Analyzing the Relationship between Single Base Flipping and Strand Slippage near DNA Duplex Termini

Insertion–deletion (indel) mutations are caused by strand slippage between pairing primer and template strands during nucleic acid strand extension. A possible causative factor for such strand slippage is base flipping in the primer strand or template strand, for insertion or deletion mutations, respectively. A simple mechanistic description is that the “hole” in the nucleic acid duplex left behind by a flipping base is occupied by a neighboring base on the same strand, resulting in slippage with respect to its paired strand. The extent of single base flipping required for occupation of its former place in the double helix by a neighboring base is not fully understood. The present study uses restrained molecular dynamics (MD) simulations along a pseudohedihedral base flipping parameter to construct two-dimensional free energy profiles along base flipping and strand slippage geometric parameters. These profiles, generated for both cytosine and guanine single base flipping in a short repetitive indel mutation hot-spot DNA sequence, illustrate the extent of single base flipping that can allow strand slippage by one base position. Relatively minor base flipping into both the major and minor grooves can result in strand slippage. Deconstruction of the collective variable strand slippage geometric parameter into its component distances illustrates the details of how strand slippage can accompany base flipping. The trans Watson–Crick:sugar edge interaction that stabilizes cytosine flipping in this hot-spot sequence is also characterized energetically. The impact of these results on understanding sequence dependence of indel errors in nucleic acid strand extension is discussed, along with a suggestion for future studies that can generalize the present findings to all nearest-neighbor sequence contexts

Analyzing the Relationship between Single Base Flipping and Strand Slippage near DNA Duplex Termini

Insertion–deletion (indel) mutations are caused by strand slippage between pairing primer and template strands during nucleic acid strand extension. A possible causative factor for such strand slippage is base flipping in the primer strand or template strand, for insertion or deletion mutations, respectively. A simple mechanistic description is that the “hole” in the nucleic acid duplex left behind by a flipping base is occupied by a neighboring base on the same strand, resulting in slippage with respect to its paired strand. The extent of single base flipping required for occupation of its former place in the double helix by a neighboring base is not fully understood. The present study uses restrained molecular dynamics (MD) simulations along a pseudohedihedral base flipping parameter to construct two-dimensional free energy profiles along base flipping and strand slippage geometric parameters. These profiles, generated for both cytosine and guanine single base flipping in a short repetitive indel mutation hot-spot DNA sequence, illustrate the extent of single base flipping that can allow strand slippage by one base position. Relatively minor base flipping into both the major and minor grooves can result in strand slippage. Deconstruction of the collective variable strand slippage geometric parameter into its component distances illustrates the details of how strand slippage can accompany base flipping. The trans Watson–Crick:sugar edge interaction that stabilizes cytosine flipping in this hot-spot sequence is also characterized energetically. The impact of these results on understanding sequence dependence of indel errors in nucleic acid strand extension is discussed, along with a suggestion for future studies that can generalize the present findings to all nearest-neighbor sequence contexts

Partial Base Flipping Is Sufficient for Strand Slippage near DNA Duplex Termini

Strand slippage is a structural mechanism by which insertion–deletion (indel) mutations are introduced during replication by polymerases. Three-dimensional atomic-resolution structural pathways are still not known for the decades-old template slippage description. The dynamic nature of the process and the higher energy intermediates involved increase the difficulty of studying these processes experimentally. In the present study, restrained and unrestrained molecular dynamics simulations, carried out using multiple nucleic acid force fields, are used to demonstrate that partial base-flipping can be sufficient for strand slippage at DNA duplex termini. Such strand slippage can occur in either strand, i.e. near either the 3′ or the 5′ terminus of a DNA strand, which suggests that similar structural flipping mechanisms can cause both primer and template slippage. In the repetitive mutation hot-spot sequence studied, non-canonical base-pairing with exposed DNA groove atoms of a neighboring G:C base-pair stabilizes a partially flipped state of the cytosine. For its base-pair partner guanine, a similar partially flipped metastable intermediate was not detected, and the propensity for sustained slippage was also found to be lower. This illustrates that a relatively small metastable DNA structural distortion in polymerase active sites could allow single base insertion or deletion mutations to occur, and stringent DNA groove molecular recognition may be required to maintain intrinsic DNA polymerase fidelity. The implications of a close relationship between base-pair dissociation, base unstacking, and strand slippage are discussed in the context of sequence dependence of indel mutations

Partial Base Flipping Is Sufficient for Strand Slippage near DNA Duplex Termini

Strand slippage is a structural mechanism by which insertion–deletion (indel) mutations are introduced during replication by polymerases. Three-dimensional atomic-resolution structural pathways are still not known for the decades-old template slippage description. The dynamic nature of the process and the higher energy intermediates involved increase the difficulty of studying these processes experimentally. In the present study, restrained and unrestrained molecular dynamics simulations, carried out using multiple nucleic acid force fields, are used to demonstrate that partial base-flipping can be sufficient for strand slippage at DNA duplex termini. Such strand slippage can occur in either strand, i.e. near either the 3′ or the 5′ terminus of a DNA strand, which suggests that similar structural flipping mechanisms can cause both primer and template slippage. In the repetitive mutation hot-spot sequence studied, non-canonical base-pairing with exposed DNA groove atoms of a neighboring G:C base-pair stabilizes a partially flipped state of the cytosine. For its base-pair partner guanine, a similar partially flipped metastable intermediate was not detected, and the propensity for sustained slippage was also found to be lower. This illustrates that a relatively small metastable DNA structural distortion in polymerase active sites could allow single base insertion or deletion mutations to occur, and stringent DNA groove molecular recognition may be required to maintain intrinsic DNA polymerase fidelity. The implications of a close relationship between base-pair dissociation, base unstacking, and strand slippage are discussed in the context of sequence dependence of indel mutations

Partial Base Flipping Is Sufficient for Strand Slippage near DNA Duplex Termini

Strand slippage is a structural mechanism by which insertion–deletion (indel) mutations are introduced during replication by polymerases. Three-dimensional atomic-resolution structural pathways are still not known for the decades-old template slippage description. The dynamic nature of the process and the higher energy intermediates involved increase the difficulty of studying these processes experimentally. In the present study, restrained and unrestrained molecular dynamics simulations, carried out using multiple nucleic acid force fields, are used to demonstrate that partial base-flipping can be sufficient for strand slippage at DNA duplex termini. Such strand slippage can occur in either strand, i.e. near either the 3′ or the 5′ terminus of a DNA strand, which suggests that similar structural flipping mechanisms can cause both primer and template slippage. In the repetitive mutation hot-spot sequence studied, non-canonical base-pairing with exposed DNA groove atoms of a neighboring G:C base-pair stabilizes a partially flipped state of the cytosine. For its base-pair partner guanine, a similar partially flipped metastable intermediate was not detected, and the propensity for sustained slippage was also found to be lower. This illustrates that a relatively small metastable DNA structural distortion in polymerase active sites could allow single base insertion or deletion mutations to occur, and stringent DNA groove molecular recognition may be required to maintain intrinsic DNA polymerase fidelity. The implications of a close relationship between base-pair dissociation, base unstacking, and strand slippage are discussed in the context of sequence dependence of indel mutations

Analyzing the Relationship between Single Base Flipping and Strand Slippage near DNA Duplex Termini

Insertion–deletion (indel) mutations are caused by strand slippage between pairing primer and template strands during nucleic acid strand extension. A possible causative factor for such strand slippage is base flipping in the primer strand or template strand, for insertion or deletion mutations, respectively. A simple mechanistic description is that the “hole” in the nucleic acid duplex left behind by a flipping base is occupied by a neighboring base on the same strand, resulting in slippage with respect to its paired strand. The extent of single base flipping required for occupation of its former place in the double helix by a neighboring base is not fully understood. The present study uses restrained molecular dynamics (MD) simulations along a pseudohedihedral base flipping parameter to construct two-dimensional free energy profiles along base flipping and strand slippage geometric parameters. These profiles, generated for both cytosine and guanine single base flipping in a short repetitive indel mutation hot-spot DNA sequence, illustrate the extent of single base flipping that can allow strand slippage by one base position. Relatively minor base flipping into both the major and minor grooves can result in strand slippage. Deconstruction of the collective variable strand slippage geometric parameter into its component distances illustrates the details of how strand slippage can accompany base flipping. The trans Watson–Crick:sugar edge interaction that stabilizes cytosine flipping in this hot-spot sequence is also characterized energetically. The impact of these results on understanding sequence dependence of indel errors in nucleic acid strand extension is discussed, along with a suggestion for future studies that can generalize the present findings to all nearest-neighbor sequence contexts

Analyzing the Relationship between Single Base Flipping and Strand Slippage near DNA Duplex Termini

Insertion–deletion (indel) mutations are caused by strand slippage between pairing primer and template strands during nucleic acid strand extension. A possible causative factor for such strand slippage is base flipping in the primer strand or template strand, for insertion or deletion mutations, respectively. A simple mechanistic description is that the “hole” in the nucleic acid duplex left behind by a flipping base is occupied by a neighboring base on the same strand, resulting in slippage with respect to its paired strand. The extent of single base flipping required for occupation of its former place in the double helix by a neighboring base is not fully understood. The present study uses restrained molecular dynamics (MD) simulations along a pseudohedihedral base flipping parameter to construct two-dimensional free energy profiles along base flipping and strand slippage geometric parameters. These profiles, generated for both cytosine and guanine single base flipping in a short repetitive indel mutation hot-spot DNA sequence, illustrate the extent of single base flipping that can allow strand slippage by one base position. Relatively minor base flipping into both the major and minor grooves can result in strand slippage. Deconstruction of the collective variable strand slippage geometric parameter into its component distances illustrates the details of how strand slippage can accompany base flipping. The trans Watson–Crick:sugar edge interaction that stabilizes cytosine flipping in this hot-spot sequence is also characterized energetically. The impact of these results on understanding sequence dependence of indel errors in nucleic acid strand extension is discussed, along with a suggestion for future studies that can generalize the present findings to all nearest-neighbor sequence contexts

Analyzing the Relationship between Single Base Flipping and Strand Slippage near DNA Duplex Termini

Insertion–deletion (indel) mutations are caused by strand slippage between pairing primer and template strands during nucleic acid strand extension. A possible causative factor for such strand slippage is base flipping in the primer strand or template strand, for insertion or deletion mutations, respectively. A simple mechanistic description is that the “hole” in the nucleic acid duplex left behind by a flipping base is occupied by a neighboring base on the same strand, resulting in slippage with respect to its paired strand. The extent of single base flipping required for occupation of its former place in the double helix by a neighboring base is not fully understood. The present study uses restrained molecular dynamics (MD) simulations along a pseudohedihedral base flipping parameter to construct two-dimensional free energy profiles along base flipping and strand slippage geometric parameters. These profiles, generated for both cytosine and guanine single base flipping in a short repetitive indel mutation hot-spot DNA sequence, illustrate the extent of single base flipping that can allow strand slippage by one base position. Relatively minor base flipping into both the major and minor grooves can result in strand slippage. Deconstruction of the collective variable strand slippage geometric parameter into its component distances illustrates the details of how strand slippage can accompany base flipping. The trans Watson–Crick:sugar edge interaction that stabilizes cytosine flipping in this hot-spot sequence is also characterized energetically. The impact of these results on understanding sequence dependence of indel errors in nucleic acid strand extension is discussed, along with a suggestion for future studies that can generalize the present findings to all nearest-neighbor sequence contexts

Partial Base Flipping Is Sufficient for Strand Slippage near DNA Duplex Termini

Strand slippage is a structural mechanism by which insertion–deletion (indel) mutations are introduced during replication by polymerases. Three-dimensional atomic-resolution structural pathways are still not known for the decades-old template slippage description. The dynamic nature of the process and the higher energy intermediates involved increase the difficulty of studying these processes experimentally. In the present study, restrained and unrestrained molecular dynamics simulations, carried out using multiple nucleic acid force fields, are used to demonstrate that partial base-flipping can be sufficient for strand slippage at DNA duplex termini. Such strand slippage can occur in either strand, i.e. near either the 3′ or the 5′ terminus of a DNA strand, which suggests that similar structural flipping mechanisms can cause both primer and template slippage. In the repetitive mutation hot-spot sequence studied, non-canonical base-pairing with exposed DNA groove atoms of a neighboring G:C base-pair stabilizes a partially flipped state of the cytosine. For its base-pair partner guanine, a similar partially flipped metastable intermediate was not detected, and the propensity for sustained slippage was also found to be lower. This illustrates that a relatively small metastable DNA structural distortion in polymerase active sites could allow single base insertion or deletion mutations to occur, and stringent DNA groove molecular recognition may be required to maintain intrinsic DNA polymerase fidelity. The implications of a close relationship between base-pair dissociation, base unstacking, and strand slippage are discussed in the context of sequence dependence of indel mutations

Partial Base Flipping Is Sufficient for Strand Slippage near DNA Duplex Termini

Strand slippage is a structural mechanism by which insertion–deletion (indel) mutations are introduced during replication by polymerases. Three-dimensional atomic-resolution structural pathways are still not known for the decades-old template slippage description. The dynamic nature of the process and the higher energy intermediates involved increase the difficulty of studying these processes experimentally. In the present study, restrained and unrestrained molecular dynamics simulations, carried out using multiple nucleic acid force fields, are used to demonstrate that partial base-flipping can be sufficient for strand slippage at DNA duplex termini. Such strand slippage can occur in either strand, i.e. near either the 3′ or the 5′ terminus of a DNA strand, which suggests that similar structural flipping mechanisms can cause both primer and template slippage. In the repetitive mutation hot-spot sequence studied, non-canonical base-pairing with exposed DNA groove atoms of a neighboring G:C base-pair stabilizes a partially flipped state of the cytosine. For its base-pair partner guanine, a similar partially flipped metastable intermediate was not detected, and the propensity for sustained slippage was also found to be lower. This illustrates that a relatively small metastable DNA structural distortion in polymerase active sites could allow single base insertion or deletion mutations to occur, and stringent DNA groove molecular recognition may be required to maintain intrinsic DNA polymerase fidelity. The implications of a close relationship between base-pair dissociation, base unstacking, and strand slippage are discussed in the context of sequence dependence of indel mutations