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Структурообразующие мотивы в геномах прокариот

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Озолинь О. Н., Деев А. А., Масулис И. С., Часов В. В., Костяницина Е. Г., Пуртов Ю. А., Архипов И. В., Брок-Волчанский А. С. Уровни структурной организации промоторнон ДНК Escherichia coli II Биофизика. 2002. Т. 47. С. 809−819. Озолинь О. Н., Пуртов Ю. А., Брок-Волчанский А.С., Деев А. А., Лукьянов В. И. Особенности ДНК-белковых взаимодействий в транскрипционных комплексах Escherichia coli II… Читать ещё >

Структурообразующие мотивы в геномах прокариот (реферат, курсовая, диплом, контрольная)

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  • Обзор литературы
  • 1. Особенности структурной организации и биологическая роль мононуклеотидных poly (dA)n-TpeKOB
    • 1. 1. Модели структурной организации poly (dА)п-треков
    • 1. 2. Биологическая роль ро1у (<1А)п-треков
      • 1. 2. 1. poly (dA) n-треки как мишени прямого контакта с белками транскрипционного комплекса
      • 1. 2. 2. poly (dA) п-треки и суперспирализация ДНК
      • 1. 2. 3. poly (dA) п-треки и выпетливание ДНК
      • 1. 2. 4. poly (dA)n-TpeKH и терминация синтеза ДНК обратной транскриптазой ретровирусов
      • 1. 2. 5. poly (dA)n-TpeKH и температурозависимая регуляция транскрипции у патогенных бактерий
      • 1. 2. 6. poly (dA) &bdquo--треки в кинетопластной ДНК
      • 1. 2. 7. poly (dA) &bdquo--треки в участках прикрепления хроматина к ядерному белковому матриксу
      • 1. 2. 8. poly (dA) &bdquo--треки и упаковка ДНК в нуклеосомы
  • 2. Неравномерность в распределении А/Т-пар в геномах прокариот
  • 3. Общая характеристика транскрипционного цикла и роль poly (dA)n-TpeicoB в формировании и функционировании транскрипционного комплекса
    • 3. 1. Фазы транскрипционного цикла
    • 3. 2. Структура бактериальной РНК-полимеразы: субъединицы, принимающие участие в распознавании промоторов
      • 3. 2. 1. а-субъединица
      • 3. 2. 2. о-субъединицы
    • 3. 3. Особенности нуклеотидных последовательностей промоторной ДНК
      • 3. 3. 1. Консервативные гексануклеотиды
      • 3. 3. 2. «Расширенный» -10-элемент и реорганизация -10-элемента
      • 3. 3. 3. Дискриминатор
      • 3. 3. 4. UP-элемент
      • 3. 3. 5. Промоторы, узнаваемые а
  • 4. Компьютерные алгоритмы поиска промоторов прокариот
    • 4. 1. Методы, основанные на использовании искусственных нейронных сетей
    • 4. 2. Методы, основанные на использовании скрытых марковских моделей
    • 4. 3. Учёт локальных физических особенностей промоторной ДНК
    • 4. 4. Алгоритмы, основанные на использовании позиционных весовых матриц
  • 5. Методы и алгоритмы
    • 5. 1. Поиск мононуклеотидных и смешанных треков в геномах
    • 5. 2. Компьютерный поиск промоторов
    • 5. 3. Определение фоновых значений показателя промотор-подобия и характеристика степени его вариабельности
    • 5. 4. Адаптация PWM PlatProm к контексту консервативных элементов других промоторов
    • 5. 5. Унификация PlatProm
    • 5. 6. Оценка предсказательного потенциала компьютерных алгоритмов
    • 5. 7. Критерии для выявления «промоторных островков»
    • 5. 8. Оценка транскрипционной активности «смешанных промоторных островков»
    • 5. 9. Исследование ассоциации «смешанных промоторных островков» Е. coli с горизонтально перенесёнными генами
    • 5. 10. Оценка взаимодействия «смешанных промоторных островков» Е. coli с белком H-NS и РНК-полимеразой
  • 6. Результаты и обсуждение
    • 6. 1. Анализ распространения мононуклеотидных poly (dA)n- и poly (dT)rt-TpeKOB по сравнению с poly (dG)n- и ро1у^С)п-треками в геномах прокариот с различным AT/GC-составом
    • 6. 2. Сравнительный анализ встречаемости мононуклеотидных треков и смешанных W- и S-треков
    • 6. 3. Анализ распределения мононуклеотидных треков в кодирующих и некодирующих участках бактериальных геномов
    • 6. 4. Распознавание промоторов а54 Е. coli разными версиями PlatProm
    • 6. 5. Разработка метода оценки статистических значимых пороговых значений коэффициента промотор-подобия
    • 6. 6. Оценка способности унифицированной и специализированных версий PlatProm распознавать промоторы в геномах с разным GC-составом
      • 6. 6. 1. Распознавание SigA-зависимых промоторов Corynebacteriimi glutamicum
      • 6. 6. 2. Распознавание промоторов Agrobacterium tumefaciens
      • 6. 6. 3. Распознавание, а -зависимых промоторов Helicobacter pylor
    • 6. 7. Поиск участков генома с высокой плотностью потенциальных промоторов
    • 6. 8. Число и функциональные свойства «смешанных промоторных островков»

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