycosyl formation Anti- Anti- Anti- at C, syn- at G

Rotation between adjacent base pair

33º 36º -60º per dimer

Relative humidity 75% 92%

Structural features of DNAs

Triplet DNA

Hoogsteen base pair

The third strand is using Hoogsteen H-bonds to pair with bases on the first strand.

G-quartet DNA

• The telomere of DNA is a G-righ sequence, such as

5’ (TTGGGG)n 3’

• 4 G residues constitute a plane which is stabilized by Hoogsteen H-bonds.

G

G

T

T

T

T

TT

G

T G

T

T

G

5'3'

T

G-quartet of DNA

Four strands are arranged in either parallel or antiparallel manner.

§ 2.3 Supercoil Structure

• The two termini of a linear DNA could be joined to form a circular DNA.

• The circular DNA is supercoiled, and supercoil can be either positive or negative.

• Only the supercoiled DNA demonstrate biological activities.

§ 2.3.a Supercoil structure

EM image of supercoiled DNA

Circular DNAs in nature, in general, are negatively supercoiled.

§ 2.3.b Prokaryotic DNA

• Most prokaryotic DNAs are supercoiled.

• Different regions have different degrees of supercoiled structures.

• About 200 nts will have a supercoil on average.

§ 2.3.c Eukaryotic DNA

• DNA in eukaryotic cells is highly packed.

• DNA appears in a highly ordered form called chromosomes during metaphase, whereas shows a relatively loose form of chromatin in other phases.

• The basic unit of chromatin is nucleosome.

• Nucleosomes are composed of DNA and histone proteins.

Nucleosome

• DNA: ~ 200 bps

• Histone: basic proteins with many Lys and Arg residues– H2A (x2), – H2B (x2), – H3 (x2), – H4 (x2)

Beads on a string

• 146 bp of negatively supercoiled DNA winds 1 ¾ turns around a histone octomer.

• H1 histone binds to the DNA spacer.

The total length of 46 human chromosomes is about 1.7 m, and becomes 200 nm long after 5 times condensation.

§ 2.4 Functions of DNA

DNA is fundamental to individual life in terms of

• They are the material basis of life inheritance, providing the template for RNA synthesis.

• They are the information basis for biological actions, carrying the genetic information.

• DNA is able to replicate itself in a high fidelity to ensure the genetic information transfer from one generation to the next.

• DNA can be used as a template to synthesize RNA (transcription), and RNA is further used as the template to synthesize proteins (translation).

• DNA posses the inherent and the mutant properties to create the diversity and the uniformity of the biological world.

• A gene is defined as a DNA segment that encodes the genetic information required to produce functional biological products.

• A gene includes coding regions as well as non-coding regions.

• Genome is a complete set of genes of a given species.

Gene and genome

Section 3

Structures and Functions of RNA

Classification

• mRNA (messenger RNA): template for protein synthesis

• tRNA (transfer RNA): AA carrier

• rRNA (ribosomal RNA): a component of ribosome for protein synthesis

• hnRNA (heterogeneous nuclear RNA): precursor of mRNA

• snRNA (small nuclei RNA): small RNAs for processing and transporting hnRNA

Classes of eukaryotic RNAs

Unique features

• RNA is single stranded, in general.

• RNA has self-complementary intrachain base paring.

• The double helical regions of RNA are of the A-form.

• RNA is susceptible to hydrolysis.

§ 3.1 Messenger RNA

• mRNAs constitute 5% of total RNAs.

• mRNAs vary significantly in life spans.

• hnRNA is the precursor of mRNA.

mRNA is the template for protein synthesis, that is, to translate each genetic codon on mRNA into each AA in proteins. Each genetic codon is a set of three continuous nucleotides on mRNA.

AUG AAA.....AAA

5' non-coding region 3' non-coding region

coding region

5'-cap 3'-poly A tail

UAA

mRNA structure

• hnRNA contains introns and exons.

• Exons are the sequences encoding proteins, and introns are non-coding portions.

• Splicing process of hnRNA removes introns and makes mRNA become matured.

• The matured mRNA has special structure features, including 5’-cap and 3’-poly A tail.

mRNA maturation

5’-cap

O

N

NN

N

NH2

O

OCH3O

HHH

CH2

H

OP

O-

O

O

HN

N

N

O

H2N N O

OH

H H

H

CH2

HOH

O PO

O-

CH3

P

O-

O5'

2'3'

5'

mRNA chain

5’-cap addition

ppp5'NpNp

pp5'NpNp

GTP

PPi

G5'ppp5'NpNp

methylating at G7

methylating at C2' of the first andsecond nucleotides after G

forming 5'-5' triphosphategroup

removing phosphate group

m7GpppNpNp

m7Gpppm2'Npm2'Np

5’-cap addition

• Methylation can occur at different sites on G or A.

• 5’-cap can be bound with CBP, benefiting transporting from nucleus to cytoplasm.

• 5’-cap can be recognized by translation initiation factor.

• It protects the 5’-end from exonucleases.

Poly A tail

• 20-200 adenine nucleotides at 3’ end

• a un-translated sequence.

• Related with mRNA degradation that begins with poly A tail shortening.

• Associate with poly A tail binding proteins for protection

Poly A tailing

5'

（Y=pyrimidine）

AAUAAA (~20nt) YA UUGUGUGUUG 3'

5' AAUAAA (~20nt) Y

5' AAUAAA (~20nt) YAAAAAAAAA AAAAAA

signal sequencefor poly A tail GU-rich region

~250nt

5' AAUAAA (~20nt) YAAAAAAAAA

poly A binding protein

AAAAAA

cleavage site

3'

3'

ATP

PPi

hnRNA

mRNA

hnRNA splicing

intron exon

AUG AAA.....AAA

5' non-coding region 3' non-coding region

coding region

5'-cap 3'-poly A tail

UAA

Matured mRNA of eukaryote

§ 3.2 Transfer RNA

• tRNA is about 15% of total RNA.

• tRNA is 65-100 nucleotides long.

• There are at least 20 types of tRNA in one cell.

tRNA serves as an amino acid carrier to transport AA for protein synthesis.

• The overall structure is a cloveleaf, reversed L-shape structure.

• There are three loops (DHU loop, anticodon loop, TψC loop), and four stems.

• The 3-D structure is stabilized by hydrogen bonds of local intrachain base pairs on these stems.

Structure of tRNA

Reversed L-shape structure

• A tRNA molecule has an amino acid attachment site and a template-recognition site, bridging DNA and protein.

• The template-recognition site is a sequence of three bases called the anticodon complementary to the mRNA codon.

Two key sites of tRNA

Codon and anticodon

The anticodon on tRNA pairs with the codon on mRNA.

Amino acid attachment

• The OH group at the 3' end of tRNA links covalently to an amino acid.

• Only the attached AA becomes activated and capable of being transported.

Rare Bases

tRNA contains a high portion of unusual bases.

NH

N

H2C

H2C

O

O

R

Dihydrouridine（DHU）

NHHN

O

O

R

pseudouridine（）

NH

NN

N

O

NH2

R

CH3

7-Methylguanosine（mG）

1

35

5

3 1

3

5 17

• rRNA is the most abundant RNA in cells (>80%).

• rRNA assembles with numerous ribosomal proteins to form ribosomes.

§ 3.3 Ribosomal RNA

rRNA provides a proper place for protein synthesis.

• Ribosomes associate with mRNA to form a place for protein synthesis.

• Ribosomes of eukaryotes and prokaryotes are similar in shapes and functions.

Ribosomes

Components of ribosomes

Prokaryote Eukaryote

(E.coli) (Liver of mouse)

Smaller subunit 30s 40s

rRNA 16s 1542 nucleotides 18s 1874 nucleotides

proteins 21 40% of total weight 33 50% of total weight

Larger subunit 50s 60s

rRNA 23s 2940 nucleotides 28s 4718 nucleotides

5s 120 nucleotides 5.85s 160nucleotides

5s 120nucleotides

proteins 31 30% of total weight 49 35% of total weight

Ribosome of E. coli

70S ribosome

50S large subunit

23S rRNA 5S rRNA

31 proteins

16S rRNA

21 proteins30S small subunit

Secondary structure of 18S rRNA

The secondary structure of rRNA has many loops and stems, which can bind ribosomal proteins to form an assembly for protein synthesis.

m7GpppG AAA...AAA

核糖体大亚基

核糖体小亚基

E位

P位

A位

mRNA

氨基酸

核糖体移动方向

进位退位

N末端

肽链

Ribosomal complex

核糖体

合成中的多肽

5'末端

3'末端

mRNA

Polysomes

EM of polysomes

Section 4

Physical and Chemical Properties of Nucleic Acids

General properties

• Acidity– Negative backbone

• Viscosity– Concentration and aggregation effects

• Optical absorption– UV absorption due to aromatic groups

• Thermal stability– Disassociation of dsDNA (double-stranded DN

A) into two ssDNAs (single-stranded DNA)

§ 4.1 UV Absorption

Quantify DNAs or RNAs

OD260=1.0 equals to

50μg/ml dsDNA

40μg/ml ssDNA (or RNA）20μg/ml oligonucleotide

Determine the purity of nucleic acid samples

pure DNA: OD260/OD280 = 1.8

pure RNA: OD260/OD280 = 2.0

Application of OD260

Transition of dsDNA to ssDNA

The absorbance at 260nm of a DNA solution increases when a dsDNA is melted into two single strands. The change is called hyperchromicity.

Melting curve of dsDNA

DNA melting

• Melting curve: a graphic presentation of the absorbance of dsDNA at 260nm versus the temperature.

• Melting temperature (Tm): the temperature at which the UV adsorption reaches the half of the maximum value, also means that about 50% of the dsDNA is disassociated into the single-stranded DNA.

Melting curve shift

Tm of dsDNA depends on its average G+C content. The higher the G+C content, the higher the Tm.

§ 4.2 Thermal stability

• Dissociation of dsDNA into two ssDNAs is referred to as denaturation.

• Denaturation can be partially and completely.

• The nature of the denaturation is the breakage of H-bonds.

• Denaturation is a common and important process in nature.

Cooperative unwinding of DNA strands

Extremes in pH orhigh temperature

Denaturation of DNA

EM image of denatured DNA

Renaturation of DNA

Two separated complementary DNA strands can rejoin together to form a double helical form spontaneously when the temperature or pH returns to the biological range. This process is called renaturation or annealing.

§ 4.3 Hybridization

• The ability of DNA to melt and anneal reversibly is extremely important.

• An association between two different polynucleotide chains whose base sequences are complementary is referred to as hybridization.

• The stability of the hybridized strand depends on the complementary degree.

Two dsDNA molecules from different species are completely denutured by heating. When mixed and slowly cooled, complementary DNA strands of each species will associate and anneal to form normal duplexes.

• Two ssDNAs, two ssRNAs, as well as one ssDNA and one ssRNA can also be hybridized.

• Ionic strength, degree of complementary, temperature, as well as base composition, fragment length of nucleic acids will affect the hybridization.

• It is a common phenomenon in biology, and has been used as a convenient techniques in medicine and biology.

• complementary hybridization

probe: …. TAGCTGAG …target: …. ATCGACTC …

probe: …. TAGCTGAG …non-target: …. ATCAGCTC …

• mismatched hybridization

Target DNA detection

Applications

• Gene structure and expression

• Microarray or gene chip

• mRNA separation

• Gene diagnosis and therapy

• PCR technique

Section 5

Nuclease

Nucleases are enzymes that are able to hydrolyze phosphoester bonds and cleave DNA or RNA into fragments.

Definition and classification

• Deoxyribonuclease (DNase) - specially cleave DNA

Ribonuclease (RNase) - specially cleave RNA

ExonucleasesThey can cleave terminal nucleotides either from 5’-end or from 3’-end, such as enzymes used in the DNA replication.

Endonucleases They can cleave internally at either 3’ or 5’ side of a phosphate group, such as the restriction endonucleases used to construct the recombinant DNA.

Classification

5’

5’3’

3’

Endonuclease

Endonuclease

Exonuclease

Exonuclease

Applications

• Participate in DNA synthesis and repair, as well as RNA post-translational modification

• Digest nucleic acids of food for better absorption

• Degrade the invaded nucleic acids

• Construct the recombinant DNA