What is an LNA oligo?

Abstract. Locked nucleic acid (LNA) is the term for oligonucleotides that contain one or more nucleotide building blocks in which an extra methylene bridge fixes the ribose moiety either in the C3′-endo (beta-D-LNA) or C2′-endo (alpha-L-LNA) conformation.

What are oligo probes?

Definition. Oligonucleotide probes are short stretches of single-stranded DNA or RNA used to detect the presence of complementary nucleic acid sequences (target sequences) by hybridization.

What are locked nucleic acid probes?

Locked nucleic acids are modified RNA monomers. The “locked” part of their name comes from a methylene bridge bond linking the 2′ oxygen to the 4′ carbon of the RNA pentose ring (Figure 1). The bridge bond fixes the pentose ring in the 3′-endo conformation.

What are the two types of DNA probes?

Gene probes can be produced in several ways and fall broadly into three types: gene-specific probes, oligonucleotide probes and polymorphic probes. Gene-specific probes are produced from specific mRNA by the enzyme reverse transcriptase, which synthesizes a complementary DNA copy (cDNA) from mRNA.

What is LNA base?

A locked nucleic acid (LNA), also known as bridged nucleic acid (BNA), and often referred to as inaccessible RNA, is a modified RNA nucleotide in which the ribose moiety is modified with an extra bridge connecting the 2′ oxygen and 4′ carbon.

How are oligonucleotide probes produced?

Oligonucleotide probes are often prepared with covalent attachment of a reporter molecule (eg, a fluorescent dye) or affinity labels that allow them to be attached to solid supports. Probes used in homogeneous (real-time) PCR are usually oligonucleotides with a fluorescent label.

What is this oligonucleotide probe specifically called as?

Sequence-Specific Oligonucleotide Probe (SSOP) Typing. DNA from a panel of samples (96- or 384-well format) are PCR amplified using locus-specific primers. The PCR products are denatured and blotted on a series of nylon membranes and probed with a panel of allele/group-specific probes.

How many nucleotides are in a probe?

In molecular biology, a hybridization probe (HP) is a fragment of DNA or RNA of usually 15–10000 nucleotide long which can be radioactively or fluorescently labeled.

How do locked nucleic acid (LNA) DNA probes differ from oligonucleotide DNA probes?

Oligonucleotide probes containing locked nucleic acid (LNA) hybridize to complementary single-stranded target DNA sequences with an increased affinity compared to oligonucleotide DNA probes.

What is the optimal length of LNA substituted labeled probes?

Optimal length of LNA substituted labeled probes: 15-18 nucleotides (Please note that these are 5-8 bases shorter than the corresponding DNA probes). Maintain T m with LNA substitutions to match the T m of the corresponding longer DNA probes.

What is the composition of LNA in oligos?

LNA Oligos are composed of either 100% Lock Nucleic Acid (LNA) bases or a mixture of LNA and DNA bases. However, only oliognulceotides that are between 7 and 15 mers in length can be made up of 100% LNA.

What is a locked nucleic acid oligonucleotide used for?

Locked nucleic acid oligonucleotides are useful in template switching oligo designs and for strengthening target oligo binding in challenges sequence regions, such as AT-rich areas. As with locked nucleic acid qPCR probes, hybridization T m can be manipulated by the number of locked nucleic acid bases incorporated.