4. ReactionBasePairingMutationMispairing DeaminationCGUA ATHypoxanthineC DeaminationGCXanthineC AkylationCG5’-methyl C Gene scilencing or A AkylationGCO6-methyl GT OxidationGC7,8-dihydro-8-oxo GC or A UVTTAATT dimer Replication arrest X-, γ- ray Double Strand Break Replication arrest Base analog Intercalating agent Base insertion or deletion To Animation ‘Mutation by base substitution’…..

7. To Animation ‘Methyl-directed mismatch repair’

9. Topic 69 Mismatch Repair –Mismatch causes distortion of helix Recognized by a repair enzyme Repair system recognizes newly synthesized strand New strand recognized by presence of breaks DNA Repair

10. Mismatch repair (MMR) Despite extraordinary fidelity of DNA synthesis, errors do persist Such errors can be detected and repaired by the post- replication mismatch repair system Prokaryotes and eukaryotes use a similar mechanism with common structural features Defects in MMR elevate spontaneous mutation rates 10- 1000x Defects in MMR underlie human predisposition to colon and other cancers (“HNPCC”) MMR also processes mispairs that result from heteroduplex DNA formed during genetic recombination: act to exclude “homeologous” recombination

11. Mechanism of MMR CH 3 3 5' 3'5' 3' Initiation CH 3 3 5' 3'5' 3' CH 3 3 5' 3'5' 3' MutS MutL MutH Excision CH 3 3 5' 3'5' 3' CH 3 3 5' 3'5' 3' UvrD + RecJ or ExoVIIUvrD + ExoI or ExoX or ExoVII Resynthesis CH 3 3 5' 3'5' 3' CH 3 3 5' 3'5' 3' PolIII + ligase

12. Mechanism of MMR CH 3 3 5' 3'5' 3' Initiation CH 3 3 5' 3'5' 3' CH 3 3 5' 3'5' 3' MutS MutL MutH Excision CH 3 3 5' 3'5' 3' CH 3 3 5' 3'5' 3' UvrD + RecJ or ExoVIIUvrD + ExoI or ExoX or ExoVII Resynthesis CH 3 3 5' 3'5' 3' CH 3 3 5' 3'5' 3' PolIII + ligase

13. Basis of MMR recognition MutS dimer (in yeast, Msh2/Msh3 or Msh2/Msh6 heterodimer) By DNA binding expts in vitro and DNA heteroduplex repair expts in vivo: MMR can recognize all base substitutions except C:C and short frameshift loops <4 bp Transition mispairs G:T and A:C and one base loops are particularly well-recognized (these are also the most common polymerase errors)

14. 직접적인 역전

15. 광회복 To Animation ‘direct repair’

16. 절제 수선

17. 염기 절제 수선 To Animation ‘BER’

18. Topic 618 Base Excision Repair (BER) –Initiated by a DNA glycosylase Recognizes alteration Removes base by cleavage of glycosidic bond between the base and deoxyribose –Several specific types of DNA glycosylase – for specific modifications Uracil formed from hydrolytic removal of amino group of cytosine Formation of 8-hydroxyguanine – by oxygen free radicals Formation of 3-methyl adenine –Following removal of the base – remaining deoxyribose phosphate is removed by endonuclease / phosphodiesterase –Gap filled via DNA polymerase and sealed by DNA ligase DNA Repair

19. Topic 619 Base Excision Repair (BER) DNA Repair

20. Mechanism of BER

22. N N NH 2 O O H2CH2C O O N HN O O O H2CH2C O O deoxycytosine deoxyuracil 1’1’ 2’2’ 3’3’ 4’4’ 5’5’ 1 2 3 4 5 6 CH 3 thymine glycosidic bond

23. Types of lesions repaired by BER Oxidative lesions; 8-oxo-G, highly mutagenic, mispairs with A, producing GC --> TA transversions example MutY, MutM=Fpg from E. coli Deoxyuracil: from misincorporation of dU or deamination of dC-->dU, example Ung, uracil N- glycosylase Various alkylation products e. g. 3-meA These lesions are not distorting and do not block DNA polymerases Spontaneous depurination (esp. G) yield abasic sites that are repaired by second half of BER pathway

25. 뉴클레오타이드 절제 수 선 To Animation ‘nucleotide excision repair’

26. Topic 626 Nucleotide Excision Repair (NER) –A ‘cut and patch’ mechanism –Removes bulky lesions Pyrimidine dimers Chemical groups attached –Two pathways Transcription coupled pathway Global pathway DNA Repair

28. 이중가닥 절제 수선

29. 상동 재조합 To Animation ‘HR’

30. 비상동 말단연결 To Animation ‘NHEJ’

34. 장애관통 DNA 합성

35. Lesion bypass polymerization Replication-blocking lesions such as UV photodimers can be repaired by NER but pose a serious problem if they are in ssDNA As a last resort, cells employ “bypass” polymerases with loosened specificity In E. coli: DinB (PolIV) and UmuD’C (Pol V); homologs in eukaryotes; mutated in XPV These polymerases are “error-prone” and are responsible for UV-induced mutation Expression and function highly regulated: dependent on DNA damage

36. Characteristics of lesion bypass polymerases Error rate 100-10,000 x higher on undamaged templates Lack 3’ to 5’ proofreading exonuclease activity Exhibit distributive rather than processive polymerization (nt. incorporated per binding event) Support translesion DNA synthesis in vitro