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  7. Дизайн праймеров для полимеразной цепной реакции. (Краткий обзор компьютерных программ и баз данных)

Дизайн праймеров для полимеразной цепной реакции. (Краткий обзор компьютерных программ и баз данных)

Год: 2016

Страницы: 215-238

Номер: Том 8, № 3

Тип: научная статья

Рубрика: Статьи

Авторы: Чемерис Алексей Викторович, Кирьянова (Забейворота) Ольга Юрьевна, Губайдуллин Ирек Марсович, Чемерис Дмитрий Алексеевич

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Аннотация:

За три десятилетия своего существования полимеразная цепная реакция (ПЦР) стала практически вездесущей. Приблизительно в каждой восьмой работе, где анализируется ДНК, применяется имеющий огромное множество вариаций метод ПЦР. Олигонуклеотидные праймеры являются крайне важной составляющей любой полимеразной цепной реакции, и существует целый ряд требований к их дизайну. В настоящее время для этой цели в основном используются базирующиеся на различных алгоритмах специализированные компьютерные программы, число которых уже превышает полторы сотни. Многие программы для дизайна праймеров существуют в виде бесплатных web-сервисов, также их дистрибутивы могут быть получены от разработчиков или скачаны с соответствующих сайтов, нередко авторы открывают для всех желающих доступ к исходным кодам своих разработок. Ряд программ доступен из коммерческих источников. С накоплением информации о нуклеотидных последовательностях отдельных генов и целых геномов обязательным этапом подбора стала проверка праймеров с помощью программы BLAST на вероятность их неспецифического связывания с матрицей, что позволяет в дальнейшем избежать появления нецелевых продуктов полимеразной цепной реакции. Существующие программы позволяют вести дизайн праймеров для различных модификаций  этого метода, среди которых мультиплексная, вырожденная, метабисульфитная ПЦР, ПЦР в реальном времени, ПЦР с последующим клонированием множественных фрагментов, в том числе безлигазным, ПЦР для проведения сайт-направленного мутагенеза, ПЦР, нацеленная на выявление мутаций, инделов, однонуклеотидного полиморфизма ДНК и др. Проводится многопараметрический анализ свойств олигонуклеотидов in silico (определение температуры плавления, выявление вторичных структур, димеров и т. п.). Разработаны программы, осуществляющие дизайн олигонуклеотидных праймеров с различными модификациями, например, содержащих рибонуклеотиды, LNA-нуклеотиды. В последнее время стали появляться программы дизайна праймеров, учитывающие уровень плоидности генома конкретного вида организма. В статье приведено большое число ссылок на web-сервисы компьютерных программ для дизайна праймеров. Кратко охарактеризованы некоторые базы данных, в которых накапливается информация о последовательностях хорошо зарекомендовавших себя праймеров. Цитированная литература составила более 240 источников. В данной работе рассматриваются программные комплексы, и отчасти некоторые алгоритмы, которые применяются для подбора праймеров. Основой любого современного программного комплекса, эффективного алгоритма является математическое описание в виде систем алгебраических, дифференциальных уравнений, интегрально-дифференциальных уравнений.

Ключевые слова:

ПЦР, праймер, температура отжига праймеров, температура плавления, олигонуклеотид, дизайн праймеров, компьютерная программа, алгоритм, база данных, банк данных

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