INTRODUCTION POLYNUCLEOTIDE CONFORMATION IN NUCLEIC ACID #DNA CONFORMATION #RNA CONFORMATION FORCES STABILIZING NUCEIC ACID STRUCTURE POLYSACCHARIDE CONFORMATION IN POLYSACCHARIDE #ORDERED CONFORMATION #DISRDERED CONFORMATION ANALYSIS TECHNIQUES #NMR #X-RAY DIFFRACTION CONCLUSION REFRENCES

1. Polysaccharide &
Polynucleotide
Conformational Properties
By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )

2. INTRODUCTION
POLYNUCLEOTIDE
CONFORMATION IN NUCLEIC ACID
#DNA CONFORMATION
#RNA CONFORMATION
 FORCES STABILIZING NUCEIC ACID STRUCTURE
POLYSACCHARIDE
CONFORMATION IN POLYSACCHARIDE
#ORDERED CONFORMATION
#DISRDERED CONFORMATION
ANALYSIS TECHNIQUES
#NMR
#X-RAY DIFFRACTION
CONCLUSION
REFRENCES

3. CONFORMATION ?

4.  A polynucleotide molecule is a biopolymer composed of
nucleotide monomers covalently bonded in a chain.
 A longer nucleic acid is called a polynucleotide.
NUCLEOTIDE
 Nucleotides have three characteristic components:
(1) a nitrogenous (nitrogen-containing) base,
(2) a pentose,
(3) a phosphate
+ + PHOSPHET GROUPNITROGEN BASE + PENTOSE SUGAR
NUCLEOSIDE NUCLEOTIDE

6.  Nucleic acids are composed of nucleotide monomers, which
themselves are built from a phosphate group, a sugar, and a
nitrogenous base. The bases are of two types, pyrimidines
(single ringed) and purines (double ringed).
 There are two classes of nucleic acids, deoxyribonucleic acid
(DNA) & ribonucleic acid(RNA).

7.  Primary Structure of Nucleic
Acids
The sequence or order of the
nucleotides defines the primary
structure of DNA and RNA. The
nucleotides of the polymer are
linked by phosphodiester bonds
connecting through the oxygen
on the 5' carbon of one to the
oxygen on the 3'carbon of
another. The Oxygen and
Nitrogen atoms in the backbone
give DNA and RNA "polarity" .

8.  Secondary Structure of Nucleic Acids
In secondary structure pairing nitrogen base is take place.
A purine base always pairs with a pyrimidine base or more
specificallyGuanosine (G) with Cytosine (C) and Adenine (A) with
Thymine (T) or Uracil(U). The G-C pair has three hydrogen bonds
while the A-T pair has two hydrogen bonds.

9.  TERTIARY STRUCTURE
The complex folding of large chromosomes within
eukaryotic chromatin & bacterial nucleotides is tertiary
structure.

10. Deoxyribonucleic acid, or DNA, like proteins, is a
linear macromolecule found in all living cells. In
contrast to proteins, however, it is build up of
only 4 different types of building blocks, called
nucleotides. Nucleotides are composed of a base,
being either a purine or pyrimidine group, and a
2'-deoxyribosyl-tri-phosphate.
A DNA helix can have the A, B, or Z
conformation.
The biologically most common form of DNA is
known as B-DNA, which has the structural
features first noted by James Watson and Francis
Crick together with Rosalind Franklin and others.

12.  The structure of B-DNA is biological
predominant form of DNA.
 It consist of right handed double helix
whose two antiparallel sugar- phosphate
chains wrap around the periphery of the
helix.
 The core of the helix is occupied by A-T
and G-C Watson-Crick base pair.
 The plane of the base pair lies
perpendicular to the helix axis.
 20-Å-diameter double helix.
 The B-DNA is a right handed, anti-parallel
double helix with 2nm in diameter.

13.  Two deep grooves between its
sugar-phosphate chains –
minor grooves
major grooves
 10bp per turn
 a twist of 36° per bp
 0.34nm (3.4Å) per base
 pitch 3.4nm (34Å)
 diameter 2.0nm
 base plane tilt away from being
perpendicular to helix axis 6°

14.  A conformational change can be induced
in DNA when the relative humidity of the
sample is lowered below 75%. This double
helix forms called A-form.
 The A form is a wider and flatter helix, the
base pair plane is tilted with respect to the
helix axis, the helix also exhibits a minor
and major groove with the
several structural parameters.

15.  11bp per turn
 a twist of 33° per turn
 0.26nm per base
 pitch of 2.8nm
 diameter 2.6nm (has an axial hole)
 base plane tilt away from being
perpendicular to helix axis 20°

16.  Z-DNA helix has a left
handed conformation .
 Z-DNA, has 12 Watson–
Crick base pairs per turn,
a pitch of 44 Å, a deep
minor groove, and no
discernible major groove.
 12bp per turn
 0.37nm per base
 pitch 4.5nm
 diameter 1.8nm
 base tilt 7°

17.  Fiber diffraction and NMR studies have shown that
complementary polynucleotides with alternating purines and
pyrimidines, such as poly d(GC) poly d(GC) or poly d(AC)
poly d(GT), assume the Z conformation at high salt
concentrations.
 The salt stabilizes Z-DNA relative to B-DNA by reducing the
electrostatic repulsions between closest approaching
phosphate groups on opposite strands (which are 8 Å apart
in Z-DNA and 12 Å apart in B-DNA).

19.  A rather common type of DNA sequence
is a palindrome.
 Such sequences are self-complementary
within each strand and therefore have
the potential to form hairpin or
cruciform(cross-shaped) structures

21.  A particularly exotic DNA
structure, known as H-DNA, is
found in polypyrimidine or
polypurine tracts that also
incorporate a mirror repeat. A
simple example is a long stretch
of alternating T and C residues.
 Two of the three strands in the
H-DNA triple helix contain
pyrimidines and the third
contains purines.

22.  The conformation of a nucleotide
unit is specified by the six torsion
angles of the sugar–phosphate
backbone and the torsion angle
describing the orientation of the base
around the glycosidic bond.
 The rotation of a base around its
glycosidic bond (angle ) is greatly
hindered.
 Purine residues have two sterically
permissible orientations known as
the syn (Greek: with) and anti
(Greek: against) conformations.

23.  Only the conformation of pyrimidines is stable, because, in the syn
conformation,the sugar residue sterically interferes with the
pyrimidine’s C2 substituent.
 In most double-helical nucleic acids, all bases are in the anti
conformation.
 The exception is Z-DNA , in which the alternating pyrimidine and
purine residues are anti and syn, this is one reason why the
repeating unit of Z-DNA is a dinucleotide.

24.  The secondary structure of RNA consists of a
single polynucleotide.
 Single stranded RNA can fold back on itself
so that complementary sequences base pair
to form double-stranded stems with single-
stranded loops.
 Weak interactions, especially base-stacking
interactions, play a major role in stabilizing
RNA structures.
 Where complementary sequences are
present, the predominant double-stranded
structure is an A-form right-handed double
helix. Z-form helices have been made in the
laboratory (under very high-salt or high-
temperature conditions). The B form of RNA
has not been observed.

26.  A double-stranded nucleic acid structure is stabilized by
hydrogen bonding between base pairs, by stacking
interactions, and by ionic inter
 Hydrogen Bonds Only Weakly Stabilize Nucleic Acid
Structures.
 Stacking Interactions Result from Hydrophobic Forces.
 Cations Shield the Negative Charges of Nucleic Acids.

27.  Polusccharide chains are generally formed by repeated sequence
of monomers and oligomers.
 Insoluble in water, tasteless, linear or branched.
 Classified -Homoglycans
Heteroglycans
 depending upon the kind of monosaccharides present. Depending
upon the function, they are classified as storage and structural
polysaccharides.

28.  The conformation of any individual monosaccharide is relatively
fixed in the polysaccharide chain,.
 The sugar residues linked through glycosidic linkage will rotate
around the glycosidic bond and tend to adopt an orientation of
lower or lowest energies.
 primary structure will assume a characteristic geometrical shape
in space, such as ribbon or helix.
 These shapes or conformations polysaccharides assume are
described as the secondary structures.
 There are two general classes of conformation for polysaccharides:
 Ordered Conformation
 Disordered Conformation
 Polysaccharide chains with well-defined secondary structures may
interact with each other to form tertiary structures ,which are
ordered organizations involving a group of polysaccharide chains.

29.  Conformation of Homo polysaccharide Chains: Liner Conformation
 According to Rees,the secondary structure of homoglycans are
classified into four conformational types based on the dihedral angle
formed between the bonds to and from each residue across the
sugar ring.
 ribbon-like, hollow helix, crumpled, and loosely jointed types.

31.  Polysaccharide chains in which the
dihedral angle is close to 180°.
 For a (1→4) linked β-D-glucosyl
residue and a (1→4) linked α D-
galactosyl residue, the bonds from
one sugar residue to it two
bridging oxygens are parallel to
each other and form a zig-zag
configuration.
 These type of polysccharide usually
have a ribbon like structure.
Examples of these types of
homoglycans are found in plant
cell walls, such as cellulose, xylan,

34.  If the bonds to and from each unit are no longer parallel to one
another, but adopt a U-turn form, as in (1→3)-linke β-D-
glucopyranose and (1→4)-linkedα-D- glucopyranose the resultant
structure is likely to be a hollow helix type.

35.  Theoretically, (1→2)-linked polysaccharides will have the
dihedral angle around 60° and will assume crumpled
ribbon conformations with restricted flexibility.
 Such linkages are rare, although they do occur in the
rhamnogalacturonic acid sequences in pectin, and in some
bacterial polysaccharides.
 The (1→6)-linked polysaccharides have an additional
element of flexibility because the residues are linked
through three rather than two covalent linkages (Figure
1.24). This additional bond tends to favor extended
flexiblecoil conformations, which are less amenable to
ordered packing.

36.  Random coil formation

37.  NMR
 X-RAY DIFFRACTION

38.  Nuclear magnetic resonance spectroscopy, most commonly known
as NMR spectroscopy, is a research technique that exploits
the magnetic properties of certain atomic nuclei. It determines the
physical and chemical properties of atoms or the molecules in which
they are contained.
 It is applicable to any kind of sample that contains nuclei possessing
spin. Suitable samples range from small compounds analyzed with
1-dimensional proton or carbon-13 NMR spectroscopy to large
proteins or nucleic acids using 3 or 4-dimensional techniques.
 The resonant frequency, energy of the absorption, and the intensity
of the signal are proportional to the strength of the magnetic field.

40.  X-ray crystallography is a method used for
determining the atomic and molecular
structure of a crystal, in which the
crystalline atoms cause a beam of X-
rays to diffract into many specific
directions.
 By measuring the angles and intensities of
these diffracted beams,
a crystallographer can produce a three-
dimensional picture of the density
of electrons within the crystal.

42. CONCLUSIONS

43. BOOK WRITER
PRINCIPLE OF BIOCHEMISTRY NELSON & COX 5th edition
FUNDAMENTALS OF BIOCHEMISTRY VOET D, VOET J G, PRATT CN ON W
2nd edition
FUNDAMENTALS OF BIOCHEMISTRY H.P.GAJERA, S.V.PATEL,
B. A. GOLAKIYA
RESEARCH PAPER
•“CONFORMATIONS IN POLYSACCHARIDES AND COMPLEX CARBOHYDRATES”
Edward Atkins, UNIVERSITY OF BRISTOL .
•“UNDERSTANDING THE STRUCTURE OF POLYSACCHARIDES”-
Qi Wang and Steve W. Cui