Base Excision Repair

Core Concept

Base excision repair (BER) removes damaged or inappropriate DNA bases — such as oxidized, alkylated, or deaminated bases and uracil — that do not distort the helix. A lesion-specific DNA glycosylase flips the damaged base out and cleaves its glycosidic bond, leaving an abasic (AP) site. The sugar-phosphate backbone is then nicked, the gap is processed, and the correct nucleotide is reinserted by a DNA polymerase and sealed by ligase. BER is the cell's main defense against the thousands of spontaneous and reactive-oxygen-species-induced base lesions that arise daily.

Key Components

• DNA glycosylases (e.g., uracil-DNA glycosylase/UNG, OGG1 for 8-oxoguanine) — recognize and excise specific damaged bases.
• AP endonuclease (APE1) — nicks the backbone 5′ to the abasic site.
• DNA polymerase β (short patch) — the main BER polymerase; removes the baseless sugar and inserts the correct base.
• DNA polymerase δ/ε and PCNA (long patch) — replace a 2–10 nucleotide flap in long-patch BER.
• Flap endonuclease (FEN1) — removes the displaced flap in long-patch BER.
• DNA ligase III/XRCC1 (short patch) or ligase I (long patch) — seal the final nick.

Mechanism

Each glycosylase recognizes a narrow class of lesions and cleaves the N-glycosidic bond, creating an apurinic/apyrimidinic (AP) site. APE1 then cuts the backbone, generating a nick with a 3′-OH and a 5′-deoxyribose phosphate. In short-patch BER, polymerase β removes the sugar-phosphate and inserts one correct nucleotide, and ligase III/XRCC1 seals the nick. In long-patch BER (when the 5′ end is blocked or modified), polymerase δ/ε displaces a short flap that FEN1 removes, and ligase I seals the longer gap.

How It Works

1. A base is damaged (e.g., cytosine deaminated to uracil, or guanine oxidized to 8-oxoguanine).
2. A specific DNA glycosylase flips the damaged base out of the helix and hydrolyzes its glycosidic bond, leaving an AP site.
3. AP endonuclease 1 incises the backbone 5′ to the AP site, creating a 3′-OH and a 5′-deoxyribose phosphate.
4. Short-patch: DNA polymerase β removes the 5′-deoxyribose phosphate and inserts the correct nucleotide.
5. DNA ligase III (with XRCC1) seals the nick.
6. Alternatively, long-patch: pol δ/ε (with PCNA) extends several nucleotides, FEN1 clips the displaced flap, and ligase I seals.

Energy and Directionality

BER consumes dNTPs (for resynthesis) and ATP (for ligation and some glycosylase/processing steps); the initial glycosylase cleavage does not require external energy beyond the chemistry of bond hydrolysis. Directionality is defined by the lesion: repair proceeds from the damaged base outward, always resynthesizing 5′→3′ off the intact complementary strand, so the correct sequence is restored from the undamaged template. The choice of short- versus long-patch depends on the state of the 5′ terminus.

Experimental Evidence

• Uracil incorporation — enzymes that remove uracil from DNA were first detected because dUTP misincorporation is toxic; UNG-deficient cells accumulate uracil.
• Knockout studies — mice lacking individual glycosylases or APE1 show elevated mutation rates and, for APE1, embryonic lethality, proving BER's essential role.
• OGG1 and 8-oxoguanine — deletion of OGG1 increases G→T transversions, the signature mutation of oxidative damage.
• In vitro reconstitution — purified glycosylase, APE1, pol β, and ligase complete short-patch repair on defined substrates, confirming the pathway order.

Technique

BER activity is assayed with synthetic oligonucleotides containing a single defined lesion, incubating with cell extracts or purified enzymes and resolving products by gel electrophoresis. Comet assay measures overall DNA strand breaks, and glycosylase-specific assays (e.g., aldehyde-reactive probes) quantify AP sites. Whole-genome sequencing of knockout cells reveals the mutation spectra attributable to each enzyme.

How it works

1. A base is damaged (e.g., cytosine deaminated to uracil, or guanine oxidized to 8-oxoguanine).
2. A specific DNA glycosylase flips the damaged base out of the helix and hydrolyzes its glycosidic bond, leaving an AP site.
3. AP endonuclease 1 incises the backbone 5′ to the AP site, creating a 3′-OH and a 5′-deoxyribose phosphate.
4. Short-patch: DNA polymerase β removes the 5′-deoxyribose phosphate and inserts the correct nucleotide.
5. DNA ligase III (with XRCC1) seals the nick.
6. Alternatively, long-patch: pol δ/ε (with PCNA) extends several nucleotides, FEN1 clips the displaced flap, and ligase I seals.

Common confusions

• "BER and mismatch repair do the same job" — MMR fixes mispaired but normal bases after replication; BER removes chemically damaged bases.
• "NER and BER are interchangeable" — NER handles bulky, helix-distorting lesions (e.g., UV dimers); BER handles small, non-distorting base damage.
• "The glycosylase removes the whole nucleotide" — it removes only the base; APE1 then cuts the backbone.
• "Only one polymerase is used" — short-patch uses pol β; long-patch uses pol δ/ε with PCNA and FEN1.
• "BER errors don't matter" — unrepaired oxidative lesions drive G→T mutations and age-related genome instability.

Quick review

• BER targets damaged bases (uracil, 8-oxoguanine, alkylated/deaminated bases).
• Glycosylase → AP site → APE1 nick → pol β (short) or pol δ/ε (long) → ligase.
• Short-patch: 1 nucleotide; long-patch: 2–10 nt flap removed by FEN1.
• Restores sequence from the intact template; consumes dNTPs and ATP.
• Essential against endogenous/oxidative damage; defects raise mutation rates.