Guanidinium ion is a toxic cellular metabolite. The ykkC-III riboswitch, an mRNA stretch, regulat... more Guanidinium ion is a toxic cellular metabolite. The ykkC-III riboswitch, an mRNA stretch, regulates the gene expression by undergoing a conformational change in response to the binding of a free guanidinium ion and thereby plays a potentially important role in alleviating guanidinium toxicity in cells. An experimental crystal structure of the guanidinium-bound aptamer domain of the riboswitch from Thermobifida Fusca revealed the overall RNA architecture and mapped the specific noncovalent interactions that stabilize the ligand within the binding pocket aptamer. However, details of how the aptamer domain discriminates the cognate ligand from its closest structurally analogous physiological metabolites (arginine and urea), and how the binding of cognate ligand arrays information from the aptamer domain to the expression platform for regulating the gene expression, are not well understood. To fill this void, we perform a cumulative of 2 μs all-atom explicit-solvent molecular dynamics (MD) simulations on the full aptamer domain, augmented with quantum-chemical calculations on the ligand-binding pocket, to compare the structural and dynamical details of the guanidinium-bound state with the arginine or urea bound states, as well as the unbound (open) state. Analysis of the ligand-binding pocket reveals that due to unfavorable interactions with the binding-pocket residues, urea cannot bind the aptamer domain and thereby cannot alter the gene expression. Although interaction of the guanidyl moiety of arginine within the binding pocket is either comparable or stronger than the guanidinium ion, additional non-native hydrogen-bonding networks, as well as differences in the dynamical details of the arginine-bound state, explain why arginine cannot transmit the information from the aptamer domain to the expression platform. Based on our simulations, we propose a mechanism of how the aptamer domain communicates with the expression platform. Overall, our work provides interesting insights into the ligand recognition by a specific class of riboswitches and may hopefully inspire future studies to further understand the gene regulation by riboswitches.
A comprehesive computational study is presented with the goal to design and analyze model chalcog... more A comprehesive computational study is presented with the goal to design and analyze model chalcogen-bonded modified nucleobase pairs that replace one or two Watson–Crick hydrogen bonds of the canonical A:T or G:C pair with chalcogen bond(s).
DFT calculations are employed to quantify the influence of the presence, number, nature and posit... more DFT calculations are employed to quantify the influence of the presence, number, nature and position of posttranscriptional methylation on stacking strength of RNA bases. We carry out detailed potential energy scans of the variation in stacking energies with characteristic geometrical parameters in three categories of forty stacked dimers- canonical base homodimers (N||N), methylated base homodimers (mN||mN) and heterodimers of canonical bases and methylated counterparts (N||mN). Our analysis reveals that neutral methylation invariably enhances the stacking of bases. Further, N||mN stacking is stronger than mN||mN stacking, and charged N||mN exhibit strongest stacking among all dimers. This indicates that methylations greatly enhance stacking when dispersed in RNA sequences containing identical bases. Comparison of stacks involving singly- and doubly-methylated purines reveals that incremental methylation enhances the stacking in neutral dimers. Although methylation at the carbon position of neutral pyrimidine dimers greatly enhances the stacking, methylation on the 5-membered ring imparts better stacking compared to methylation on the 6-membered ring in adenine dimers. However, methylation at the ring nitrogen (N1) provides better stacking than the amino group (N2) in guanine dimers. Our results thus highlight subtle structural effects of methylation on RNA base stacking, and will enhance our understanding of the physicochemical principles of RNA structure and dynamics.
The origin of genetic material on earth is an age-old, entangled mystery that lacks a unanimous e... more The origin of genetic material on earth is an age-old, entangled mystery that lacks a unanimous explanation. Recent studies have suggested that noncanonical bases such as barbituric acid (BA), melamine (MM), cyanuric acid (CA), and 2,4,6-triaminopyrimidine (TAP) may have undergone molecular selection within the "prebiotic soup" to spontaneously form supramolecular assemblies, which then covalently assembled into an RNA-like polymer (preRNA). However, information on the role of intrinsic interactions of these candidate heterocycles in their molecular selection as the components of preRNA, and the subsequent transition from preRNA to RNA, is currently missing in the literature. To fill this gap in our knowledge on the origin and evolution of primitive genetics, the present work employs density functional theory (B3LYP-D3) to evaluate and compare the stacking propensities of dimers containing prebiotic noncanonical (BA, MM, CA, and TAP) and/or canonical RNA bases (A, C, G, and U). Our detailed analysis of the variation in stacking strength with respect to four characteristic geometrical parameters between the monomers [i.e., the vertical distance, the angle of rotation, and (two) displacements in the x and y directions] reveals that stacking between nonidentical bases is preferred over identical bases for both prebiotic-prebiotic and canonical-canonical dimers. This not only underscores the similarity between the fundamental chemical properties of preRNA and RNA constituents but also supports the likelihood of the evolution of modern (RNA) genetics from primitive (preRNA) genetics. Furthermore, greater average stacking stabilization of canonical dimers than that of dimers containing one canonical and one preRNA nucleobase (by ∼5 kJ mol-1) or dimers solely containing preRNA nucleobases (by ∼12 kJ mol-1) indicates that enhanced stacking is an important factor that may have spurred the evolution of preRNA to an intermediate informational polymer to RNA. More importantly, our study identifies the central roles of CA, BA, and TAP in stacking stabilization within the preRNA and of BA in stacking interactions within the intermediate polymers and suggests that these heterocycles may have played distinct roles in various stages during the evolution from preRNA to RNA. Overall, our results highlight the significance of stacking interactions in the selection of nucleobase components of preRNA.
The astonishing diversity in folding patterns of RNA three-dimensional (3D) structures is crafted... more The astonishing diversity in folding patterns of RNA three-dimensional (3D) structures is crafted by myriads of noncovalent contacts, of which base pairing and stacking are the most prominent. A systematic and comprehensive classification and annotation of these interactions is necessary for a molecular-level understanding of their roles. However, unlike in the case of base pairing, where a widely accepted nomenclature and classification scheme exists in the public domain, currently available classification schemes for base-base stacking need major enhancements to comprehensively capture the necessary features underlying the rich stacking diversity in RNA. Here, we extend the previous stacking classification based on nucleobase interacting faces by introducing a structurally intuitive geometry-cum topology-based scheme. Specifically, a stack is first classified in terms of the geometry described by the relative orientation of the glycosidic bonds, which generates eight basic stacking geometric families for heterodimeric stacks and six of those for homodimeric stacks. Further annotation in terms of the identity of the bases and the region of involvement of purines (five-membered, six-membered, or both rings) leads to the enumeration of 384 distinct RNA base stacks. Based on our classification scheme, we present an algorithm for automated identification of stacks in RNA crystal structures and analyze the stacking context in selected RNA structures. Overall, the work described here is expected to greatly facilitate the structure-based RNA research.
Abstract Hydrogen bonding between amino acids and nucleobases is important for RNA–protein recogn... more Abstract Hydrogen bonding between amino acids and nucleobases is important for RNA–protein recognition. As a first step toward understanding the physicochemical features of these contacts, the present work employs density functional theory calculations to critically analyze the intrinsic structures and strength of all theoretically possible model hydrogen-bonded complexes involving RNA nucleobase edges and polar amino acid side chains. Our geometry optimizations uncover a number of unique complexes that involve variable hydrogen-bonding characteristics, including conventional donor–acceptor interactions, bifurcated interactions and single hydrogen-bonded contacts. Further, significant strength of these complexes in the gas phase (−27 kJ mol−1 to −226 kJ mol−1) and solvent phase (−19 kJ mol−1 to −78 kJ mol−1) points toward the ability of associated contacts to provide stability to RNA–protein complexes. More importantly, for the first time, our study uncovers the features of complexes involving protonated nucleobases, as well as those involving the weakly polar cysteine side chain, and thereby highlights their potential importance in biological processes that involve RNA–protein interactions. Additional analysis on select base pair-amino acid complexes uncovers the ability of amino acid side chain to simultaneously interact with both nucleobases of the base pair, and highlights the greater strength of such interactions compared to base-amino acid interactions. Overall, our analysis provides a basic physicochemical framework for understanding the molecular basis of nucleic acid–protein interactions. Further, our quantum chemical data can be used to design better algorithms for automated search of these contacts at the RNA–protein interface. Communicated by Ramaswamy H. Sarma
Exposure to aristolochic acid I and II (AAI and AAII) has been implicated in aristolochic acid ne... more Exposure to aristolochic acid I and II (AAI and AAII) has been implicated in aristolochic acid nephropathy and urothelial carcinoma. The toxicological effects of AAs are attributed to their ability to form aristolacatam (AL)-purine DNA adducts. Among these lesions, the AL-adenine (ALI-N6-A and ALII-N6-A) adducts cause the 'signature' A→T transversion mutations associated with AA genotoxicity. To provide the currently-missing structural basis for the induction of these signature mutations, the present work uses classical all-atom molecular dynamics (MD) simulations to examine different (i.e., pre-insertion, insertion and post-extension) stages of replication past the most abundant AA adduct (ALI-N6-A) by a representative lesion-bypass DNA polymerase (Dpo4). Our analysis reveals that before dNTP incorporation (i.e., pre-insertion step), ALI-N6-A adopts a nearly-planar conformation at the N6-linkage and the ALI-moiety intercalates within the DNA helix. Since this conformation occupies the dNTP binding site, the same planar lesion conformation results in significant distortion of the polymerase active site at the insertion step and therefore replication will likely not be successful. However, if ALI-N6-A undergoes a small conformational change to introduce nonplanarity at the N6-linkage during the insertion step, minimal distortion occurs in the Dpo4 active site upon incorporation of dATP. This insertion and subsequent extension would initially lead to A:A mismatches, and then result in A→T transversion mutations during the second round of replication. In contrast, if a large conformation flip of the ALI-moiety occurs at the insertion step to reorient the bulky moiety from an intercalated position into the major groove, (non-mutagenic) dTTP incorporation will be favored. MD simulations on post-extension complexes reveal that damaged DNA will likely further rearrange during later replication steps to acquire a base-displaced intercalated conformation that is similar to that previously reported for (unbound) ALI-N6-A adducted DNA, with the exception of slight nonplanarity at the lesion site. Overall, our results provide a structural explanation for both the successful non-mutagenic lesion bypass and the preferential misincorporation of dATP opposite ALI-N6-A, and thereby rationalize the previously-reported induction of A→T signature transversion mutations associated with AAs. This work should thereby inspire future biochemical experiments and modeling studies on the replication of this important class of DNA lesions by related human translesion synthesis polymerases.
ABSTRACTThe astonishing diversity in folding patterns of RNA 3D structures is crafted by myriads ... more ABSTRACTThe astonishing diversity in folding patterns of RNA 3D structures is crafted by myriads of noncovalent contacts, of which base pairing and stacking are the most prominent. Although the classification scheme proposed by Leontis and Westhof (RNA (2001), 7, 499–512) has been widely accepted for annotation of RNA base pairs, the absence of an unambiguous classification system for base stacks appears to be a roadblock for exploring the stacking diversity in RNA. Here we provide a structurally-intuitive and unambiguous geometry cum topology based classification scheme for base stacking, where a base stack is classified in terms of interacting nucleobase faces and the relative orientation of the glycosidic bonds. This generates eight or six basic stacking geometrical families for heterodimeric or homodimeric stacks. Further classification in terms of the identity of the bases, and the nature of involvement of the purines (5-membered, 6-membered or both rings) leads to 384 distinct...
The study explores radical-assisted formations of the nucleobase components of primitive genetics... more The study explores radical-assisted formations of the nucleobase components of primitive genetics from cyanamide and related precursors in impact events.
In the present work, 67 crystal structures of the aptamer domains of RNA riboswitches are chosen ... more In the present work, 67 crystal structures of the aptamer domains of RNA riboswitches are chosen for analysis of the structure and strength of hydrogen bonding (pairing) interactions between nucleobases constituting the aptamer binding pockets and the bound ligands. A total of 80 unique base:ligand hydrogen-bonded pairs containing at least two hydrogen bonds were identified through visual inspection. Classification of these contacts in terms of the interacting edge of the aptamer nucleobase revealed that interactions involving the Watson–Crick edge are the most common, followed by the sugar edge of purines and the Hoogsteen edge of uracil. Alternatively, classification in terms of the chemical constitution of the ligand yields five unique classes of base:ligand pairs: base:base, base:amino acid, base:sugar, base:phosphate, and base:other. Further, quantum mechanical (QM) geometry optimizations revealed that 67 out of 80 pairs exhibit stable geometries and optimal deviations from the...
Ochratoxin A (OTA) is a ubiquitous food toxin associated with chronic nephropathy in humans and r... more Ochratoxin A (OTA) is a ubiquitous food toxin associated with chronic nephropathy in humans and renal carcinogenicity in rodents. The mutational spectra of cells exposed to OTA reveal that one-base deletions comprise the largest percentage (73%) of the total mutations that occur upon OTA exposure. To contribute towards understanding the prevalence of OTA-induced one-base deletion mutations, the present work uses molecular dynamics (MD) simulations to analyze the conformational preferences of one-base deletion duplexes containing OT-G, the major OTA adduct (addition product) at the C8-site of guanine. Specifically, the influence of OT-G in four possible ionization states and three sequence contexts (G1, G2 and G3 in the NarI (5'-G1G2CG3CC-3'), a prokaryotic mutational hotspot sequence) on the structure of the adducted DNA is investigated. Our data reveals that the damaged helices are stable in two (B-type (B) and stacked (S)) conformations that are structurally similar to those adopted by common N-linked C8-guanine lesions. However, the adduct ionization state and sequence context affect the degree of helical distortion and the B/S conformational heterogeneity, which will impact the lesion repair and replication outcomes. This finding correlates with the experimentally-reported tissue-specific mutagenicity of OTA exposure. Nevertheless, regardless of the adduct conformation, ionization state or sequence context, more stable lesion-site interactions and lack of disruption of the flanking base pairs in the one-base deletion duplexes compared to the corresponding two-base deletion helices rationalize the greater abundance of OTA induced one-base deletions. Overall, our work provides valuable structural insights that help explain the experimentally-observed mutagenicity associated with OTA.
Exposure to ochratoxin A (OTA) is associated with chronic renal diseases and carcinogenesis. The ... more Exposure to ochratoxin A (OTA) is associated with chronic renal diseases and carcinogenesis. The deleterious effects of OTA have been linked to its covalent binding at the C8 position of guanine (G) to form a DNA adduct (OT-G), which causes various mutations. To contribute toward understanding the complex mutagenic profile of OTA, the present work uses a robust computational approach to characterize postreplication DNA structures containing OT-G mismatched with canonical nucleobases. Our MD simulations provide insight into the effects of the opposing base, adduct ionization state, and flanking base on duplex structural features for the competing (major groove (B-type), wedge (W), and stacked (S)) conformers. For the B-type duplexes, our data suggest that significantly more stable lesion-site hydrogen bonding may lead to preferential insertion of an opposing cytosine (C) if the OT moiety is directed toward the major groove at the replication fork. Although the W conformation is consistently predicted to be less stable than the B conformer, a G mismatch is likely the most stable and least distorted replication outcome when the bulky moiety is directed into the DNA minor groove. These findings directly correlate with the limited contribution of substitution mutations to the overall mutagenic profile of OTA and suggest that the dominant mutations are G → C transversions. In contrast, stable S conformers that are known precursors to small (one- or two-base) deletion mutations are found when the lesion is opposite cytosine, adenine, or thymine, which directly correlates with the large number of deletion mutations previously reported for animals exposed to OTA. Nevertheless, the predicted sequence and ionization-dependent distortion of the S conformer points toward the dependence of the repair propensity on the cellular environment, which rationalizes the reported tissue specific OTA-induced toxicity.
The present work investigates the effects of the size and shape of the nitrogen-containing aromat... more The present work investigates the effects of the size and shape of the nitrogen-containing aromatic (NCA) skeleton on the structure of DNA damaged through adduct formation at C8 of 2'-deoxyguanosine (dG), a common DNA lesion associated with chemical carcinogenesis. Specifically, density functional theory (DFT) calculations (B3LYP-D3) and molecular dynamics (MD) simulations (AMBER) are performed on seven model adducts with systematic expansion of the NCA moiety. DFT calculations reveal that the NCA moiety shape affects the structure at the nucleobase-carcinogen linkage. Approximately 4.5 μs of MD simulations on damaged oligonucleotides adopting three established conformational themes (namely, B, W, and S) illustrate that the structure and lesion-site stabilization strongly depend on the NCA moiety shape and size, which provides insight into the repair propensity of C8-dG adducted DNA. Our results add bulky moiety shape to the growing list of previously established effects on the conformational and repair outcomes of damaged DNA (i.e., size, ionization state, substitution, linker type, and DNA sequence). Furthermore, this work illustrates the utility of a systematic set of model DNA lesions for understanding the structure-activity relationship for DNA damaged by carcinogens of different sizes and shapes, which should be used in future studies of the cellular processing of damaged DNA.
In the present work, sixty seven crystal structures of the aptamer domains of RNA riboswitches, a... more In the present work, sixty seven crystal structures of the aptamer domains of RNA riboswitches, are chosen for analysis of the structure and strength of hydrogen bonding (pairing) interactions between nucleobases constituting the aptamer binding pockets and the bound ligands. A total of eighty unique base:ligand hydrogen bonded pairs containing at least two hydrogen bonds were identified through visual inspection. Classification of these contacts in terms of the interacting edge of the aptamer nucleobase revealed that interactions involving the Watson-Crick edge are the most common, followed by the sugar edge of purines and the Hoogsteen edge of uracil. Alternatively, classification in terms of the chemical constitution of the ligand yields five unique classes of base:ligand pairs: base:base, base:amino acid, base:sugar, base:phosphate and base:other. Further, quantum mechanical (QM) geometry optimizations revealed that sixty seven out of eighty pairs exhibit stable geometries and o...
Guanidinium ion is a toxic cellular metabolite. The ykkC-III riboswitch, an mRNA stretch, regulat... more Guanidinium ion is a toxic cellular metabolite. The ykkC-III riboswitch, an mRNA stretch, regulates the gene expression by undergoing a conformational change in response to the binding of a free guanidinium ion and thereby plays a potentially important role in alleviating guanidinium toxicity in cells. An experimental crystal structure of the guanidinium-bound aptamer domain of the riboswitch from Thermobifida Fusca revealed the overall RNA architecture and mapped the specific noncovalent interactions that stabilize the ligand within the binding pocket aptamer. However, details of how the aptamer domain discriminates the cognate ligand from its closest structurally analogous physiological metabolites (arginine and urea), and how the binding of cognate ligand arrays information from the aptamer domain to the expression platform for regulating the gene expression, are not well understood. To fill this void, we perform a cumulative of 2 μs all-atom explicit-solvent molecular dynamics (MD) simulations on the full aptamer domain, augmented with quantum-chemical calculations on the ligand-binding pocket, to compare the structural and dynamical details of the guanidinium-bound state with the arginine or urea bound states, as well as the unbound (open) state. Analysis of the ligand-binding pocket reveals that due to unfavorable interactions with the binding-pocket residues, urea cannot bind the aptamer domain and thereby cannot alter the gene expression. Although interaction of the guanidyl moiety of arginine within the binding pocket is either comparable or stronger than the guanidinium ion, additional non-native hydrogen-bonding networks, as well as differences in the dynamical details of the arginine-bound state, explain why arginine cannot transmit the information from the aptamer domain to the expression platform. Based on our simulations, we propose a mechanism of how the aptamer domain communicates with the expression platform. Overall, our work provides interesting insights into the ligand recognition by a specific class of riboswitches and may hopefully inspire future studies to further understand the gene regulation by riboswitches.
A comprehesive computational study is presented with the goal to design and analyze model chalcog... more A comprehesive computational study is presented with the goal to design and analyze model chalcogen-bonded modified nucleobase pairs that replace one or two Watson–Crick hydrogen bonds of the canonical A:T or G:C pair with chalcogen bond(s).
DFT calculations are employed to quantify the influence of the presence, number, nature and posit... more DFT calculations are employed to quantify the influence of the presence, number, nature and position of posttranscriptional methylation on stacking strength of RNA bases. We carry out detailed potential energy scans of the variation in stacking energies with characteristic geometrical parameters in three categories of forty stacked dimers- canonical base homodimers (N||N), methylated base homodimers (mN||mN) and heterodimers of canonical bases and methylated counterparts (N||mN). Our analysis reveals that neutral methylation invariably enhances the stacking of bases. Further, N||mN stacking is stronger than mN||mN stacking, and charged N||mN exhibit strongest stacking among all dimers. This indicates that methylations greatly enhance stacking when dispersed in RNA sequences containing identical bases. Comparison of stacks involving singly- and doubly-methylated purines reveals that incremental methylation enhances the stacking in neutral dimers. Although methylation at the carbon position of neutral pyrimidine dimers greatly enhances the stacking, methylation on the 5-membered ring imparts better stacking compared to methylation on the 6-membered ring in adenine dimers. However, methylation at the ring nitrogen (N1) provides better stacking than the amino group (N2) in guanine dimers. Our results thus highlight subtle structural effects of methylation on RNA base stacking, and will enhance our understanding of the physicochemical principles of RNA structure and dynamics.
The origin of genetic material on earth is an age-old, entangled mystery that lacks a unanimous e... more The origin of genetic material on earth is an age-old, entangled mystery that lacks a unanimous explanation. Recent studies have suggested that noncanonical bases such as barbituric acid (BA), melamine (MM), cyanuric acid (CA), and 2,4,6-triaminopyrimidine (TAP) may have undergone molecular selection within the "prebiotic soup" to spontaneously form supramolecular assemblies, which then covalently assembled into an RNA-like polymer (preRNA). However, information on the role of intrinsic interactions of these candidate heterocycles in their molecular selection as the components of preRNA, and the subsequent transition from preRNA to RNA, is currently missing in the literature. To fill this gap in our knowledge on the origin and evolution of primitive genetics, the present work employs density functional theory (B3LYP-D3) to evaluate and compare the stacking propensities of dimers containing prebiotic noncanonical (BA, MM, CA, and TAP) and/or canonical RNA bases (A, C, G, and U). Our detailed analysis of the variation in stacking strength with respect to four characteristic geometrical parameters between the monomers [i.e., the vertical distance, the angle of rotation, and (two) displacements in the x and y directions] reveals that stacking between nonidentical bases is preferred over identical bases for both prebiotic-prebiotic and canonical-canonical dimers. This not only underscores the similarity between the fundamental chemical properties of preRNA and RNA constituents but also supports the likelihood of the evolution of modern (RNA) genetics from primitive (preRNA) genetics. Furthermore, greater average stacking stabilization of canonical dimers than that of dimers containing one canonical and one preRNA nucleobase (by ∼5 kJ mol-1) or dimers solely containing preRNA nucleobases (by ∼12 kJ mol-1) indicates that enhanced stacking is an important factor that may have spurred the evolution of preRNA to an intermediate informational polymer to RNA. More importantly, our study identifies the central roles of CA, BA, and TAP in stacking stabilization within the preRNA and of BA in stacking interactions within the intermediate polymers and suggests that these heterocycles may have played distinct roles in various stages during the evolution from preRNA to RNA. Overall, our results highlight the significance of stacking interactions in the selection of nucleobase components of preRNA.
The astonishing diversity in folding patterns of RNA three-dimensional (3D) structures is crafted... more The astonishing diversity in folding patterns of RNA three-dimensional (3D) structures is crafted by myriads of noncovalent contacts, of which base pairing and stacking are the most prominent. A systematic and comprehensive classification and annotation of these interactions is necessary for a molecular-level understanding of their roles. However, unlike in the case of base pairing, where a widely accepted nomenclature and classification scheme exists in the public domain, currently available classification schemes for base-base stacking need major enhancements to comprehensively capture the necessary features underlying the rich stacking diversity in RNA. Here, we extend the previous stacking classification based on nucleobase interacting faces by introducing a structurally intuitive geometry-cum topology-based scheme. Specifically, a stack is first classified in terms of the geometry described by the relative orientation of the glycosidic bonds, which generates eight basic stacking geometric families for heterodimeric stacks and six of those for homodimeric stacks. Further annotation in terms of the identity of the bases and the region of involvement of purines (five-membered, six-membered, or both rings) leads to the enumeration of 384 distinct RNA base stacks. Based on our classification scheme, we present an algorithm for automated identification of stacks in RNA crystal structures and analyze the stacking context in selected RNA structures. Overall, the work described here is expected to greatly facilitate the structure-based RNA research.
Abstract Hydrogen bonding between amino acids and nucleobases is important for RNA–protein recogn... more Abstract Hydrogen bonding between amino acids and nucleobases is important for RNA–protein recognition. As a first step toward understanding the physicochemical features of these contacts, the present work employs density functional theory calculations to critically analyze the intrinsic structures and strength of all theoretically possible model hydrogen-bonded complexes involving RNA nucleobase edges and polar amino acid side chains. Our geometry optimizations uncover a number of unique complexes that involve variable hydrogen-bonding characteristics, including conventional donor–acceptor interactions, bifurcated interactions and single hydrogen-bonded contacts. Further, significant strength of these complexes in the gas phase (−27 kJ mol−1 to −226 kJ mol−1) and solvent phase (−19 kJ mol−1 to −78 kJ mol−1) points toward the ability of associated contacts to provide stability to RNA–protein complexes. More importantly, for the first time, our study uncovers the features of complexes involving protonated nucleobases, as well as those involving the weakly polar cysteine side chain, and thereby highlights their potential importance in biological processes that involve RNA–protein interactions. Additional analysis on select base pair-amino acid complexes uncovers the ability of amino acid side chain to simultaneously interact with both nucleobases of the base pair, and highlights the greater strength of such interactions compared to base-amino acid interactions. Overall, our analysis provides a basic physicochemical framework for understanding the molecular basis of nucleic acid–protein interactions. Further, our quantum chemical data can be used to design better algorithms for automated search of these contacts at the RNA–protein interface. Communicated by Ramaswamy H. Sarma
Exposure to aristolochic acid I and II (AAI and AAII) has been implicated in aristolochic acid ne... more Exposure to aristolochic acid I and II (AAI and AAII) has been implicated in aristolochic acid nephropathy and urothelial carcinoma. The toxicological effects of AAs are attributed to their ability to form aristolacatam (AL)-purine DNA adducts. Among these lesions, the AL-adenine (ALI-N6-A and ALII-N6-A) adducts cause the 'signature' A→T transversion mutations associated with AA genotoxicity. To provide the currently-missing structural basis for the induction of these signature mutations, the present work uses classical all-atom molecular dynamics (MD) simulations to examine different (i.e., pre-insertion, insertion and post-extension) stages of replication past the most abundant AA adduct (ALI-N6-A) by a representative lesion-bypass DNA polymerase (Dpo4). Our analysis reveals that before dNTP incorporation (i.e., pre-insertion step), ALI-N6-A adopts a nearly-planar conformation at the N6-linkage and the ALI-moiety intercalates within the DNA helix. Since this conformation occupies the dNTP binding site, the same planar lesion conformation results in significant distortion of the polymerase active site at the insertion step and therefore replication will likely not be successful. However, if ALI-N6-A undergoes a small conformational change to introduce nonplanarity at the N6-linkage during the insertion step, minimal distortion occurs in the Dpo4 active site upon incorporation of dATP. This insertion and subsequent extension would initially lead to A:A mismatches, and then result in A→T transversion mutations during the second round of replication. In contrast, if a large conformation flip of the ALI-moiety occurs at the insertion step to reorient the bulky moiety from an intercalated position into the major groove, (non-mutagenic) dTTP incorporation will be favored. MD simulations on post-extension complexes reveal that damaged DNA will likely further rearrange during later replication steps to acquire a base-displaced intercalated conformation that is similar to that previously reported for (unbound) ALI-N6-A adducted DNA, with the exception of slight nonplanarity at the lesion site. Overall, our results provide a structural explanation for both the successful non-mutagenic lesion bypass and the preferential misincorporation of dATP opposite ALI-N6-A, and thereby rationalize the previously-reported induction of A→T signature transversion mutations associated with AAs. This work should thereby inspire future biochemical experiments and modeling studies on the replication of this important class of DNA lesions by related human translesion synthesis polymerases.
ABSTRACTThe astonishing diversity in folding patterns of RNA 3D structures is crafted by myriads ... more ABSTRACTThe astonishing diversity in folding patterns of RNA 3D structures is crafted by myriads of noncovalent contacts, of which base pairing and stacking are the most prominent. Although the classification scheme proposed by Leontis and Westhof (RNA (2001), 7, 499–512) has been widely accepted for annotation of RNA base pairs, the absence of an unambiguous classification system for base stacks appears to be a roadblock for exploring the stacking diversity in RNA. Here we provide a structurally-intuitive and unambiguous geometry cum topology based classification scheme for base stacking, where a base stack is classified in terms of interacting nucleobase faces and the relative orientation of the glycosidic bonds. This generates eight or six basic stacking geometrical families for heterodimeric or homodimeric stacks. Further classification in terms of the identity of the bases, and the nature of involvement of the purines (5-membered, 6-membered or both rings) leads to 384 distinct...
The study explores radical-assisted formations of the nucleobase components of primitive genetics... more The study explores radical-assisted formations of the nucleobase components of primitive genetics from cyanamide and related precursors in impact events.
In the present work, 67 crystal structures of the aptamer domains of RNA riboswitches are chosen ... more In the present work, 67 crystal structures of the aptamer domains of RNA riboswitches are chosen for analysis of the structure and strength of hydrogen bonding (pairing) interactions between nucleobases constituting the aptamer binding pockets and the bound ligands. A total of 80 unique base:ligand hydrogen-bonded pairs containing at least two hydrogen bonds were identified through visual inspection. Classification of these contacts in terms of the interacting edge of the aptamer nucleobase revealed that interactions involving the Watson–Crick edge are the most common, followed by the sugar edge of purines and the Hoogsteen edge of uracil. Alternatively, classification in terms of the chemical constitution of the ligand yields five unique classes of base:ligand pairs: base:base, base:amino acid, base:sugar, base:phosphate, and base:other. Further, quantum mechanical (QM) geometry optimizations revealed that 67 out of 80 pairs exhibit stable geometries and optimal deviations from the...
Ochratoxin A (OTA) is a ubiquitous food toxin associated with chronic nephropathy in humans and r... more Ochratoxin A (OTA) is a ubiquitous food toxin associated with chronic nephropathy in humans and renal carcinogenicity in rodents. The mutational spectra of cells exposed to OTA reveal that one-base deletions comprise the largest percentage (73%) of the total mutations that occur upon OTA exposure. To contribute towards understanding the prevalence of OTA-induced one-base deletion mutations, the present work uses molecular dynamics (MD) simulations to analyze the conformational preferences of one-base deletion duplexes containing OT-G, the major OTA adduct (addition product) at the C8-site of guanine. Specifically, the influence of OT-G in four possible ionization states and three sequence contexts (G1, G2 and G3 in the NarI (5'-G1G2CG3CC-3'), a prokaryotic mutational hotspot sequence) on the structure of the adducted DNA is investigated. Our data reveals that the damaged helices are stable in two (B-type (B) and stacked (S)) conformations that are structurally similar to those adopted by common N-linked C8-guanine lesions. However, the adduct ionization state and sequence context affect the degree of helical distortion and the B/S conformational heterogeneity, which will impact the lesion repair and replication outcomes. This finding correlates with the experimentally-reported tissue-specific mutagenicity of OTA exposure. Nevertheless, regardless of the adduct conformation, ionization state or sequence context, more stable lesion-site interactions and lack of disruption of the flanking base pairs in the one-base deletion duplexes compared to the corresponding two-base deletion helices rationalize the greater abundance of OTA induced one-base deletions. Overall, our work provides valuable structural insights that help explain the experimentally-observed mutagenicity associated with OTA.
Exposure to ochratoxin A (OTA) is associated with chronic renal diseases and carcinogenesis. The ... more Exposure to ochratoxin A (OTA) is associated with chronic renal diseases and carcinogenesis. The deleterious effects of OTA have been linked to its covalent binding at the C8 position of guanine (G) to form a DNA adduct (OT-G), which causes various mutations. To contribute toward understanding the complex mutagenic profile of OTA, the present work uses a robust computational approach to characterize postreplication DNA structures containing OT-G mismatched with canonical nucleobases. Our MD simulations provide insight into the effects of the opposing base, adduct ionization state, and flanking base on duplex structural features for the competing (major groove (B-type), wedge (W), and stacked (S)) conformers. For the B-type duplexes, our data suggest that significantly more stable lesion-site hydrogen bonding may lead to preferential insertion of an opposing cytosine (C) if the OT moiety is directed toward the major groove at the replication fork. Although the W conformation is consistently predicted to be less stable than the B conformer, a G mismatch is likely the most stable and least distorted replication outcome when the bulky moiety is directed into the DNA minor groove. These findings directly correlate with the limited contribution of substitution mutations to the overall mutagenic profile of OTA and suggest that the dominant mutations are G → C transversions. In contrast, stable S conformers that are known precursors to small (one- or two-base) deletion mutations are found when the lesion is opposite cytosine, adenine, or thymine, which directly correlates with the large number of deletion mutations previously reported for animals exposed to OTA. Nevertheless, the predicted sequence and ionization-dependent distortion of the S conformer points toward the dependence of the repair propensity on the cellular environment, which rationalizes the reported tissue specific OTA-induced toxicity.
The present work investigates the effects of the size and shape of the nitrogen-containing aromat... more The present work investigates the effects of the size and shape of the nitrogen-containing aromatic (NCA) skeleton on the structure of DNA damaged through adduct formation at C8 of 2'-deoxyguanosine (dG), a common DNA lesion associated with chemical carcinogenesis. Specifically, density functional theory (DFT) calculations (B3LYP-D3) and molecular dynamics (MD) simulations (AMBER) are performed on seven model adducts with systematic expansion of the NCA moiety. DFT calculations reveal that the NCA moiety shape affects the structure at the nucleobase-carcinogen linkage. Approximately 4.5 μs of MD simulations on damaged oligonucleotides adopting three established conformational themes (namely, B, W, and S) illustrate that the structure and lesion-site stabilization strongly depend on the NCA moiety shape and size, which provides insight into the repair propensity of C8-dG adducted DNA. Our results add bulky moiety shape to the growing list of previously established effects on the conformational and repair outcomes of damaged DNA (i.e., size, ionization state, substitution, linker type, and DNA sequence). Furthermore, this work illustrates the utility of a systematic set of model DNA lesions for understanding the structure-activity relationship for DNA damaged by carcinogens of different sizes and shapes, which should be used in future studies of the cellular processing of damaged DNA.
In the present work, sixty seven crystal structures of the aptamer domains of RNA riboswitches, a... more In the present work, sixty seven crystal structures of the aptamer domains of RNA riboswitches, are chosen for analysis of the structure and strength of hydrogen bonding (pairing) interactions between nucleobases constituting the aptamer binding pockets and the bound ligands. A total of eighty unique base:ligand hydrogen bonded pairs containing at least two hydrogen bonds were identified through visual inspection. Classification of these contacts in terms of the interacting edge of the aptamer nucleobase revealed that interactions involving the Watson-Crick edge are the most common, followed by the sugar edge of purines and the Hoogsteen edge of uracil. Alternatively, classification in terms of the chemical constitution of the ligand yields five unique classes of base:ligand pairs: base:base, base:amino acid, base:sugar, base:phosphate and base:other. Further, quantum mechanical (QM) geometry optimizations revealed that sixty seven out of eighty pairs exhibit stable geometries and o...
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Papers by Purshotam Sharma