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Learning Objectives:
Nu cle oside s& Nu cle otide s
Reading
Handout of Chapter 2: Bases, Nucleosides,and Nucleotides
Chapters 2, 3,4 from Neidle
Be able t o draw all 5 nucleotides with correct numbering (G, A, T, U, C)
Know the difference between nucleoside and nucleotide
Know ribose and deoxyribose numbering
Recognize methylation as a major modification
Know different sugar puckers
A-form usually 3'-endo, 2'-exo
B-form usually 3'-exo, 2'-endo
How does sugar pucker change distance between phosphates?
Know difference between syn and anti - when do you see syn?
Know all the hydrogen bond donors and accept ors in the Watson-Crick base pairs
How do donors and accept ors change when the enol form of the bases are found vs. the
ket o form?
What base groups are found in the major and minor grooves?
Be able t o draw the Watson-Crick base pairs
Understand Hoogsten pairing and what face of the bases are used for this type of bonding
Define pKa and if I give you the pKas for a nucleoside you can raw the protonation states
Understand the importance of stacking to duplex stability
A-DNA vs. B-DNA vs. Z-DNA
Know bp/turn, if each is right- or left-handed, sugar pucker, syn or anti
configuration of glycosyl bond, groove widths and depths
Know the base movements - propeller, twist , roll, tilt
Recognize a palindrome sequence - be able to postulate a cruciform structure
Recognize a mirror repeat - be able t o postulate a hairpin structure
Know how G quartets are stabilized and that they involve 4 G residues
Be able t o recognize a sequence's ability to form H-DNA or a third strand that can bind
by Hoogsteen pairing to form a triplex
Nucleosides & Nucleotides
Nucleotides:
1. Nitrogenous base
2. Pentose
3. Phosphate
Nucleosides:
1. Nitrogenous base
2. Pentose
Nucleotides & Nucleic Acids
Nitrogenous bases are either pyrimidines or purines
Nucleotides & Nucleic Acids
Nitrogenous bases are either pyrimidines or purines
Properties of Nucleotides/Bases
Compound
Uracil
Cytosine
Thymine
Adenine
Guanine
Deoxycytidine 5’-phosphate
Thymidine 5’-phosphate
Deoxyadenosine 5’-phosphate
Deoxyguanosine 5’-phosphate
Mol. Weight
112.09
111.10
126.11
135.11
151.15
321.24
322.21
331.22
347.23
Melt Pt (˚C)
338
320-5
326
360-5
365
187
142
360 (salt)
Naturally Occurring Modified Bases in tRNA
Adenine
1-methyladenosine
N6-methyladenosine
Inosine (deaminated adenosine)
1-methylinosine
Guanine
1-methylguanosine
N2-methylguanosine
N2, N2 -dimethylguanosine
7-methylguanosine
Cytosine
3-methylcytidine
5-methylcytidine
2-thiocytidine
N4-acetylcytidine
Uracil
Ribosylthymine (5-methyluridine)
5-methoxyuridine
5,6-dihydrouridine
4-thiouridine
5-methyl-2-thiouridine
Pseudouridine (uracil attached to ribose at C5)
DNA Methylation
Natural DNA contains:
5-methylcytosine
N6-methyladenine
N4-methylcytosine
5-hydroxymethyluracil
Sequence-specific methylation after DNA synthesis
0% to 100% methylation
5-methylcytosine (favors Z-DNA in CG sequences)
Bacteria: methylation distinguishes self from foreign DNA (methylation
after synthesis)
base-base mismatch repair (nonmethylated strand scanned)
Higher Eukaryotes: 5-methylcytosine is only methylated form found
predominately at CpG
role in gene expression (undermethylated  increase in transcription)
Nucleotides & Nucleic Acids
Ribose sugars can be either 2’-deoxy (DNA)
Nucleotides & Nucleic Acids
Ribose sugars ... or have a 2’-OH (RNA)
TAUTOMERS
H
H
H
H
H
HOOGSTEEN
Nucleotides & Nucleic Acids
Nucleotides & Nucleic Acids
Hydrogen bonding patterns in RNA and DNA
Involve ring N, carbonyls, amino groups
Permits complementary association of 2 strands of nucleic acid
(structure of DNA by Watson & Crick)
Uridine (RNA)
Nucleotides & Nucleic Acids
Chargaff’s rules 1940s
1. Base composition of DNA varies from one species to another
2. DNA from different tissues of same species have same base
composition
3. Base composition of DNA in given species does not change with
age, nutritional state, environment
4. In all cellular DNAs, regardless of species, the number of
adenosine residues is equal to the number of thymidine residues
(A=T), and the number of guanosines = cytidines (G=C)
A + G (purines) = C + T (pyrimidines)
pKa values in nucleosides/tides
Base
(site of protonation)
Adenine (N1)
Cytosine (N3)
Guanine (N7)
Guanine (N1)
Thymine (N3)
Uracil (N3)
Nucleoside
3.52
4.17
3.3
9.42
9.93
9.38
3’-Nucleotide
5’-Nucleotide
3.70
4.43
(3.5)
9.84
9.96
3.88
4.56
(3.6)
10.00
10.47
10.06
Data relate to 20 ˚C and zero salt concentration
They correspond to loss of a proton for pKa > 9 and capture of a proton for pKa < 5
Nucleotides & Nucleic Acids
Properties of RNA and DNA
Bases hydrophobic at neutral pH, hydrophobic stacking interactions
Stabilize 3D structure of nucleic acids
Nucleotides & Nucleic Acids
Properties of RNA and DNA
Nitrogenous rings are mostly planar
Resonance in cyclic rings allow nucleotide bases to absorb UV light