PCR-i praimerite kvaliteedimudeli integreerimine Primer3-e disainimetoodikasse
Date
2015
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Abstract
Polümeraasi ahelreaktsiooni (PCR) edukas toimumine sõltub praimerite lähtejärjestusega seondumise stabiilsusest ja spetsiifilisusest. Praimeridisaini protsessis tuleb seega jälgida, et disainitaval praimeril ei oleks uuritavas genoomis palju mittespetsiifilisi seondumiskohti. Käesoleva töö raames koostati mudel, mis hindaks praimeri mittetöötamise tõenäosust, lähtudes selle potentsiaalsete seondumiskohtade arvust uuritavas genoomis. Seejärel implementeeriti maskeerimisalgoritm, mis kasutaks loodud mudelit lähtejärjestusest ebasobivate praimeri seondumiskohtade maskeerimiseks. Kirjeldatud algoritm integreeriti praimeridisaini programmi Primer3. Maskeerimisfunktsiooni kasutamine praimeridisaini kontekstis vähendas disainitavate praimerite keskmist mittetöötamise tõenäosust enam kui kaks korda.
The success rate of polymerase chain reaction (PCR) is highly dependent on the binding specificity and stability of the primers currently in use. Primers with more binding sites tend to have higher failure rates. In the current study a model for predicting primer failure rates based on the number of their binding sites was fit. Next, the model was used in an algorithm which would mask the regions of a given input sequence that are unsuitable for primer design. The described algorithm was then integrated to Primer3 software where it was tested in the context of primer design. Our results show that by using the masking functionality one can reduce the primer failure rate more than two times.
The success rate of polymerase chain reaction (PCR) is highly dependent on the binding specificity and stability of the primers currently in use. Primers with more binding sites tend to have higher failure rates. In the current study a model for predicting primer failure rates based on the number of their binding sites was fit. Next, the model was used in an algorithm which would mask the regions of a given input sequence that are unsuitable for primer design. The described algorithm was then integrated to Primer3 software where it was tested in the context of primer design. Our results show that by using the masking functionality one can reduce the primer failure rate more than two times.