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N. R. Jena et al.
preferred mode of protein translocation. Recent studies involving both experimental
and theoretical analyses performed on model systems in vitro suggest that proteins
diffuse by employing the sliding mechanism when the length of DNA is less than
100 base pairs and by hopping if it is longer than 100 base pairs [191, 192]. It is also
possible that proteins may undergo rotation along the helix axis of DNA during its
translocation [193].
3.5.2 Target Recognition
Once a protein reaches the target site on DNA, it needs to recognize the lesion
completely, as it can be a simple base lesion or a bulky cross-link product or an
abasic lesion. Depending on the nature of the lesion, repair proteins adopt different
strategies to accurately identify them. In the case of a simple base lesion, lesion
recognition and repair occur by the nucleotide flipping mechanism where the base
and the sugar get flipped out of the DNA double helix into the active site of the
protein for further processing [194–199]. Two different mechanisms of nucleotide
flipping have been proposed in some recent experimental and theoretical studies
where either a protein is directly involved in base flipping or base flipping occurs
without the involvement of a protein. According to the first mechanism, specific
binding of a protein with DNA at the lesion site followed by subsequent squeezing
can make the lesion extrahelical in DNA [200]. Alternatively, after binding to DNA,
proteins may recruit one or more amino acid residues to intercalate into the DNA
to push the damaged nucleotide out of the helix into its active site [201–203]. The
space thus generated due to the affected base extrusion is ultimately filled by an
amino acid that provides the necessary interaction required to stabilize the complementary base on one of the DNA strands [201–213]. It is proposed that due to a base
modification, DNA gets locally distorted. This distortion is sensed by the protein
during its translocation. As a result, the protein specifically binds at the lesion site
and the protein translocation ends after recognizing the correct nucleotide. Several enzymes such as different DNA glycosylases like human (hOGG1) or bacterial
(FPG) 8-oxoguanine-DNA glycosylase, human (AAG) and bacterial (AlkA/AlkB)
alkyl adenine-DNA glycosylase, uracil-DNA glycosylase (UDG) [204–216], etc.
and different DNA transferases like O6-alkylguanine-DNA alkyltransferase (AGT)
[217], cytosine-5-methyltransferase [218, 219], etc. are proposed to identify and
process the base lesion following the above mentioned mechanism. In addition to
the above mentioned enzymes, endonuclease V (EndoV) [220, 221], which repairs
bulky DNA lesions like thymine dimers has also been proposed to identify and
process the lesion by the above protein facilitated nucleotide flipping mechanism.
According to the second mechanism of nucleotide flipping, intrinsic dynamics
of DNA pushes the modified base significantly out of the DNA double helix, which
then gets captured by the protein during its translocation on the DNA surface [222,
223]. This is argued to be possible due to differences in stabilities of base pairs and
stacking interactions between the modified and complementary bases in DNA. In
this situation, the repair protein may undergo conformational changes in such a
N. R. Jena et al.
preferred mode of protein translocation. Recent studies involving both experimental
and theoretical analyses performed on model systems in vitro suggest that proteins
diffuse by employing the sliding mechanism when the length of DNA is less than
100 base pairs and by hopping if it is longer than 100 base pairs [191, 192]. It is also
possible that proteins may undergo rotation along the helix axis of DNA during its
translocation [193].
3.5.2 Target Recognition
Once a protein reaches the target site on DNA, it needs to recognize the lesion
completely, as it can be a simple base lesion or a bulky cross-link product or an
abasic lesion. Depending on the nature of the lesion, repair proteins adopt different
strategies to accurately identify them. In the case of a simple base lesion, lesion
recognition and repair occur by the nucleotide flipping mechanism where the base
and the sugar get flipped out of the DNA double helix into the active site of the
protein for further processing [194–199]. Two different mechanisms of nucleotide
flipping have been proposed in some recent experimental and theoretical studies
where either a protein is directly involved in base flipping or base flipping occurs
without the involvement of a protein. According to the first mechanism, specific
binding of a protein with DNA at the lesion site followed by subsequent squeezing
can make the lesion extrahelical in DNA [200]. Alternatively, after binding to DNA,
proteins may recruit one or more amino acid residues to intercalate into the DNA
to push the damaged nucleotide out of the helix into its active site [201–203]. The
space thus generated due to the affected base extrusion is ultimately filled by an
amino acid that provides the necessary interaction required to stabilize the complementary base on one of the DNA strands [201–213]. It is proposed that due to a base
modification, DNA gets locally distorted. This distortion is sensed by the protein
during its translocation. As a result, the protein specifically binds at the lesion site
and the protein translocation ends after recognizing the correct nucleotide. Several enzymes such as different DNA glycosylases like human (hOGG1) or bacterial
(FPG) 8-oxoguanine-DNA glycosylase, human (AAG) and bacterial (AlkA/AlkB)
alkyl adenine-DNA glycosylase, uracil-DNA glycosylase (UDG) [204–216], etc.
and different DNA transferases like O6-alkylguanine-DNA alkyltransferase (AGT)
[217], cytosine-5-methyltransferase [218, 219], etc. are proposed to identify and
process the base lesion following the above mentioned mechanism. In addition to
the above mentioned enzymes, endonuclease V (EndoV) [220, 221], which repairs
bulky DNA lesions like thymine dimers has also been proposed to identify and
process the lesion by the above protein facilitated nucleotide flipping mechanism.
According to the second mechanism of nucleotide flipping, intrinsic dynamics
of DNA pushes the modified base significantly out of the DNA double helix, which
then gets captured by the protein during its translocation on the DNA surface [222,
223]. This is argued to be possible due to differences in stabilities of base pairs and
stacking interactions between the modified and complementary bases in DNA. In
this situation, the repair protein may undergo conformational changes in such a