DNA models of trinucleotide frameshift deletions: the formation of loops and bulges at the primer–template junction

Abstract

Although mechanisms of single-nucleotide residue deletion have been investigated, processes involved in the loss of longer nucleotide sequences during DNA replication are poorly understood. Previous reports have shown that in vitro replication of a 3′-TGC TGC template sequence can result in the deletion of one 3′-TGC. We have used low-energy circular dichroism (CD) and fluorescence spectroscopy to investigate the conformations and stabilities of DNA models of the replication intermediates that may be implicated in this frameshift. Pyrrolocytosine or 2-aminopurine residues, site-specifically substituted for cytosine or adenine in the vicinity of extruded base sequences, were used as spectroscopic probes to examine local DNA conformations. An equilibrium mixture of four hybridization conformations was observed when template bases looped-out as a bulge, i.e. a structure flanked on both sides by duplex DNA. In contrast, a single-loop structure with an unusual unstacked DNA conformation at its downstream edge was observed when the extruded bases were positioned at the primer–template junction, showing that misalignments can be modified by neighboring DNA secondary structure. These results must be taken into account in considering the genetic and biochemical mechanisms of frameshift mutagenesis in polymerase-driven DNA replication.

Spectroscopic studies of position-specific DNA “breathing” fluctuations at replication forks and primer-template junctions

“…We have also recently used low energy CD and fluorescence measurements of a cytosine derivative, pyrrolocystosine, to characterize the formation of a 3Ј-TGC loop in oligonucleotides that model a 3-nt frameshift deletion (24).…”

A Polymerase – Tautomeric Model for Targeted Frameshift Mutations: Deletions Formation during Error-prone or SOS Replication of Double-stranded DNA Containing cis-syn Cyclobutane Thymine Dimers

“…The Streisinger model [41] is now the best-grounded model of frameshift mutations [42][43][44] suggesting gaps and DNA strand slippage during synthesis as the causes of mutations. It is shown that deletions formation due to the appearance of template bases looped-out as a bulge [44].…”

“…It is shown that deletions formation due to the appearance of template bases looped-out as a bulge [44]. The second model [45,46] states that certain ( 1)-frameshifts are initiated by a nucleotide misincorporation.…”

A Polymerase Tautomeric Model for Radiation Induced Bystander Effects: A Model for Untargeted Base Substitution Mutagenesis during Error Prone and SOS Replication of Double Stranded DNA Containing Thymine and Adenine in Rare Tautomeric Forms

“…Specialized DNA polymerases may make errors that give rise to mutations [71,72]. In addition, the translesion synthesis can be conducted using constitutive DNA polymerases [148][149][150].…”

“…It is not clear why some cyclobutane pyrimidine dimers do not cause mutations, while others, seemingly the exact cause of transition or transversion mutations, or the just the same cyclobutane pyrimidine dimers cause frame shift mutations. The mechanism of formation the targeted frame shift mutations does not clear [69][70][71][72][73]. Even the mechanisms of formation of the targeted base substitution mutations are not entirely clear.…”