DNA

CONFORMATION
ANDRIANI
Department Biochemistry and Molecular
Biology
PREFACE…..

Linus Pauling
 In the early 1950s, he
proposed that regions of
protein can fold into a
secondary structure
 a-helix

 To elucidate this structure,

he built ball-and-stick
models
 Refer to Figure 9.12b
Rosalind Franklin
 She worked in the
same laboratory as
Maurice Wilkins

 The diffraction pattern

she obtained suggested
several structural
features of DNA
 Helical The diffraction pattern is interpreted
(using mathematical theory)
 More than one strand This can ultimately provide
 10 base pairs per information concerning the
structure of the molecule
complete turn
Erwin Chargaff’s Experiment
Interpreting the Data

 The compelling observation was that

 Percent of adenine = percent of thymine
 Percent of cytosine = percent of guanine

 This observation became known as Chargaff’s rule

 It was crucial evidence that Watson and Crick used to
elucidate the structure of DNA
Watson and Crick
 Stick and ball experimental for DNA conformation

 A critical question was how the two (or more strands)

would interact
 An early hypothesis proposed that the strands
interact through phosphate-Mg++ crosslinks
Watson and Crick
 They then built models with the
 Sugar-phosphate backbone on the outside
 Bases projecting toward each other

 They first considered a structure with identical

bases in the opposite strand
 ie., A to A, T to T, C to C, and G to G

 They then realized that the hydrogen bonding of A

and T resembled that between C and G
• Watson dan Crick (1953)
Model struktur DNA : double helix
BASE PAIRING
 ikatan hidrogen bukan
ikatan kovalen

 Stabilitas DNA ditentukan

oleh pH, kadar garam, suhu,
dan kadar pasangan basa
G-C
STRUKTUR NUKLEOTIDA
Nukleosida :
gula + basa
Nukleotida :
Nukleosida +
fosfat
STRUKTUR DOUBLE HELIX MERUPAKAN POLINUKLEUTIDA ANTIPARALEL
The DNA Double Helix

the minor
groove, is 12 Å
wide
the major
groove, is 22 Å
wide
DUA POLINUKLEOTIDA BERIKATAN ANTIPARALEL
MEMBENTUK STRUKTUR DOUBLE HELIX DNA

T
STRUKTUR ALTERNATIF KONFORMASI DNA
Tiga jenis bentuk putaran double helix DNA
1 basa berputar 36°  10 basa = 360°

1. DNA tipe B
2. DNA tipe A
3. DNA tipe Z
• Right handed DNA
• Paling banyak
• Right handed DNA
ditemukan di dalam
• 11pb/putaran
sel
• Lebih kompak
Left handed DNA
• 10pb/putaran
• Central pore
• Zigzag appearance
dibagian bawah
 DNA TIPE A DNA TIPE B DNA TIPE Z

Bases
Bases substantially
substantially tilted relative
tilted relative to the central
to the central axis
axis

Bases relatively
perpendicular to the
central axis

Sugar-phosphate
backbone follows a
zigzag pattern

Its formation is
favored by
GG-rich
sequences, at high
salt concentrations
Cytosine
methylation, at low
salt concentrations
In the late 1950s, Alexander Rich et al
discovered triplex DNA

 Triplex DNA formation

T binds to an is sequence specific
AT pair in
biological DNA
 The pairing rules are

 Triplex DNA has been

implicated in several
cellular processes
C binds to a
CG pair in
 Replication,
biological DNA transcription,
recombination
 Cellular proteins that
specifically recognize
triplex DNA have been
recently discovered
 VARIASI STRUKTUR DNA
Tipe Pasangan Rotasi/Pasa Diameter Kondisi Terjadinya
ngan Basa
Untaian Basa/Putaran Untaian Kelembapan Dalam
relatif Larutan

A 11 +32,7 23 A’ 75 % K+, Na+,

B 10 +36,0 19 A’ 92 % Kadar
Garam
Rendah

C 9,33 +38,6 19 A’ 66 % -
Z 12 -30,0 18 A’ - Kadar
Garam
Tinggi
Ribonucleic acid (RNA)
STRUKTUR RNA RNA single strand  RNA double strand
Complementary regions
Held together by
hydrogen bonds

Noncomplementary regions
Also called
Have bases projecting away hair-pin
from double stranded regions
 STRUKTUR RNA
PSEUDOKNOT

Pseudoknot dibentuk oleh

pasangan basa antara
sekuens yang saling
komplementer
Mengapa DNA Lebih Stabil dibanding RNA?
Ada tidaknya ikatan hidrogen antara untai yang
berlawanan

Ada tidaknya pengaruh tumpukan pasangan basa satu

sama lain yang berinteraksi

Ikatan phospohodiester sebagai backbone structure

 orientasi single strand
A-Form DNA vs B-Form DNA
Tipe B
1. Pada kadar garam rendah  tipe A
2. Pada kadar garam tinggi  tipe Z

Pembentukan double strand dari single strand:

1. H RNA = 40 kJ/mol per bp; S RNA = 105 J/mol per bp
2. H DNA = 35 kJ/mol per bp; S DNA = 90 J/mol per bp

Kestabilan konformasi DNA tipe A dan B bukan karena gula

ribosanya, melainkan krn konformasinya
 Many factors
contribute to the
tertiary structure of
RNA Molecule contains
 For example single- and double-
stranded regions
 Base-pairing and These spontaneously
base stacking within interact to produce
the RNA itself this 3-D structure

 Interactions with
ions, small
molecules and large
proteins

 depicts the tertiary structure of tRNAphe

 The transfer RNA that carries phenylalanine
THANK YOU…
Structural features of the three major forms of DNA (Wikipedia)

Geometry attribute A-DNA B-DNA Z-DNA

Helix sense right-handed right-handed left-handed

Repeating unit 1 bp 1 bp 2 bp
Rotation/bp 32.7° 35.9° 60°/2
bp/turn 11 10.5 12
Inclination of bp to +19° −1.2° −9°
axis
Rise/bp along axis 2.3 Å (0.23 nm) 3.32 Å (0.332 nm) 3.8 Å (0.38 nm)
Pitch/turn of helix 28.2 Å (2.82 nm) 33.2 Å (3.32 nm) 45.6 Å (4.56 nm)
Mean propeller +18° +16° 0°
twist
C: anti,
Glycosyl angle anti anti G: syn
C: C2'-endo,
Sugar pucker C3'-endo C2'-endo G: C2'-exo
Diameter 23 Å (2.3 nm) 20 Å (2.0 nm) 18 Å (1.8 nm)
DNA TIPE B
 memiliki major groove dan
minor groove

 struktur yang dikemukakan

oleh Watson dan Crick

 Ditemukan lebih banyak

pada kondisi fisiologis
DNA TIPE A

 Major groove lebih besar

 Biasanya terdapat pada tRNA

dan hibrid DNA-RNA

DNA TIPE Z
 kerangka gula-posfat
berbentuk zigzag

 rangkaian basa G-C dan A-C

yang berulang

 ditemukan pada kondisi

fisiologis jika termetilasi pada
basa Cytosin

Lebih bermuatan negatif

Ribonucleic acid (RNA)

Rantai belakang glukosa= Ribosa

Basa Urasil menggantikan Timin

Fungsi RNA:
1. Materi geentik (virus)
2. Bertindak sebagai molekul
intermediate (mRNA), adaptor
(tRNA), struktur (rRNA) and katalis
(ribozime)
The Data