# What are degenerate primers used for?

What are degenerate primers used for? A degenerate primer is mixture of primers that has substitution of different bases sequence (they are similar not same). They are usefull if need to amplify a gene from

## What are degenerate primers used for?

A degenerate primer is mixture of primers that has substitution of different bases sequence (they are similar not same). They are usefull if need to amplify a gene from similar organism. So it possible amplify different sequence which represent different protein sequence.

## What is degenerate base?

Degenerate base means more than one base possibility at a particular position, this is usually the case when a DNA sequence is derived from amino acid sequence with codon based sequence.

What is a genetic primer?

A primer is a short nucleic acid sequence that provides a starting point for DNA synthesis. In living organisms, primers are short strands of RNA. The primers are removed before DNA replication is complete, and the gaps in the sequence are filled in with DNA by DNA polymerases.

How many bases should a degenerate primer match?

2) Target an area approximately 200-500 base pairs in length for optimal PCR amplification. 3) Position forward and reverse primers in more conserved regions – the less degenerate, the further apart these can be. 4) Include between 6 and 7 amino acids in the primers, equating to ~15-20 base pairs.

### How do you calculate degeneracy of a primer?

To compute degeneracy, multiply the degeneracies of each of the contributing AA. For example, if you have a primer which matches the AA sequence D E W V P, this would correspond to a degeneracy of 2 * 2 * 1 * 4 * 4 = 64.

### What does K mean in a primer?

K = G or T. M = A or C. B = C or G or T. D = A or G or T. H = A or C or T.

What are universal bases?

Since 1990s, a variety of compounds known as universal bases, including hypoxanthine, nitroazoles, isocarbostyril analogues, azole carboxamides and aromatic triazole analogues have been developed and employed in degenerate PCR primers, microarray probes, ligation and triplexes.

Which is the best definition of a degenerate primer?

Definition of degenerate primers A degenerate primer is defined as: “A mix of oligonucleotide sequences in which some positions contain a number of possible bases, giving a population of primers with similar sequences that cover all possible nucleotide combinations for a given protein sequence” (Iserte 2013).

#### How can I make my own degenerate primer?

To design your own set of degenerate primers, follow some basic guidelines: 1) Align multiple amino acid sequences using free online software such as EBIClustalO. 2) Target an area approximately 200-500 base pairs in length for optimal PCR amplification.

#### What is the medical definition of a degenerate?

Medical Definition of degenerate. (Entry 1 of 3) 1a : having declined (as in nature, character, structure, or function) from an ancestral or former state especially : having deteriorated progressively (as in the process of evolution) especially through loss of structure and function. b : having sunk to a lower and usually corrupt and vicious state.

How long should a degenerate primer be for PCR?

Degenerate primers are designed to match an amino acid sequence. A DNA sequence and its corresponding amino acid sequence would be For PCR, you need two conserved regions for locating the forward and reverse primers. These should each be at least 5 AA long (preferably 6 or 7 AA long) and fairly close together.