A novel method to quantify base substitution mutations at the 10 −6 per bp level in DNA samples

2017 ◽  
Vol 403 ◽  
pp. 152-158 ◽  
Author(s):  
Satoshi Yamashita ◽  
Naoko Iida ◽  
Hideyuki Takeshima ◽  
Naoko Hattori ◽  
Masahiro Maeda ◽  
...  
Keyword(s):  
Base Substitution ◽  
Novel Method ◽  
Substitution Mutations

scholarly journals The effect of attachment site mutations on strand exchange in bacteriophage lambda site-specific recombination.

Genetics ◽  
1989 ◽  
Vol 122 (4) ◽  
pp. 727-736
Author(s):  
C E Bauer ◽  
J F Gardner ◽  
R I Gumport ◽  
R A Weisberg
Keyword(s):  
Attachment Site ◽  
Strand Exchange ◽  
Segregation Pattern ◽  
Base Substitution ◽  
Base Pairs ◽  
Multiple Mutation ◽  
Attachment Sites ◽  
Dna Strands ◽  
Substitution Mutations ◽  
Overlap Region

Abstract Recombination of phage lambda attachment sites occurs by sequential exchange of the DNA strands at two specific locations. The first exchange produces a Holliday structure, and the second resolves it to recombinant products. Heterology for base substitution mutations in the region between the two strand exchange points (the overlap region) reduces recombination; some mutations inhibit the accumulation of Holliday structures, others inhibit their resolution to recombinant products. To see if heterology also alters the location of the strand exchange points, we determined the segregation pattern of three single and one multiple base pair substitution mutations of the overlap region in crosses with wild type sites. The mutations are known to differ in the severity of their recombination defect and in the stage of strand exchange they affect. The three single mutations behaved similarly: each segregated into both products of recombination, and the two products of a single crossover were frequently nonreciprocal in the overlap region. In contrast, the multiple mutation preferentially segregated into one of the two recombinant products, and the two products of a single crossover appeared to be fully reciprocal. The simplest explanation of the segregation pattern of the single mutations is that strand exchanges occur at the normal locations to produce recombinants with mismatched base pairs that are frequently repaired. The segregation pattern of the multiple mutation is consistent with the view that both strand exchanges usually occur to one side of the mutant site. We suggest that the segregation pattern of a particular mutation is determined by which stage of strand exchange it inhibits and by the severity of the inhibition.

Study on the expression of specific chimeric-orfs of C type cytoplasmic male sterile in maize

2013 ◽  
Vol 61 (1-4) ◽  
pp. 25-36 ◽  
Author(s):  
Jiyue Wang ◽  
Lihua Zeng ◽  
Shengqing Wang ◽  
Jing Wang ◽  
Yanli Lu ◽  
...  
Keyword(s):  
Base Substitution ◽  
Pcr Analysis ◽  
Male Sterile ◽  
Maintainer Line ◽  
Cytoplasmic Male Sterile ◽  
Real Time Quantitative Pcr ◽  
Substitution Mutations ◽  
Membrane Spanning ◽  
Insertion Mutations ◽  
Online Software

In the present study, a mutated chimericorf364, namedorf366-c, was identified in a maize C type cytoplasmic male sterile line (CMS-C) by PCR and RT-PCR. Four base pair adjacent base substitution mutations (CAAA to TTTT) and eight bp insertion mutations were found inorf366-ccompared withorf364. ORF366-C was predicted to contain one membrane-spanning domain using TMHMM online software. Real-time quantitative PCR analysis showed thatorf366-cwas upregulated in the CMS-C line in comparison to its maintainer line at the uninucleate stage. The protokaryotic protein expression oforf366-cinEscherichia colishowed that ORF366-C could be a cytotoxic protein. All the results indicated thatorf366-cmay be associated with maize CMS-C.

A MAJOR ROLE FOR BACTERIOPHAGE T4 DNA POLYMERASE IN FRAMESHIFT MUTAGENESIS

Genetics ◽  
1983 ◽  
Vol 103 (3) ◽  
pp. 353-366
Author(s):  
Lynn S Ripley ◽  
Nadja B Shoemaker
Keyword(s):  
Dna Polymerase ◽  
Dna Sequences ◽  
Frameshift Mutation ◽  
Bacteriophage T4 ◽  
Base Substitution ◽  
Temperature Sensitive ◽  
Polymerase Gene ◽  
Frameshift Mutagenesis ◽  
Substitution Mutations ◽  
Polymerase Mutants

ABSTRACT T4 DNA polymerase strongly influences the frequency and specificity of frameshift mutagenesis. Fifteen of 19 temperature-sensitive alleles of the DNA polymerase gene substantially influenced the reversion frequencies of frameshift mutations measured in the T4 rII genes. Most polymerase mutants increased frameshift frequencies, but a few alleles (previously noted as antimutators for base substitution mutations) decreased the frequencies of certain frameshifts while increasing the frequencies of others. The various patterns of enhanced or decreased frameshift mutation frequencies suggest that T4 DNA polymerase is likely to play a variety of roles in the metabolic events leading to frameshift mutation. A detailed genetic study of the specificity of the mutator properties of three DNA polymerase alleles (tsL56, tsL98 and tsL88) demonstrated that each produces a distinctive frameshift spectrum. Differences in frameshift frequencies at similar DNA sequences within the rII genes, the influence of mutant polymerase alleles on these frequencies, and the presence or absence of the dinucleotide sequence associated with initiation of Okazaki pieces at the frameshift site has led us to suggest that the discontinuities associated with discontinuous DNA replication may contribute to spontaneous frameshift mutation frequencies in T4.

scholarly journals Template-directed base pairing of 2-chloro-2'-deoxyadenosine catalyzed by AMV reverse transcriptase.

1998 ◽  
Vol 45 (2) ◽  
pp. 587-593 ◽  
Author(s):  
A M Bukowska-Maciejewska ◽  
J T Kuśmierek
Keyword(s):  
Binding Energy ◽  
Reverse Transcriptase ◽  
Kinetic Parameters ◽  
Active Site ◽  
Base Substitution ◽  
Base Pairing ◽  
Lymphoid Malignancies ◽  
Order Of Magnitude ◽  
The Difference ◽  
Substitution Mutations

2-Chloro-2'-deoxyadenine (2CldA) is used for treatment of several lymphoid malignancies. Since this drug is incorporated into DNA, we have undertaken studies on base pairing of 2-chloroadenine (2ClA). 2CldA phosphoramidite was synthesized and used for preparation of 25-mer templates with 2ClA located at site 21 from the 3'-end. Kinetic parameters (Km and Vmax) for the incorporation of deoxynucleoside-5'-triphosphates by AMV reverse transcriptase opposite the 2ClA template, as well as for the extension of 2ClA.T pair, were determined. The efficiency (Vmax/Km) of incorporation of dGTP, dCTP, and dATP opposite 2ClA is at least one order of magnitude lower than opposite unmodified A. The efficiency of incorporation of dTTP opposite 2ClA is about 30-fold lower than opposite A and extension of 2ClA.T pair is 3-fold lower than of A.T pair. From the analysis of the parameters of dTTP incorporation we conclude that formation of 2ClA.T pair is thermodynamically, but not kinetically controlled. The difference in binding energy (deltadeltaG) between 2ClA.T and A.T pairs in the environment of the polymerase active site is 2 kcal/mol. Our results indicate that the presence of 2ClA in DNA slows down replication, but does not lead to base-substitution mutations.

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