scholarly journals Retraction: Artifactual Palindrome and Mutations Resulting from the Stable Secondary Structure of Templates in Sanger Sequencing

2021 ◽  
Vol 6 (46) ◽  
pp. 13382-13382
Author(s):  
Zhaocheng Liu ◽  
Minxue Zheng ◽  
Zhaobang Liu
Keyword(s):  
Secondary Structure ◽  
Sanger Sequencing ◽  
Stable Secondary Structure

scholarly journals Sequence-specific polypeptoids: A diverse family of heteropolymers with stable secondary structure

1998 ◽  
Vol 95 (8) ◽  
pp. 4303-4308 ◽  
Author(s):  
K. Kirshenbaum ◽  
A. E. Barron ◽  
R. A. Goldsmith ◽  
P. Armand ◽  
E. K. Bradley ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Stable Secondary Structure

scholarly journals Capped mRNAs with Reduced Secondary Structure Can Function in Extracts from Poliovirus-Infected Cells

1982 ◽  
Vol 2 (12) ◽  
pp. 1633-1638 ◽  
Author(s):  
Nahum Sonenberg ◽  
Denise Guertin ◽  
Kevin A. W. Lee
Keyword(s):  
Secondary Structure ◽  
Mosaic Virus ◽  
Hela Cells ◽  
Alfalfa Mosaic Virus ◽  
Stable Secondary Structure ◽  
Ribosome Binding ◽  
Infected Cells

Extracts from poliovirus-infected HeLa cells were used to study ribosome binding of native and denatured reovirus mRNAs and translation of capped mRNAs with different degrees of secondary structure. Here, we demonstrate that ribosomes in extracts from poliovirus-infected cells could form initiation complexes with denatured reovirus mRNA, in contrast to their inability to bind native reovirus mRNA. Furthermore, the capped alfalfa mosaic virus 4 RNA, which is most probably devoid of stable secondary structure at its 5′ end, could be translated at much higher efficiency than could other capped mRNAs in extracts from poliovirus-infected cells.

scholarly journals Two Cases of Recessive Intellectual Disability Caused by NDST1 and METTL23 Variants

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1021
Author(s):  
Amjad Khan ◽  
Zhichao Miao ◽  
Muhammad Umair ◽  
Amir Ullah ◽  
Mohammad A. Alshabeeb ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Secondary Structure ◽  
Homology Modeling ◽  
Exome Sequencing ◽  
In Silico ◽  
Brain Function ◽  
Sanger Sequencing ◽  
Autosomal Recessive ◽  
Wild Type ◽  
Genetic Condition

Intellectual disability (ID) is a highly heterogeneous genetic condition with more than a thousand genes described so far. By exome sequencing of two consanguineous families presenting hallmark features of ID, we identified two homozygous variants in two genes previously associated with autosomal recessive ID: NDST1 (c.1966G>A; p.Asp656Asn) and METTL23 (c.310T>C; p.Phe104Leu). The segregation of the variants was validated by Sanger sequencing in all family members. In silico homology modeling of wild-type and mutated proteins revealed substantial changes in the secondary structure of both proteins, indicating a possible effect on function. The identification and validation of new pathogenic NDST1 and METTL23 variants in two cases of autosomal recessive ID further highlight the importance of these genes in proper brain function and development.

scholarly journals Mutation screening of the UBE3A gene in Chinese Han population with autism

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Xue Zhao ◽  
Ran Zhang ◽  
Shunying Yu
Keyword(s):  
Secondary Structure ◽  
Sample Size ◽  
Association Analysis ◽  
Sanger Sequencing ◽  
Healthy Controls ◽  
Control Groups ◽  
Chinese Han ◽  
Han Population ◽  
Coding Regions ◽  
And Control

Abstract Background 15q11–13 region is one of the most complex chromosomal regions in the human genome. UBE3A is an important candidate gene of autism spectrum disorder (ASD), which located at the 15q11–13 region and encodes ubiquitin-protein ligase E3A. Previous studies about UBE3A gene and ASD have shown inconsistent results and few studies were performed in Chinese population. This study aimed to detect the genetic mutations of UBE3A gene in Chinese Han population with ASD and analyze genetic association between these variants and ASD. Methods The samples consisted of 192 patients with autism according to the DSM-IV diagnostic criteria and 192 healthy controls. We searched for mutations at coding sequence (CDS) regions and their adjacent non-coding regions of UBE3A gene using the high resolution melting (HRM) and Sanger sequencing methods. We further increased sample size to validate the detected variants using HRM and conducted association analysis between case and control groups. Results A known single nucleotide polymorphism (T > C, rs150331504) located at the CDS4 and a known 5 bp insertion/deletion variation (AACTC+/−, rs71127053) located at the intron region of the upstream 288 bp of the CDS2 of UBE3A gene were detected using Sanger sequencing method. The ASD samples of case group were 391 for rs71127053, 384 for rs150331504 and 384 healthy controls, which were used to make an association analysis. The results of association analysis suggested that there were no significant difference about the allele and genotype frequencies of rs71127053 and rs150331504 between case and control groups after extending the sample size. Besides, rs150331504 is a synonymous mutation and we compared the secondary structure and minimum free energy (MFE) of mRNA harboring the allele T or C of rs150331504 using RNAfold software. We found that the centroid secondary structure apparently differs along with the polymorphisms of rs150331504 T > C, the results suggested that this variant might change the secondary structure of mRNA of UBE3A gene. We did not detect mutations in other coding regions of UBE3A gene. Conclusions These findings showed that UBE3A gene might not be a major disease gene in Chinese ASD cases.

Capped mRNAs with Reduced Secondary Structure Can Function in Extracts from Poliovirus-Infected Cells

1982 ◽  
Vol 2 (12) ◽  
pp. 1633-1638
Author(s):  
Nahum Sonenberg ◽  
Denise Guertin ◽  
Kevin A. W. Lee
Keyword(s):  
Secondary Structure ◽  
Mosaic Virus ◽  
Hela Cells ◽  
Alfalfa Mosaic Virus ◽  
Stable Secondary Structure ◽  
Ribosome Binding ◽  
Infected Cells

Extracts from poliovirus-infected HeLa cells were used to study ribosome binding of native and denatured reovirus mRNAs and translation of capped mRNAs with different degrees of secondary structure. Here, we demonstrate that ribosomes in extracts from poliovirus-infected cells could form initiation complexes with denatured reovirus mRNA, in contrast to their inability to bind native reovirus mRNA. Furthermore, the capped alfalfa mosaic virus 4 RNA, which is most probably devoid of stable secondary structure at its 5′ end, could be translated at much higher efficiency than could other capped mRNAs in extracts from poliovirus-infected cells.

scholarly journals A mutation allowing an mRNA secondary structure diminishes translation of Saccharomyces cerevisiae iso-1-cytochrome c.

1985 ◽  
Vol 5 (8) ◽  
pp. 1839-1846 ◽  
Author(s):  
S B Baim ◽  
D F Pietras ◽  
D C Eustice ◽  
F Sherman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Secondary Structure ◽  
Cytochrome C ◽  
Mrna Secondary Structure ◽  
Wild Type ◽  
Stable Secondary Structure ◽  
Yeast Saccharomyces Cerevisiae ◽  
Wild Type Level ◽  
Altered Protein

The CYC1-239-O mutation in the yeast Saccharomyces cerevisiae produces a -His-Leu- replacement of the normal -Ala-Gly- sequence at amino acid positions 5 and 6, which lie within a dispensable region of iso-1-cytochrome c; this mutation can accommodate the formation of a hairpin structure at the corresponding site in the mRNA. The amount of the altered protein was diminished to 20% of the wild-type level, whereas the amount of the mRNA remained normal. However, in contrast to the normal CYC1+ mRNA that is associated mainly with four to seven ribosomes, the bulk of the CYC1-239-O mRNA is associated with one to four ribosomes. These results suggest that the stable secondary structure within the translated region of the CYC1 mRNA diminishes translation by inhibiting elongation.

scholarly journals Absence of a Stable Secondary Structure Is Not a Limitation for Photoswitchable Inhibitors of β-Arrestin/β-Adaptin 2 Protein-Protein Interaction

2015 ◽  
Vol 22 (1) ◽  
pp. 31-37 ◽  
Author(s):  
Andrés Martín-Quirós ◽  
Laura Nevola ◽  
Kay Eckelt ◽  
Sergio Madurga ◽  
Pau Gorostiza ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Protein Interaction ◽  
Stable Secondary Structure ◽  
Protein Protein Interaction
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