Lecture 6 - Nucleic Acid: DNA:II | Molecular Biology (DNA) by ILLL, DU - Biotechnology Engineering (BT) PDF Download

 Page 1


 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
0 
 
 
 
 
 
 
 
 
 
 
 
MOLECULAR BIOLOGY 
LESSON NAME: Nucleic acids:  DNA II 
LESSON DEVELOPER: Dr. Mansi Verma 
COLLEGE/DEPT: Sri Venkateswara College 
University of Delhi 
 
 
 
 
 
 
 
 
 
 
 
Page 2


 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
0 
 
 
 
 
 
 
 
 
 
 
 
MOLECULAR BIOLOGY 
LESSON NAME: Nucleic acids:  DNA II 
LESSON DEVELOPER: Dr. Mansi Verma 
COLLEGE/DEPT: Sri Venkateswara College 
University of Delhi 
 
 
 
 
 
 
 
 
 
 
 
 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
1 
Table of Contents 
          
? Introduction 
o Types of DNA 
o B-form 
o A-form 
o Z-form 
o C-form  
? Unusual structures of DNA 
? Forms of DNA molecule 
? Topology of DNA 
? Topology of covalently closed circular DNA (cccDNA)  
? Tautomeric forms of bases 
? Major and Minor grooves of DNA 
? TOPOISOMERASES: The molecular engineers to relax supercoiled DNA 
? Denaturation and Renaturation: DNA kinetics  
o Effect of temperature on strand separation 
o Measuring the rate of DNA kinetics 
o Parameters for renaturation of DNA 
? Summary 
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
? Web links 
? Answers 
 
 
 
 
 
 
 
 
Introduction 
Page 3


 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
0 
 
 
 
 
 
 
 
 
 
 
 
MOLECULAR BIOLOGY 
LESSON NAME: Nucleic acids:  DNA II 
LESSON DEVELOPER: Dr. Mansi Verma 
COLLEGE/DEPT: Sri Venkateswara College 
University of Delhi 
 
 
 
 
 
 
 
 
 
 
 
 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
1 
Table of Contents 
          
? Introduction 
o Types of DNA 
o B-form 
o A-form 
o Z-form 
o C-form  
? Unusual structures of DNA 
? Forms of DNA molecule 
? Topology of DNA 
? Topology of covalently closed circular DNA (cccDNA)  
? Tautomeric forms of bases 
? Major and Minor grooves of DNA 
? TOPOISOMERASES: The molecular engineers to relax supercoiled DNA 
? Denaturation and Renaturation: DNA kinetics  
o Effect of temperature on strand separation 
o Measuring the rate of DNA kinetics 
o Parameters for renaturation of DNA 
? Summary 
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
? Web links 
? Answers 
 
 
 
 
 
 
 
 
Introduction 
 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
2 
Previous chapter explained the salient features of DNA.  The features described by Watson 
and Crick were of B-type DNA. Later, various forms of DNA were discovered which will be 
discussed in this chapter.   We will learn about the different forms of DNA, effect of 
tautomeric forms of bases on base pairing, role of major and minor grooves of DNA and the 
renaturation kinetics.  
Learn about the basics of DNA by clicking the link 
https://www.youtube.com/watch?v=uXdzuz5Q-hs&x-yt-ts=1422327029&x-yt-cl=84838260  
 
Types of DNA 
The pentose sugar in a nucleotide exists in a closed five-membered ring i.e., furanose form, 
due to which the pentose ring can acquire a variety of conformations called as “puckered”. 
In case of nucleotides, four carbons of the pentose sugar exists in same plane whereas only 
one carbon (either C-2’ or C-3’) acquire endo or exo positions in the same plane with 
respect to C-5’, thus forming four puckered conformations (Fig. 1).    
 
Base
C-2’ Exo
C-2’ Endo
C-5’
C-3’
C-4’
C-1’
C-2’
C-3’ exo
Base
C-3’ Endo
C-5’
C-4’
C-1’
a)
b)
 
Fig. 1: Furanose ring in nucleotides in different puckered 
conformations. Note that four carbons (C1’, C2’/C3’,C4’ and C5’) remains  in the same plane 
for a given conformation. But only C2’ or C3’ can acquire endo (same) or exo (opposite) side with 
respect to C5’ atom. (Source: Author) 
 
 
The base of nucleotide (at N-1 for pyrimidines and at N-9 for purines) in joined to the first 
carbon (C-1) of a pentose sugar by N-glycosyl bond. The torsion in this bond leads to syn 
and anti conformations of bases (Fig. 2), and therefore is responsible for the different forms 
of DNA i.e, right handed and left handed forms.  
Page 4


 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
0 
 
 
 
 
 
 
 
 
 
 
 
MOLECULAR BIOLOGY 
LESSON NAME: Nucleic acids:  DNA II 
LESSON DEVELOPER: Dr. Mansi Verma 
COLLEGE/DEPT: Sri Venkateswara College 
University of Delhi 
 
 
 
 
 
 
 
 
 
 
 
 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
1 
Table of Contents 
          
? Introduction 
o Types of DNA 
o B-form 
o A-form 
o Z-form 
o C-form  
? Unusual structures of DNA 
? Forms of DNA molecule 
? Topology of DNA 
? Topology of covalently closed circular DNA (cccDNA)  
? Tautomeric forms of bases 
? Major and Minor grooves of DNA 
? TOPOISOMERASES: The molecular engineers to relax supercoiled DNA 
? Denaturation and Renaturation: DNA kinetics  
o Effect of temperature on strand separation 
o Measuring the rate of DNA kinetics 
o Parameters for renaturation of DNA 
? Summary 
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
? Web links 
? Answers 
 
 
 
 
 
 
 
 
Introduction 
 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
2 
Previous chapter explained the salient features of DNA.  The features described by Watson 
and Crick were of B-type DNA. Later, various forms of DNA were discovered which will be 
discussed in this chapter.   We will learn about the different forms of DNA, effect of 
tautomeric forms of bases on base pairing, role of major and minor grooves of DNA and the 
renaturation kinetics.  
Learn about the basics of DNA by clicking the link 
https://www.youtube.com/watch?v=uXdzuz5Q-hs&x-yt-ts=1422327029&x-yt-cl=84838260  
 
Types of DNA 
The pentose sugar in a nucleotide exists in a closed five-membered ring i.e., furanose form, 
due to which the pentose ring can acquire a variety of conformations called as “puckered”. 
In case of nucleotides, four carbons of the pentose sugar exists in same plane whereas only 
one carbon (either C-2’ or C-3’) acquire endo or exo positions in the same plane with 
respect to C-5’, thus forming four puckered conformations (Fig. 1).    
 
Base
C-2’ Exo
C-2’ Endo
C-5’
C-3’
C-4’
C-1’
C-2’
C-3’ exo
Base
C-3’ Endo
C-5’
C-4’
C-1’
a)
b)
 
Fig. 1: Furanose ring in nucleotides in different puckered 
conformations. Note that four carbons (C1’, C2’/C3’,C4’ and C5’) remains  in the same plane 
for a given conformation. But only C2’ or C3’ can acquire endo (same) or exo (opposite) side with 
respect to C5’ atom. (Source: Author) 
 
 
The base of nucleotide (at N-1 for pyrimidines and at N-9 for purines) in joined to the first 
carbon (C-1) of a pentose sugar by N-glycosyl bond. The torsion in this bond leads to syn 
and anti conformations of bases (Fig. 2), and therefore is responsible for the different forms 
of DNA i.e, right handed and left handed forms.  
 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
3 
 
Anti
Syn
 
Fig.2: Anti and syn conformations of bases due to rotation in 
glycosidic bonds. (Source: Author) 
 
a) B-form of DNA 
B-form is the most common form of DNA and can be observed under high humidity 
conditions. Watson and Crick model was based on this form, with the helix turn at every 3.4 
nm and the distance between two adjacent base pairs is 0.34 nm. Hence, there are about 
10 pairs per turn with a right handed helix rotation. The turns generate wide major groove 
and narrow minor groove. Total diameter of helix is 23.7 Å.  
b) A-form of DNA 
In less humid conditions, like solution with higher salt concentrations or with alcohol, DNA 
conformation changes from B to A-form.  Although the helix rotation stays the same (i.e., 
right handed), but other conformational alterations are seen (Fig. 3). A-DNA is 
comparatively short and broad, with the distance between two adjacent base pairs reduced 
to 0.23 nm, resulting in 11 pairs per turn with the helix turn at every 33.6 Å. A-DNA forms 
are usually seen in during DNA-protein interactions. For example, TATA box (present 10 bp 
upstream of transcription site and is the place of attachment for TATA-binding protein 
(TBP)) acquires A-form of DNA when TBP binds to it.  (Even RNA attains A-form similar to 
A-DNA when it forms hairpin loops!).  
c) Z-form of DNA  
In both A and B-forms, glycosidic bond is always in anti- conformation, whereas in Z-DNA, 
due to repeating of purines and pyrimidines, the gycosidic bond acquires syn- conformation 
at purine residue and anti- conformation at pyrimidine residue. Syn- conformation accounts 
for base-flipping in Z-DNA. This alternative syn and anti conformations results in zig-zag 
Page 5


 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
0 
 
 
 
 
 
 
 
 
 
 
 
MOLECULAR BIOLOGY 
LESSON NAME: Nucleic acids:  DNA II 
LESSON DEVELOPER: Dr. Mansi Verma 
COLLEGE/DEPT: Sri Venkateswara College 
University of Delhi 
 
 
 
 
 
 
 
 
 
 
 
 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
1 
Table of Contents 
          
? Introduction 
o Types of DNA 
o B-form 
o A-form 
o Z-form 
o C-form  
? Unusual structures of DNA 
? Forms of DNA molecule 
? Topology of DNA 
? Topology of covalently closed circular DNA (cccDNA)  
? Tautomeric forms of bases 
? Major and Minor grooves of DNA 
? TOPOISOMERASES: The molecular engineers to relax supercoiled DNA 
? Denaturation and Renaturation: DNA kinetics  
o Effect of temperature on strand separation 
o Measuring the rate of DNA kinetics 
o Parameters for renaturation of DNA 
? Summary 
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
? Web links 
? Answers 
 
 
 
 
 
 
 
 
Introduction 
 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
2 
Previous chapter explained the salient features of DNA.  The features described by Watson 
and Crick were of B-type DNA. Later, various forms of DNA were discovered which will be 
discussed in this chapter.   We will learn about the different forms of DNA, effect of 
tautomeric forms of bases on base pairing, role of major and minor grooves of DNA and the 
renaturation kinetics.  
Learn about the basics of DNA by clicking the link 
https://www.youtube.com/watch?v=uXdzuz5Q-hs&x-yt-ts=1422327029&x-yt-cl=84838260  
 
Types of DNA 
The pentose sugar in a nucleotide exists in a closed five-membered ring i.e., furanose form, 
due to which the pentose ring can acquire a variety of conformations called as “puckered”. 
In case of nucleotides, four carbons of the pentose sugar exists in same plane whereas only 
one carbon (either C-2’ or C-3’) acquire endo or exo positions in the same plane with 
respect to C-5’, thus forming four puckered conformations (Fig. 1).    
 
Base
C-2’ Exo
C-2’ Endo
C-5’
C-3’
C-4’
C-1’
C-2’
C-3’ exo
Base
C-3’ Endo
C-5’
C-4’
C-1’
a)
b)
 
Fig. 1: Furanose ring in nucleotides in different puckered 
conformations. Note that four carbons (C1’, C2’/C3’,C4’ and C5’) remains  in the same plane 
for a given conformation. But only C2’ or C3’ can acquire endo (same) or exo (opposite) side with 
respect to C5’ atom. (Source: Author) 
 
 
The base of nucleotide (at N-1 for pyrimidines and at N-9 for purines) in joined to the first 
carbon (C-1) of a pentose sugar by N-glycosyl bond. The torsion in this bond leads to syn 
and anti conformations of bases (Fig. 2), and therefore is responsible for the different forms 
of DNA i.e, right handed and left handed forms.  
 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
3 
 
Anti
Syn
 
Fig.2: Anti and syn conformations of bases due to rotation in 
glycosidic bonds. (Source: Author) 
 
a) B-form of DNA 
B-form is the most common form of DNA and can be observed under high humidity 
conditions. Watson and Crick model was based on this form, with the helix turn at every 3.4 
nm and the distance between two adjacent base pairs is 0.34 nm. Hence, there are about 
10 pairs per turn with a right handed helix rotation. The turns generate wide major groove 
and narrow minor groove. Total diameter of helix is 23.7 Å.  
b) A-form of DNA 
In less humid conditions, like solution with higher salt concentrations or with alcohol, DNA 
conformation changes from B to A-form.  Although the helix rotation stays the same (i.e., 
right handed), but other conformational alterations are seen (Fig. 3). A-DNA is 
comparatively short and broad, with the distance between two adjacent base pairs reduced 
to 0.23 nm, resulting in 11 pairs per turn with the helix turn at every 33.6 Å. A-DNA forms 
are usually seen in during DNA-protein interactions. For example, TATA box (present 10 bp 
upstream of transcription site and is the place of attachment for TATA-binding protein 
(TBP)) acquires A-form of DNA when TBP binds to it.  (Even RNA attains A-form similar to 
A-DNA when it forms hairpin loops!).  
c) Z-form of DNA  
In both A and B-forms, glycosidic bond is always in anti- conformation, whereas in Z-DNA, 
due to repeating of purines and pyrimidines, the gycosidic bond acquires syn- conformation 
at purine residue and anti- conformation at pyrimidine residue. Syn- conformation accounts 
for base-flipping in Z-DNA. This alternative syn and anti conformations results in zig-zag 
 Nucleic acids:  DNA II 
 
              Institute of Life Long Learning, University of Delhi  
4 
look (Fig. 3) and hence give left handed helix appearance. Unlike B-DNA, major and minor 
grooves of Z-DNA show very little difference. The significance of Z-DNA is believed to 
provide torsional strain relief during active transcription. Intercalation of EtBr in the DNA 
also leads to Z-form.  Z-DNA is also suspected to play role in regulating gene expression 
and recombination.    
d) C-form of DNA 
C conformation is commonly observed as a low humidity form of the lithium salt, but 
resembles B-form of DNA (Fig. 3).  
The difference in A-, B- and Z-DNA is summarized in Table 1.  
 
Fig. 3: Forms of DNA: A-, B-, C- and Z-DNA. A, B and C DNA are right 
handed whereas Z-DNA is left handed. 
(Source:http://nar.oxfordjournals.org/content/31/17/5108/F9.expansion) Free for 
educational purpose 
 
Table 1: Major differences in A, B and Z forms of DNA.  
 A form B form Z form