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Site-Specific Self-Catalyzed DNA Depurination: A Biological Mechanism That Leads to Mutations and Creates Sequence Diversity.

Abstract Self-catalyzed DNA depurination is a sequence-specific physiological mechanism mediated by spontaneous extrusion of a stem-loop catalytic intermediate. Hydrolysis of the 5'G residue of the 5'GA/TGG loop and of the first 5'A residue of the 5'GAGA loop, together with particular first stem base pairs, specifies their hydrolysis without involving protein, cofactor, or cation. As such, this mechanism is the only known DNA catalytic activity exploited by nature. The consensus sequences for self-depurination of such G- and A-loop residues occur in all genomes examined across the phyla, averaging one site every 2,000-4,000 base pairs. Because apurinic sites are subject to error-prone repair, leading to substitution and short frameshift mutations, they are both a source of genome damage and a means for creating sequence diversity. Their marked overrepresentation in genomes, and largely unchanging density from the lowest to the highest organisms, indicate their selection over the course of evolution. The mutagenicity at such sites in many human genes is associated with loss of function of key proteins responsible for diverse diseases.
PMID
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Authors

Mayor MeshTerms

Polymorphism, Genetic

Keywords

DNA self-catalysis

abasic sites

adenine and guanine self-depurination sequences

cruciform extrusion

inverted repeat sequences

modulating sequence factors

Journal Title annual review of biochemistry
Publication Year Start




PMID- 28654322
OWN - NLM
STAT- MEDLINE
DA  - 20170627
DCOM- 20170704
LR  - 20170704
IS  - 1545-4509 (Electronic)
IS  - 0066-4154 (Linking)
VI  - 86
DP  - 2017 Jun 20
TI  - Site-Specific Self-Catalyzed DNA Depurination: A Biological Mechanism That Leads 
      to Mutations and Creates Sequence Diversity.
PG  - 461-484
LID - 10.1146/annurev-biochem-070611-095951 [doi]
AB  - Self-catalyzed DNA depurination is a sequence-specific physiological mechanism
      mediated by spontaneous extrusion of a stem-loop catalytic intermediate.
      Hydrolysis of the 5'G residue of the 5'GA/TGG loop and of the first 5'A residue
      of the 5'GAGA loop, together with particular first stem base pairs, specifies
      their hydrolysis without involving protein, cofactor, or cation. As such, this
      mechanism is the only known DNA catalytic activity exploited by nature. The
      consensus sequences for self-depurination of such G- and A-loop residues occur in
      all genomes examined across the phyla, averaging one site every 2,000-4,000 base 
      pairs. Because apurinic sites are subject to error-prone repair, leading to
      substitution and short frameshift mutations, they are both a source of genome
      damage and a means for creating sequence diversity. Their marked
      overrepresentation in genomes, and largely unchanging density from the lowest to 
      the highest organisms, indicate their selection over the course of evolution. The
      mutagenicity at such sites in many human genes is associated with loss of
      function of key proteins responsible for diverse diseases.
FAU - Fresco, Jacques R
AU  - Fresco JR
AD  - Department of Molecular Biology, Princeton University, Princeton, New Jersey
      08544; email: [email protected] , [email protected]
FAU - Amosova, Olga
AU  - Amosova O
AD  - Department of Molecular Biology, Princeton University, Princeton, New Jersey
      08544; email: [email protected] , [email protected]
LA  - eng
PT  - Journal Article
PT  - Review
PL  - United States
TA  - Annu Rev Biochem
JT  - Annual review of biochemistry
JID - 2985150R
RN  - 0 (DNA, Catalytic)
RN  - 0 (DNA, Cruciform)
RN  - 0 (DNA, Single-Stranded)
RN  - 0 (beta-Globins)
RN  - 5Z93L87A1R (Guanine)
RN  - JAC85A2161 (Adenine)
SB  - IM
MH  - Adenine/*metabolism
MH  - Biological Evolution
MH  - Bloom Syndrome/*genetics/metabolism/pathology
MH  - Catalysis
MH  - DNA Repair
MH  - DNA, Catalytic/*genetics/metabolism
MH  - DNA, Cruciform/genetics/metabolism
MH  - DNA, Single-Stranded/genetics/metabolism
MH  - Guanine/*metabolism
MH  - Humans
MH  - Hydrolysis
MH  - Inverted Repeat Sequences
MH  - Mutation
MH  - *Polymorphism, Genetic
MH  - Werner Syndrome/*genetics/metabolism/pathology
MH  - beta-Globins/genetics/metabolism
OTO - NOTNLM
OT  - DNA self-catalysis
OT  - abasic sites
OT  - adenine and guanine self-depurination sequences
OT  - cruciform extrusion
OT  - inverted repeat sequences
OT  - modulating sequence factors
EDAT- 2017/06/28 06:00
MHDA- 2017/07/05 06:00
CRDT- 2017/06/28 06:00
AID - 10.1146/annurev-biochem-070611-095951 [doi]
PST - ppublish
SO  - Annu Rev Biochem. 2017 Jun 20;86:461-484. doi:
      10.1146/annurev-biochem-070611-095951.