alexa Amplicon Secondary Structure Formation and Elongation during the Process of Sequencing | OMICS International | Abstract
ISSN: 0974-276X

Journal of Proteomics & Bioinformatics
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Research Article

Amplicon Secondary Structure Formation and Elongation during the Process of Sequencing

Elham Davoudi-Dehaghani1,2, Sirous Zeinali2,3*, Nejpb Mahdieh3,4, Atefeh Shirkavand5 and Hamideh Bagherian3

1Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran

2Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran

3Medical Genetics Lab, Kawsar Human Genetics Research Center, No. 41 Majlesi St., Vali Asr St., Tehran, Iran

4Growth and Development Research Center, Tehran University of Medical Sciences, Iran

5Department of Biology, Faculty of Sciences, Razi University, Kermanshah, Iran

*Corresponding Author:
Sirous Zeinali
Department of Molecular Medicine
Biotechnology Research Center, Pasteur Institute of Iran
Pasteur St., Tehran, Iran, Postal Code: 1595645513
Tel: 989121372040
Fax: 982188939140
E-mail: [email protected]

Received Date: July 07, 2012; Accepted Date: August 23, 2012; Published Date: August 25, 2012

Citation: Davoudi-Dehaghani E, Zeinali S, Mahdieh N, Shirkavand A, Bagherian H (2012) Amplicon Secondary Structure Formation and Elongation during the Process of Sequencing. J Proteomics Bioinform 5: 204-207. doi: 10.4172/jpb.1000236

Copyright: © 2012 Davoudi-Dehaghani E, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Understanding the exact mechanism involved in different molecular processes such as replication, transcription and recombination, as well as improving different applications of single stranded DNA, requires increasing of our knowledge regarding different properties of single stranded DNA secondary structure. Despite some efforts in this field, our understanding of the exact mechanism is still very limited. During our investigation on hearing loss, we encountered an unusual sequencing result for exon 5 of TMC1 gene in a patient suspected of having mutation in this gene. BLASTN was used to find out the origin of extra segment seen in the sequencing result. The Mfold web server was used to investigate if secondary structure formation of the amplicon during sequencing can be the cause of this elongation. Our investigation on the DNA sequence revealed that the extra sequence was an inverted repeat of the first 270 nucleotides inserted just after the sequence of the reverse primer. To investigate the origin of this repeat, we run the original PCR product on an agarose gel and no size increase was observed. This suggested that the inverted repeat has been formed during sequencing as a result of secondary structure formation and subsequent extension during sequencing. Despite of the above the Mfold web server did not predict this hypothetical structure. However, when we submitted RNA equivalent for this sequence, the above server suggested formation of several secondary structures in which one of them was very similar to the one which had been predicted. Inability of the Mfold to predict DNA secondary structure for our sequence may lie in its thermodynamic parameters. This finding, during DNA sequencing, suggests that single stranded DNA elongation in the presence of dNTPs and DNA polymerase can be used as a new way for studying the secondary structure in the single stranded DNA.

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