nucleobases. The length of the strands also plays a role: the longer the strands (i.e.,
the more nucleobases there are to interact), the more stable is the double helix.
1.1.2 Conformations of DNA
DNA can have different conformations (A-, B-, or Z-DNA), which vary in handedness, number of base pairs per helix turn, and diameter as proved by X-ray
diffraction studies [28]. DNA in its native state is a semi-flexible long thin rod,
only about 2 nm in diameter (B- and Z-DNA), with a persistence length (mechanical property quantifying the stiffness of a polymer) of about 50 nm [29, 30], which
depends on ionic strength [31], DNA sequence [32], and temperature [33].
The conformation of the double helix can be studied using various spectroscopic
methods such as circular dichroism (CD) [34], infrared (IR), Raman, ultraviolet
(UV), visible absorption spectroscopy, and nuclear magnetic resonance (NMR)
spectroscopy [35].
1.1.3 Topologies of DNA
DNA can be chromosomal or extra-chromosomal (plasmid DNA). Plasmid DNA
(pDNA) is a double-stranded DNA (dsDNA) that can replicate independently of the
chromosomal DNA, and is usually constituted of hundreds to a few thousand base
pairs. Artificial plasmids are widely used in gene therapy in order to drive the
replication of recombinant DNA sequences within host organisms. pDNA can
adopt various conformations (linear, circular, or supercoiled) according to the
over- or underwinding of a DNA strand (Scheme 2). DNA supercoiling is important
for DNA packaging within all cells. Because the length of DNA can be thousands of
times that of a cell, supercoiling of DNA allows DNA compaction, therefore much
more genetic material can be packaged into the cell or nucleus (in eukaryotes).
The commercial calf thymus DNA (ctDNA) often used in physico-chemical
studies is a linear DNA that can be isolated from calf thymus, an organ that has a
very high yield of DNA.
The various topologies of DNA (supercoiled, circular, linear) can be
discriminated by various methods such as electrophoresis and by microscopy
techniques such as electron microscopy (EM) [36], cryogenic transmission electron
microscopy (cryo-TEM) [37], and atomic force microscopy (AFM) [38].
1.1.4 DNA Condensation in Nature
Interpolyelectrolyte complexes form spontaneously upon mixing of solutions of
oppositely charged polyelectrolytes, the main driving force being the gain of
entropy because of the release of small counterions as well as the electrostatic
interactions. This entropy-driven process creates an exceedingly tricky problem of
how to package the genetic material in a stable non-aggregating form with synthetic
108
A. Bertin
the more nucleobases there are to interact), the more stable is the double helix.
1.1.2 Conformations of DNA
DNA can have different conformations (A-, B-, or Z-DNA), which vary in handedness, number of base pairs per helix turn, and diameter as proved by X-ray
diffraction studies [28]. DNA in its native state is a semi-flexible long thin rod,
only about 2 nm in diameter (B- and Z-DNA), with a persistence length (mechanical property quantifying the stiffness of a polymer) of about 50 nm [29, 30], which
depends on ionic strength [31], DNA sequence [32], and temperature [33].
The conformation of the double helix can be studied using various spectroscopic
methods such as circular dichroism (CD) [34], infrared (IR), Raman, ultraviolet
(UV), visible absorption spectroscopy, and nuclear magnetic resonance (NMR)
spectroscopy [35].
1.1.3 Topologies of DNA
DNA can be chromosomal or extra-chromosomal (plasmid DNA). Plasmid DNA
(pDNA) is a double-stranded DNA (dsDNA) that can replicate independently of the
chromosomal DNA, and is usually constituted of hundreds to a few thousand base
pairs. Artificial plasmids are widely used in gene therapy in order to drive the
replication of recombinant DNA sequences within host organisms. pDNA can
adopt various conformations (linear, circular, or supercoiled) according to the
over- or underwinding of a DNA strand (Scheme 2). DNA supercoiling is important
for DNA packaging within all cells. Because the length of DNA can be thousands of
times that of a cell, supercoiling of DNA allows DNA compaction, therefore much
more genetic material can be packaged into the cell or nucleus (in eukaryotes).
The commercial calf thymus DNA (ctDNA) often used in physico-chemical
studies is a linear DNA that can be isolated from calf thymus, an organ that has a
very high yield of DNA.
The various topologies of DNA (supercoiled, circular, linear) can be
discriminated by various methods such as electrophoresis and by microscopy
techniques such as electron microscopy (EM) [36], cryogenic transmission electron
microscopy (cryo-TEM) [37], and atomic force microscopy (AFM) [38].
1.1.4 DNA Condensation in Nature
Interpolyelectrolyte complexes form spontaneously upon mixing of solutions of
oppositely charged polyelectrolytes, the main driving force being the gain of
entropy because of the release of small counterions as well as the electrostatic
interactions. This entropy-driven process creates an exceedingly tricky problem of
how to package the genetic material in a stable non-aggregating form with synthetic
108
A. Bertin