Nucleic Acids
Classification<br>
DNA
Double-strand: stability<br>
Why 2'-deoxyribose<br>
RNA can form phosphodiester bonds within one molecule (with C2 and C3)<br>
Why T instead of U?<br>
RNA<br>
Single-strand: Different functions<br>
Noncoding-RNA<br>
rRNA
tRNA
snRNA: mRNA splicing<br>
snoRNA: rRNA processing<br>
siRNA, gRNA, Xist, Virus RNA<br>
Structure
Phosphodiester bonds<br>
DNA
bp sequence<br>
Palindrome
Mirror repeat<br>
Hairpin
Cruciform
Phosphate: Hydrophilic<br>
Base pair: Hydrophobic<br>
Double helix<br>
Different forms<br>
A-DNA
B-DNA<br>
Z-DNA<br>
Groove<br>
Minor groove: A&T<br>
Major groove: C&G<br>
Unusual DNA structure<br>
Triple helix<br>
H DNA<br>
Hoogsteen pairs<br>
Watson-crick pairs<br>
Four DNA strands<br>
Guanosine tetraplex<br>
Tend to appear at sites where important events in DNA metabolism are initiated or regulated<br>
RNA
SS
bulge
internal loop<br>
hairpin
DS
hairpin double helix<br>
Function
UV absorption<br>
DNA 260/280=1.8<br>
RNA 260/280=2.0<br>
Double-helical DNA&RNA can be denatured<br>
Nucleic acid hybrid & Probe<br>
UV can induce the formation of pyrimidine dimers<br>
Size
Single strand: nt, nucleotides<br>
Double strand: bp, kb<br>
Oligonucleotide: <50bp<br>
Normally a DNA molecule can have 10^8 bp<br>
Nucleic Acid-Based Biotech
Probe
DNA sequencing<br>
Sanger method<br>
Use ddNTP to end fragments and then do electrophoreisis to identify the fragment's length<br>
Automating DNA sequencing<br>
Lable the ddNTPs with fluorescent molecules, separate with gel and use laser to identify each band<br>
Chemistry cycle<br>
Detect the first nucleotide by using laser to excite the labeled molecule<br>
Nucleic acid synthesis<br>
PCR
DNA cloning<br>
Genome alterations<br>
Nucleotides
Structure
Nucleoside
Composition
Base
Classification
Pyrimidine(Py)
Uracil, U<br>
Cytosine, C<br>
Thymine, T<br>
Purine(Pu)
Adenine, A<br>
Guanine, G<br>
Metabolism
Py metabolism<br>
Pu metabolism<br>
C=N Tautomerism
C8 in Pu can form double bonds with N7 or N9<br>
N7=C8: 9H-purine<br>
N9=C8: 7H-purine<br>
Proportion: 50% each<br>
A and G in DNA and RNA, the sugar links to N9<br>
Keto-enol tautomerism (G)<br>
Keto: 2-aminohypoxanthine<br>
Enol: 2-amino-6-hydroxypurine<br>
Pentose
D-ribose
both are β-furanose<br>
Phosphate
Function
Building blocks of genetic materials<br>
Energy carriers<br>
ATP
Central role of energy metabolism<br>
GTP
Drives protein synthesis<br>
CTP<br>
Drives lipid synthesis<br>
UTP<br>
Drives carbohydrate metabolism<br>
Signaling molecules<br>
cGMP<br>
Visual sense<br>
cAMP<br>
Olfactory sensation, taste sense<br>
Allosteric effectors<br>
Other Functions of Nucleotides
Adenine nucleotides are components of many enzyme cofactors<br>
Coenzyme A: β-Mercaptoethylamine+Pantothenic acid+3'P-ADP<br>
NAD+: Nicotinamide adenine dinucleotide<br>
Brief History
1928--Griffith's transformation experiment
Diplococcus pneumoniae in vivo (mice)
1944--Avery-MacLeod-McCarty experiment
D. pneumoniae tranformation in vitro
1952--Hershey&Chase experiment (T2 phages)
1953--Watson&Crick determined DNA structure
1958-- Crick discovered central dogma
1975-- Sanger developed DNA sequencing
1983-- Mullis PCR
2012-- CRISPR/Cas9
