Sequencing and Alignment of DENV-2 E Protein

For the DENV-2 strains used in this study, E protein was amplified using SuperScript™ III One-Step RT-PCR System with Platinum™ Taq DNA Polymerase (Thermo Fisher Scientific, Waltham, MA, USA), according to the manufacturer’s instructions and previously reported primer sequences and protocols [54 (link)]. Amplicons were sequenced using the Sanger method (Macrogen Inc., Seoul, Korea). Sequences were assembled and edited with the Lasergene software, and a BLAST search was performed using the online platform Dengue Virus Typing Tool v.3.82. Subsequently, reference sequences retrieved from NCBI and the sequences under study were aligned with CLUSTAL W using MEGA v7. To determine nucleotide differences between strains, 1308 nucleotides corresponding to 435 amino acids of the E protein of the DENV-2 New Guinea C (AB609589) and DENV-2 16,681 (NC001474) strains were compared with those of the strains assessed here (DENV-2/NG and DENV-2/16681, respectively).

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Monsalve-Escudero L.M., Loaiza-Cano V., Zapata-Cardona M.I., Quintero-Gil D.C., Hernández-Mira E., Pájaro-González Y., Oliveros-Díaz A.F., Diaz-Castillo F., Quiñones W., Robledo S, & Martinez-Gutierrez M. (2021). The Antiviral and Virucidal Activities of Voacangine and Structural Analogs Extracted from Tabernaemontana cymosa Depend on the Dengue Virus Strain. Plants, 10(7), 1280.

Publication 2021

SuperScript™ III One-Step RT-PCR System Platinum™ Taq DNA Polymerase Sanger method

Amino acids Dengue virus Dna polymerase iii Nucleotides Platinum Primer Protein Protein c Rt pcr Strains

Corresponding Organization : Universidad Cooperativa de Colombia

Other organizations : University of Cartagena, University of Atlántico, Universidad de Antioquia

Top 5 similar protocols

Variable analysis

independent variables

Primer sequences and protocols used for E protein amplification

dependent variables

E protein sequences of DENV-2 strains

control variables

Manufacturer's instructions for SuperScript™ III One-Step RT-PCR System with Platinum™ Taq DNA Polymerase
Previously reported primer sequences and protocols [54]

controls

Positive control: DENV-2 New Guinea C (AB609589) strain
Negative control: DENV-2 16,681 (NC001474) strain

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