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The structure and character of the
nucleic acid
School of Life Science
Shandong University
Ch2 &6: The structure and character
of the nucleic acid
1. Nucleic Acids convey genetic information
2. DNA structure
3. DNA topology
4. RNA structure
1. Nucleic Acids convey genetic
information
What were the hereditary
factors that transmitted the
different traits from one
generation to the next?
The molecules should be stability that
the gene demanded, yet be sufficient
complexity to convey genetic
information, be capable of permanent,
sudden change to the mutant forms
that must provide the basis of evolution.
1.1. DNA can carry genetic specificity
1.1 Experiment of Transformation of Streptococcus
pneumoniae(肺炎链球菌)
——from 1928-1944，a story written for 16 years
There are 2 forms of S. pneumoniae.
smooth: the bacteria have a polysaccharide
capsule（多糖的荚膜） that protects
them from the immune system. It also
gives the colonies a smooth appearance.
rough: the bacteria lack the capsule and are
destroyed by the immune system. They
produce rough colonies.
Streptococcus pneumoniae
Figure 2-1
Transformation of a genetic characteristics of a
bacterial cell by addition of heat-killed cells of a
genetically different strain.
Figure 2-2
Isolation of a chemically
pure transforming agent
严谨的实验设计
——DNA是主要的遗传物
质
1.2. Viral genes are
also nucleic acids
2. DNA structure
2.1. DNA is composed of two polynucleotide
chains （多聚核苷酸链）
DNA is composed two
polynucleotide chains
are twisting around
each other in the form
of a double helix
p102 Figure 6-1
The monomers in polynucleotide chains are
nucleotides.
Each nucleotide has 3 parts:
a 5 carbon sugar
a nitrogen base
a phosphate
Formation of nucleotide by removal of
water
磷酸酯键
糖苷键
dehydration
synthesis
脱水合成
p103 Figure 6-2
When you write the sequence of a
piece of DNA, you always begin
with the 5’ end.
sugar
phosphate
backbone
phosphodiester
bond
(d)
CAG
(c)
The composition and
sequence of the base
pairs affects what type of
structure the DNA forms
2. 2 Each base has its preferred tautomeric
form
Amino
imino (亚氨基)
keto
enol
p105 Figure 6-5
Each of the bases can exist in
two alternative tautomeric
states. These states are in
equilibrium.
Most of the time the base is
in the normal state. Only
rarely are the altered forms
present.
The altered forms can form
different hydrogen bonds, so
tautomerization can cause
mutations during DNA
synthesis
2.3. The two strands of the Double Helix are
held together by base pairing in an
antiparallel orientation
p104 Figure 6-3
This antiparallel orientation a
stereochemical (立体化学的)
consequence of the way that AT and G-C pair with each other.
The size of an A:T pair is the same as the
size of a G:C pair.
This means that both can fit in the space
between the sugar-phosphate backbones.
2.4. The two chains of the double helix
have complementary sequences
“Waston-Crick” pairing
Cytosine
Adenine
Guanine
Thymine
The strictness of the rules for
“Waston-Crick” pairing derives
from the complementarity both
of shape and of hydrogen
bonding properties between
adenine and thymine and
between guanine and cytosine.
P106 Figure 6-6
2.5. Hydrogen Bonding Is Important for
Base Pairing
Adenine hydrogen bonds to
thymine. It does not form
hydrogen bonds with cytosine
Thus, the adenine always
binds to thymine and never to
cytosine. The hydrogen bonds
determine which bases will
pair with each other
p107 Figure 6-7
2.6. Base can flip out from double helix
It is energetically favorable for
bases to form hydrogen bonds in
DNA
However, sometimes a single base
pair will move to stick out the side
of the double helix. This is called
base flipping (碱基外掷)
Base flipping is important in some
systems of DNA repair
p107 Figure 6-8
2.7. DNA is usually a right-handed
double helix
p107 Figure 6-9
Please read the Box6-1， p108
2.8. The double helix has
minor and major grooves
270
180
Why？
--geometry
几何学
2.9. The major groove is rich in chemical
information
The edges of each base pair are exposed in the major
and minor grooves, creating a pattern of hydrogen
bond donors and acceptors and of van der Waals
surfaces that identifies the base pair.
These patterns of hydrogen bonding and shapes allow
proteins to bind to specific DNA sequences. Amino
acids in a protein can form noncovalent bonds with
the base pairs in the major groove.
A: H-bond acceptors
D: H-bond donors
H: non-polar hydrogens
M: methyl groups
p109 Figure 6-10
2.10. The double helix exists in multiple
conformations
DNA can exist in 3
different structures:
A DNA
B DNA
Z DNA
p111 Figure 6-11
Under physiological conditions, DNA is generally in
the B form. It has 10 base pairs per turn and major
and minor grooves.
When there is less water available and binds to
some proteins, DNA is often in the A form. it has 11
base pairs per turn, so it is more compact.
Z DNA forms when the DNA sequence has
alternating purines and pyrimidines and there are
high concentrations of positive ions (such as Na+)
that form ionic bonds with the negative phosphates.
It has 12 base pairs per turn. And it has a lefthanded helix .
The between the purine and pyrimidine base
pairs of a right-hand helix.
normal
p111 Figure 6-12
propeller twist
2.11. DNA sometimes form a left-handed
helix
反式
There are two ways the
base connects to the
deoxyribose. The Nglycosylic bond can be
in the syn or the anti
conformation.
p113 Figure 6-13
顺式
2.12.DNA strands can separate and reassociate
（denaturation and Renaturation）
Native: the normal structure of a nucleic acid in nature.
Denaturation (Melting，熔解): A process of the
hydrogen bonds in DNA were broken which cause the two
strands separate.
----heat, high pH, etc
Renaturation (Annealing，退火) : A process of the
single strands meet their complementary strands and reform regular double helices.
Hybridization: The capacity of single DNA strands to reform artificial hybrid DNA molecules from two different
sources
----complementary sequence
techniques！
The absorbance at 260nm for diferent nucleotides
When the Double stranded DNA
has an absorbance (A260) of 1.0,
the same concentrate:
Single stranded DNA has an
absorbance (A260) of 1.37.
Free nucleotides have an
absorbance (A260) of 1.60.
RNA have an absorbance (A260)
higher than DNA
Purity：A260/A280:
dsDNA--1.8； pure RNA--2.0；protein--0.5
共轭双键
hyperchromicity—增色效应
When the temperature of a
solution of DNA is raised above
its melting temperature (usually
more than 80 oC), the doublestranded DNA unwinds to form
single-stranded DNA. The bases
become unstacked and can thus
absorb more light. The
absorbance at 260 nm markedly
increases, the phenomenon is
known as hyperchromic.
One way to study the denaturation of DNA is
to measure its absorbance of UV light.
This reflects the
unwinding of the DNA
double helix, since the
stacked base pairs
absorb less light
When the temperature
is lowered, the
absorbance decreases,
reflecting that the DNA
is again stacking.
变性过程中DNA构型的变化规律
RNA: the absorbance increases gradually and irregularly
DNA: the absorbance increases cooperatively.
Plotting A260 versus temperature on a graph
gives you a melting curve.－溶解曲线
Tm is 85oC
The melting
temperature (Tm)
is defined as the
point where half
of the DNA is
denatured.
The melting temperature is a characteristic of each
DNA——Tm值是DNA的特征常数，与下面的因素
有关。
1) Tm depends on G·C percentage. the higher the G·C
percentage, the greater the Tm. (more energy is
required to break the extra hydrogen bonds).
2) Tm depends on DNA length. the longer the DNA, the
greater the Tm
3) Effect of [Salt] on Tm，the higher the salt
concentration of the solution, the greater the Tm
Increasing G-C content
E.coli 52%
Pneumococcus
38% G+C
S. marcescens 58%
M.phlei 66%
Temperrature (℃)
For oligos 4-18 nucleotides
Tm = (A+T) 2 ℃ + (G+C) 4 ℃
73%
40%
51%
low
salt
high
salt
p107 Figure 6-7
Why？
dsDNA和ssDNA表现出不同的变性曲线
Renaturation
When DNA is heated it denatures and the two
strands separate.
Then when the DNA is slowly cooled the
complementary strands renature.
复性条件：
For renaturation to occur the DNA must be at
the right temperature ①— one that allows
some base pairing to occur but that is high
enough to prevent single stranded DNA from
binding to itself. (破坏链内氢键的形成)
The optimal temperature is based on the G-C
content② of the DNA and is about 5o C below
the melting temperature (Tm) ——8-18nt
Renaturation also requires the correct salt
concentration③. The negatively charged
phosphates in the DNA backbone repel each
other. Na+ or Mg++ ions bind to the phosphates
and neutralize the charges.
0.15-.5M NaCl works well
Renaturation occurs best at high concentrations
of DNA ④ .
Renaturation requires time⑤for the
complementary strand to pair. Longer time
allows more annealing to occur up to a point.
复性机制：
At the molecular level
renaturation occurs in 2 steps.
First there is an initial slow step of
base pair binding often called
nucleation(成核作用). If the DNA
is complementary, the second step
which is often called zippering is
fast.
复性过程是一个随机混合的过程
In renaturation a DNA strand will hydrogen bond to a
complementary DNA strand in solution. This will likely
not be the original DNA strand that it was bound to
before it was denatured. 大部分复性分子都不是原
配的。
 Similar to measuring
denaturation, renaturation
can also be studied by
measuring A260. As the
strands of DNA renature, the
absorbance will decrease.－－
减色效应
复
性
分
数
C/C0
复性速度常数
起始浓度X时间,C0t
复性分数 C/C0 是C0t的函数，
这函数曲线称为C0t曲线。
——C指单链DNA的浓度
① DNA复性过程
遵循二级反应动
力学
DNA序列的复杂性影响k值
DNA序列的复杂性（complexity）X: 最长的没有重复
序列的核酸对的数值
5 kb Repeats (20% total)
100 kb fragment
Repeat DNA = 5 kb
Longest non-repeat DNA = 100kb - 20 kb = 80 kb
Difference in complexity = 80/5 = 16
DNA with many repeated
sequences will renature
much faster than DNA
with no repeated
sequences.
Eukaryotic genomes
have several sequence
components
重复度
②
复性与DNA的（复杂程度）
重复序列有关，组分复性
越快复杂性越低。
Explanation of complexity
1－C/C0
C0t values are directly proportional to the
complexity of the genome.
2.13.Some DNA molecules are circles
Examples:
• The chromosome of the small monkey DNA
virus SV40.
• Most bacterial chromosomes.
• Plasmids: The small autonomously replicating
genetic elements outside of chromosomes.
3. DNA topology
 At the time of the discovery of the double helix structure of DNA,
scientists thought all DNA molecules were linear and had two
free ends.
 But there were some circular DNA molecules in nature (plasmid,
bacteria chromosome, etc).
 The ends of linear DNA can freely rotate to adjust to changes in
the number of times the strands are twisted around each other,
but in circular DNA this is not possible.
 In circular DNA the number of times the DNA strands are
twisted around each other cannot change.
Closed circular DNA cannot
unwind. It is topologically
constrained.
Species of cccDNA：
 Plasmid and circular bacterial chromosomes
 Linear DNA molecules of eukaryotic
chromosomes due to their extreme length,
entrainment (缠卷) in chromatin and interaction
with other cellular components (Ch 7)
3.1. Linking number is an invariant topological
property of covalently closed, circular DNA
(cccDNA，共价闭合环状DNA)
Linking number (交叉数、环绕数) ------ The
number of times one strand have to be passed
through the other strand in order for the two
strands to be entirely separated from each other.
一条链绕另一条链环绕的次数（Lk）
Lk0 is the linking number of fully relaxed cccDNA
under physiological conditions
Linking number=0
Linking number=1
Linking number=2
3.2. Linking number(Lk) is composed of Twist
and Writhe
The linking number is the sum of the twist (扭
曲)and the writhe（翻腾）.
Twist(Tw)is the number of times one strand
completely wraps around the other strand.
Writhe(Wr) is the number of times that the long
axis of the double helical DNA crosses over itself
in 3-D space.
Lk= Tw + Wr
There are 2 kinds of writhe:
Interwound
互相盘绕的
Please read p118－120 for detail
Spiral盘旋
Relaxed Closed
circular DNA
Negatively
Superoiled
Local
disruption of
base pairing
p118 Figure 6-17
3.2. Lk0 is the Linking number of fully relaxed
cccDNA under physiological conditions
• Lk0 for such a molecule is the number of base
pairs divided by 10.5. Since in a relaxed state in
solution the two polynucleotide strands wrap
around each other such that there are 10.5 base
pairs per turn. For a cccDNA of 10,500 base pairs,
Lk=+1000.
• If there are more or less than 10.5 base pairs per
turn, the DNA is supercoiled.
3.3 DNA in cells is negatively supercoiled
Adding twists to the DNA causes it to be supercoiled or
superhelical. 增旋而形成的超螺旋为正超螺旋
Unwinding the DNA causes a negative superhelix. 解旋
而形成的超螺旋为负超螺旋
• Circular DNA molecules purified from both
bacteria and eukaryotes are usually negatively
supercoiled, having values of of about -0.06.
ơ =(Lk-Lk0)/Lk0
• The only organisms that have been found to
have positively supercoiled DNA are certain
thermophiles, microorganisms that live under
conditions of extreme high temperatures.
3.4. Topoisomerases can relax supercoiled
Topoisomerases are enzymes that can change
the linking number of DNA by making single
or double stranded nicks.
There are 2 kinds of topoisomerases:
Type I make a single stranded cut in the DNA.
Type II make a double stranded cut in the DNA.
Properties of the topoisomerase：
Type I (Topo I)-⑴每次只切开一条链，⑵每次改变
一个超螺旋，⑶反应不需要能量，
Type II (Topo II)- ⑴每次切开两条链，⑵每次改变2
个超螺旋，⑶需要能量， Topo II can catenate
and decatenate cccDNA molecules.
3.5. Topoisomerases
cleave DNA using a
covalent tyrosineDNA intermediate
P124Figure 6-24
Properties of the topoisomerase：
3.6. DNA topoisomers can be separated
by electrophoresis
Relaxed or nick DNA
p125 Figure 6-26
The speed of the DNA molecules
migrate increases as the number
of superhelical turns increases
4. RNA Structure
4.1. RNA contains ribose and
uracil and is usually singlestranded
Sequence complementarity: inter- and
intra-molecular base pairing
4.2. RNA chains fold back on themselves to
form local regions of double helix similar to
A-form DNA
Because RNA is single stranded, it
often will base pair to itself
between short segments of
complementary sequences, which
adopt one of the various stem-loop
structures
hairpin
bulge
loop
Non-Watson-Crick G:U base pairs represent
additional regular base pairing in RNA, which
enriched the capacity for self-complementarity.
A example of hydrogenbonding that allows
unusual triples base pairing
Unconventional base pairing, such as
base triples, base-backbone interactions
in RNA.
tetraloop(UUCG)---- Special interactions
水平线：
碱基堆积作用
2
3
1
U:G对
4
4.3. RNA can fold up into complex tertiary
structures
The base pair in the single stranded produce the
secondary (base pairing) and tertiary (3 dimensional
conformation) of the RNA molecule. Pseudoknots
（“假结”）are complex secondary structure
resulted from base pairing of discontiguous RNA
segments.
Pseudoknot
4.4. Some RNAs are enzymes ---- Ribozymes
Ribozymes are RNA molecules that adopt
complex tertiary structure and serve as
biological catalysts.
RNase P and self-splicing introns are
ribozymes
Please read p130－132 for detail
The hammerhead ribozyme cleaves RNA by
formation of a 2’,3’ cyclic phosphate
tertiary structures of
the hammerhead
ribozyme
Biological roles of RNA
a) RNA is the genetic material of some viruses
b) RNA functions as the intermediate (mRNA) between the
gene and the protein-synthesizing machinery.
c) RNA functions as an adaptor (tRNA) between the codons
in the mRNA and amino acids.
d) Through sequence complementarity, RNA serves as a
regulatory molecule to bind to and interfere with the
translation of certain mRNAs; or as a recognition
molecule to guide many post-transcriptional processing
steps.
e) Through the tertiary structures, some RNAs function as
enzymes to catalyze essential reactions in the cell.
Thinking-----
Did life evolve from an RNA world?