![]() PCR-based GW can be employed when it is possible to select at least one sequence-specific primer (SSP) that anneals to the DNA of interest. The first applications of PCR as an alternative to hybridization were reported in the late 1980s 1. PCR-based methods are currently predominant among GW techniques because they are rapid and their use avoids construction of large libraries. use of a sequenced fragment as a probe for hybridization). The initial GW technology also utilized libraries and screening (e.g. Before the advent of next-generation sequencing (NGS), capturing of unknown DNA was based on GW or screening of genomic libraries. Genome walking (GW) refers to a collection of methods that capture unknown (unsequenced) genomic regions that are contiguous with and adjacent to a known DNA sequence. In our experience, PST-PCR had higher throughput and greater convenience in comparison to other GW methods. Using PST-PCR, previously unknown regions (the promoter and intron 1) of the VRN1 gene of Timothy-grass ( Phleum pratense L.) were captured for sequencing. In contrast to traditional genome walking methods, PST-PCR is rapid (two to three hours to produce GW fragments) as it uses only one or two PCR rounds. Changing the annealing temperature to switch the amplification phases at a defined cycle controls the balance between sensitivity and specificity. The thermal cycling profile has a linear amplification phase and an exponential amplification phase differing in annealing temperature. Upstream of the palindromes there is a degenerate sequence (8–12 nucleotides long) defined adapters are present at the 5′-termini. The PST primers have palindromic sequences at their 3′-ends. The walking primers (PST primers) match palindromic sequences (PST sites) that are randomly distributed in natural DNA. PST-PCR is based on a distinctive design of walking primers and special thermal cycling conditions. A novel PCR-based method, palindromic sequence-targeted PCR (PST-PCR), was developed. ![]() The proposed method has been tested using the bacterial (3891 KB bases) and human chromosomal sequences (Chr-18: 74366 kb and Chr-Y: 25554 kb) and the computation time for finding the palindromic sequences is in milli seconds.Ĭomplimentarity Even-numbered Genome Palindrome.Genome walking (GW) refers to the capture and sequencing of unknown regions in a long DNA molecule that are adjacent to a region with a known sequence. The new method uses less memory and thereby it increases the overall speed and efficiency. Thus, a new method has been developed using dynamic programming to fetch the palindromic nucleic acid sequences. A typical nucleotide palindromic sequence would be TATA (5' to 3') and its complimentary sequence from 3' to 5' would be ATAT. For example, both the strands i.e the strand going from 5' to 3' and its complementary strand from 3' to 5' must be complementary. For a nucleotide sequence to be considered as a palindrome, its complementary strand must read the same in the opposite direction. Among these sequences, palindromic nucleic acid sequences are one such type that have been studied in detail and found to influence a wide variety of genomic characteristics. ![]() Various types of sequences in the human genome are known to play important roles in different aspects of genomic functioning.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |