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Nucleic Acid Structure
Dr. Helen Berman
September 16, 2002
•Components
•Sugar
•Base
•Phosphate
•5’ to 3’ direction
•RNA
ribose
•DNA
deoxyribose
•Numbering
Voet, Donald and Judith G. Biochemistry.
John Wiley & Sons, 1990, p. 792.
•Names
•Numbering
•Bonding character
•Position of hydrogen
•tautomers
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 18.
Tautomeric structures
•Keto vs inol
•How do we know?
•Different hydrogen
bonding patterns
Saenger, Wolfram. Principles of Nucleic Acid Structure.
Springer-Verlag New York Inc., 1984, p. 113.
•pK of nucleotides
•Effects on bases
N1 adenine-3.5
N3 cytosine-4.2
N7 of adenine 1.0
Saenger, Wolfram. Principles of Nucleic Acid Structure.
Springer-Verlag New York Inc., 1984, p. 109.
Geometry of
Watson Crick
base pairs
A:T and G:C
are similar
Voet, Donald and Judith G. Biochemistry.
John Wiley & Sons, 1990, p. 797.
The diversity
of hydrogen
bonding
geometries
Effects of pH
Saenger, Wolfram. Principles of Nucleic Acid Structure.
Springer-Verlag New York Inc., 1984, p. 120.
Hydrogen
bonding of WC
base pair
Definition of
Major and
Minor groove
Mechanisms of
recognition
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 90.
Base-base pair
T-A-T
C-G-C
(C must be
protonated)
Found in triple
helices
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 68.
Amino acid base pair
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 165.
Amino acid base pair
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 165.
Amino acidbase pair
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 166.
Amino acid base pair
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 166.
Base
morphology
Propeller twist
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 21.
buckle
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 21.
Base pair twist
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 22.
roll
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 22.
Backbone
conformation
Voet, Donald and Judith G. Biochemistry.
John Wiley & Sons, 1990, p. 807.
Anti vs. syn
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 27.
Change in
sugar
conformation
affects the
backbone
Voet, Donald and Judith G. Biochemistry.
John Wiley & Sons, 1990, p. 808.
Ribose ring is
never flat
Voet, Donald and Judith G. Biochemistry.
John Wiley & Sons, 1990, p. 808.
C4’-C5’-g+
Voet, Donald and Judith G. Biochemistry.
John Wiley & Sons, 1990, p. 809.
Conformation
wheel for
nucleotides
a-3 values
b-3 values
g-3 values
d-two ranges
•C3’endo
•C2’ endo
e-trans-gz-3 values
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 28.
Common
building blocks
Small changes
leading to big
differences
A DNA
B DNA
B-DNA
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 34.
A DNA
Neidle, Stephen. Nucleic Acid Structure and Recognition.
Oxford University Press, 2002, p. 36.
Ch a r ac ter ist ics of ma jo r for m s of do u b le str an de d DNA
Ove ra ll
Gr oo ve s
Polymer
characteristics
Sym m e try
Ha n d e d n e ss
Con fo r ma tio n
Stac kin g
A
sm o o th
sh o rt, fa t,
b a se s tilted
2
m ajo r dee p
m in o r sh all ow
B
sm o o th
lo ng , thin,
b a se s p e rpe nd icu la r
2
m ajo r w ide , dee p
m in o r n ar row , dee p
2 diad s
in p la n e
b e tw ee n p la n e
r ig ht
C3 ' e n d o
lo w a nt i
sin gle nu cle ot ide
r e p ea t
Ba se -B a se in ea ch stra nd
2 diad s
in p la n e
b e tw ee n p la n e
r ig ht
C2 ' e n d o
h ig h a nt i
sin gle nu cle ot ide
r e p ea t
Ba se -B a se in ea ch stra nd
Z
zig -z a g
1
"mi nor gro o ve" side lin ed
by ph o sph a te s
"ma jo r g ro o ve " a to ms
face co nv e x side
1 diad
b e tw ee n p la n e
lef t
C3 ', C2 '
sy n a nt i
2 nu cle o tide
r e p ea t
int e rstr a n d b a se -b a se
int e rstr a n d b a se -su ga r