MAAP: a versatile and universal tool for genome analysis

Area of Science:

• Molecular Biology
• Genetics
• Biotechnology

Background:

• Arbitrary primers are used to generate DNA fingerprints from anonymous genomes.
• Multiple Arbitrary Amplicon Profiling (MAAP) is a technique for DNA fingerprinting and mapping.
• MAAP markers can be converted into Sequence-Characterized Amplified Regions (SCARs).

Purpose of the Study:

• To describe the MAAP technique and its applications in DNA fingerprinting and mapping.
• To explore the tailoring of MAAP profiles for monomorphic and polymorphic products.
• To investigate primer-template interactions and amplification product formation in MAAP.

Main Methods:

• Utilizing oligonucleotide primers of arbitrary sequence (> or = 5 nt) for DNA amplification.
• Employing multiple endonuclease digestion or mini-hairpin primers to enhance polymorphism detection.
• Comparing theoretical and actual amplification product numbers with varying primer and template characteristics.

Main Results:

• MAAP generates characteristic DNA fingerprints from anonymous genomes.
• MAAP profiles can be adjusted for monomorphic and polymorphic products.
• Significant deviations from theoretical amplification product counts were observed, indicating complex primer-template interactions.
• Primer annealing and extension are primarily directed by the 8 nt 3'-terminal domain, requiring 5-6 nt homology.

Conclusions:

• MAAP is a versatile tool for general DNA fingerprinting and mapping applications.
• Primer-template interactions in MAAP are complex, with extensive mismatching possible.
• The 3'-terminal primer domain plays a critical role in MAAP specificity and extension.