1. Chapter 27 Nucleotides and Nucleic acid
Contents
General structure of Nucleosides,
Nucleotides, DNA, and RNA
Hydrogen bonding vs Melting
Replication, Transcription, and Translation

2. Nucleoside
Ribose or Deoxyribose + Base

3. Nitrogen bases
Pyrimidines (C,T)
Purines (A,G)

4. Nucleotide - Adenine  Adenosin; Gauanine  Guanosin
Nucleoside + Phosphate
- Adenine  Adenosin; Gauanine  Guanosin
- Cytosine  Cytidine; Thymine  Thymidine; Uracil  Uridine

5. Other Nucleotide
ATP : Energy bank
NAD+ : CoE for Ox-Red

6. Structure of DNA and RNA
5’-End
- Polynucleotides:
DNA (Deoxyribo-nucleic acid)
RNA (Ribonucleic acid)
 Simplified structure
3’-End
Diester of phosphoric acid : pKa 2.2
- Sensitivity to hydrolysis: DNA<<<RNA (NGP)

7. Complementary Base Pairing
Charged Polymer : base pairing at high salt conc.
Number of A(C) is equal to T(G) : Chargaff’s rule
 Base pairing by HB
Melting Temperature depends on AT, CG contents
- A -- T 2 HB (10 Kcal/mol)
- C -- G 3 HB (17 Kcal/mol)
Chain growing by 5’-triphophate monomer
(similar to carboxyl anhydride)

8. )
Hydrogen bonding ~ Melting Temperature : AT, CG contents
- A -- T 2 HB (10 Kcal/mol)
- C -- G 3 HB (17 Kcal/mol

9. Double helix Distance between sugar backbone is always same
Inside ; less polar
Outside; polar, easily solvated by water
Stacked base  DNA stability : Intercalating agent

10. 30 억 base x 3.4 A = 1 m Double Helix Information repairing is easy
Replication method
40 억 조각 x 16-mer DNA needed for sequencing whole genome

11. Reparing
Replication : polymerase (replicase)

12. Replication

13. - mRNA copies genetic information (DNA  Ribosome)
Transcription:
- mRNA copies genetic information (DNA  Ribosome)
codon: 3 base code  4 3 (64) possiblities
Translation:
- mRNA acts as a template for protein synthesis
tRNA w/ anticodon carries AAs
to the protein factory (Ribosomes)

14. NC peptide bond formation (Nature) vs
CN chemical synthesis (Organic Synthesis)

15. RNA occurs as single stranded molecule : structuring by itself
mRNA: RAM memory
tRNA
rRNA
Ribozymes : RNA catalyst

16. (Systematic Evolution of Ligands by EXponential Enrichment)
SELEX
(Systematic Evolution of Ligands by EXponential Enrichment)
Library of Random Oligonuceotides
Fixed
Variable(n)
n=40 s=1024
ssNA
Random ssDNA or RNA
Negative selection
Positive selection
Removal of non-
binding ssNA
Isolation of ssNA-
targets complex
(RT) PCR
(T7 transcription)
Clone
Sequence
aptamer
Apmlification
Validation

17. Double straned DNA library Single straned DNA Library (SM)
SELEX procedure
Double straned DNA library
Single straned DNA Library (SM)
In-vitro transcription
Error prone PCR
RNA library
Binging to target protein
Binging to target protein
RNA
N cycle
In-vitro transcription
RNA elution from target
RT-PCR
Selected RNA
cDNA

18. RNA Aptamer to HCV NS5B 1# 2# 3# Sequence (Occurrence)
#1 ( 6 ) 5'- TCGATAAAAGGGGCCTGGGATTGAATCGCATGGCCGTGTC -3'
#2 ( 2 ) 5'- ACATTGTGAGGGGCTCAGGTGGATCGCATGGCCGTGTC -3'
#3 ( 3 ) 5'- TAAGAGGCTGCAGACCCTTGTGTTATACTTGAGGATTTCG -3'
#4 ( 2 ) 5'- TCGGCTAGGGGGTCTGGGCGAATCGCATTGCCGTGCATC -3'
1# # #

19. Tautomers of Guanine and Thymine
Anlalogues of Nucleoside :
AZT, DDC used as AIDS drug  1174
 drug target (retrovirus) : reverse transcriptase

20. Sequencing DNA vs Proteins
Need fragments  used for mapping
Restriction Enzymes vs Protease
DNA can be multiplied (vs Proteins)
Protein sequencing by DNA sequencing
Two methods :
Cleavage method (Gilbert, 1980 Nobel prize)
Chain Terminator method (Sanger, 1980 Nobel prize)
Restriction Endonucleases  gives primer sequence 
synthesizing DNAs to a terminating sequence 
separate by Gel-Electrophoresis and analyzed

21. Sequencing DNA

23. Radio labeled vs Fluorescence labeled

24. Laboratory synthesis of DNA
Activation by tetrazole
Oxidation by I2
Deprotections :
Pi & DMT

25. Exercise problems
18, 22, 23, 24
Good Luck! & Have Fun!