The different mobility of complementary strands depends on the proportion AC/GT

Area of Science:

• Molecular Biology
• Genetics

Background:

• Electrophoretic mobility of DNA on denaturing polyacrylamide gels is influenced by sequence composition.
• Single-stranded DNA (ssDNA) migration patterns can vary based on base content.

Purpose of the Study:

• To investigate the impact of base composition on the electrophoretic mobility of DNA fragments.
• To determine the relationship between DNA strand mobility differences and base composition in short tandem repeat (STR) loci.

Main Methods:

• Analyzing electrophoretic mobility of complementary DNA strands from polymerase chain reaction (PCR) products across 13 STR loci.
• Correlating mobility differences between strands (MD) with base composition, specifically the adenine-cytosine (AC) to guanine-thymine (GT) ratio.

Main Results:

• Complementary strands of PCR-amplified STR alleles consistently exhibited different mobilities.
• Mobility differences (MD) were found to be proportional to the AC/GT ratio in the adenine-cytosine-rich strand.
• This relationship held true even for end-polished DNA fragments.

Conclusions:

• The proportion of adenine-cytosine to guanine-thymine bases (AC/GT ratio) significantly affects ssDNA electrophoretic mobility on denaturing gels.
• In PCR-based STR typing, differential mobility of complementary strands can lead to misidentification of alleles.
• Standardized labeling of the same DNA strand and consistent use of allelic ladder markers are crucial for accurate STR analysis.