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DNA Hybridization Time Experiment in Version Space: A Comparative Analysis

Explore DNA structure and hybridization time in Version Space, detailing methods from biochemistry sources with a focus on Tm value measurement, reassociation kinetics, and Cot0.5 relationship to genome size. Discover two available methods with detailed steps and considerations for optimal results. Delve into other methods such as Megaclone, Megasort, Megatype, and Mpss.

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DNA Hybridization Time Experiment in Version Space: A Comparative Analysis

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  1. Version Space의 실험적 고찰 2001.11.23 장해만

  2. Introduction • DNA structure • Hybirdization time • version space • Other methods

  3. DNA structure biochemistry 4th edition p788-793

  4. Hybirdization time biochemistry 4th edition p990 • Tm value의 측정 ds strand : 40% less than ss at 260nm • Kinetic of reassociation S : single strand S`: 상보적 seq. D : ds seq. K : 평형상수 Co: 전체DNA농도 f : ss decreases

  5. Hybridization time

  6. Hybridization time Low con. of complementary seq slow rate of reassociation Cot0.5 is directly related to the size of genome ex) mammalian genome(30억bp) ====104 Ms 10-4m sol. of DNA ===== 108 Ms (about 3 years) 10000도시 TSP : 모든 도시를 DNA로 표현 = 47 =16384; 적어도 7bp가 소요.. 7 * 10000 (weight제외) + weight(10000!) + ,,,

  7. cs ee four faculty staff five Version space Edge • Graph for All Hypothesis Vertex + Dummy strand for blunt end?

  8. Version Space • available method 1 • vertex 와 edge(PNA)를 이용, 가능한 모든 pool 합성 • positive seq. 제작 • hybridization in pool • PAGE로 위치확인 • gel elution • PCR , 적정농도의 pool 형성 ---1st generalize • 2~6 반복 ( 단, positive일 경우) • negative example ??? • DNA breaks down in gel elution

  9. Version Space • available method 2 • 가능한 모든 pool을 주문 • positive seq. 제작 (linked bead) • hybridization in pool • bead selection • enz.처리 ---- blunt end 형성 • denaturation --- 1st generalize pool • negative seq. 제작(linked bead) • pool을 일부 균등분할 / hybridize / selection / enz. cutting / PAGE • PAGE에서 나온 band sequencing • negative probe (linked bead) 제작 • 1st generalize pool과 hybrid / bead selection / discard • 농도차이에 의한 부정확한 구분?? • 비용 / 비능률

  10. Other Methods • Megaclone • Megasort • Megatype • Mpss

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