1
|
Kole K, Gupta AM, Chakrabarti J. Conformational stability and order of Hoogsteen base pair induced by protein binding. Biophys Chem 2023; 301:107079. [PMID: 37523944 DOI: 10.1016/j.bpc.2023.107079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
Abstract
Several experimental studies have shown that Hoogsteen (HG) base pair (bp) stabilizes in the presence of proteins. The molecular mechanism underlying this stabilization is not well known. This leads us to examine the stability of the HG bp in duplex DNA using all-atom molecular dynamics simulation in both the absence and presence of proteins. We use conformational thermodynamics to investigate the stability of a HG bp in duplex DNA at the molecular level. We compute the changes in the conformational free energy and entropy of DNA when DNA adopts a HG bp in its bp sequence rather than a Watson-Crick (WC) bp in both naked DNA and protein-bound DNA complex. We observe that the presence of proteins stabilizes and organizes the HG bp and the entire DNA duplex. Sugar-phosphate, sugar-base, and sugar-pucker torsion angles play key roles in stabilizing and ordering the HG bp in the protein-bound DNA complex.
Collapse
Affiliation(s)
- Kanika Kole
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Aayatti Mallick Gupta
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India.
| | - Jaydeb Chakrabarti
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India.
| |
Collapse
|
2
|
Mishra RK, Mukherjee S, Bhattacharyya D. Maturation of siRNA by strand separation: Steered molecular dynamics study. J Biomol Struct Dyn 2022; 40:13682-13692. [PMID: 34726123 DOI: 10.1080/07391102.2021.1994468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA interference, particularly siRNA induced gene silencing is becoming an important avenue of modern therapeutics. The siRNA is delivered to the cells as short double helical RNA which becomes single stranded for forming the RISC complex. Significant experimental evidence is available for most of the steps except the process of the separation of the two strands. We have attempted to understand the pathway for double stranded siRNA (dsRNA) to single stranded (ssRNA) molecules using steered molecular dynamics simulations. As the process is completely unexplored we have applied force from all possible directions restraining all possible residues to convert dsRNA to ssRNA. We found pulling one strand along the helical axis direction restraining the far end of the other strand demands excessive force for ssRNA formation. Pulling a central residue of one strand, in a direction perpendicular to the helix axis, while keeping the base paired residue fixed requires intermediate force for strand separation. Moreover, we found that in this process the force requirement is quite high for the first bubble formation (nucleation energy) and the bubble propagation energies are quite small. We believe the success rate of the design of siRNA sequences for gene silencing may increase if this mechanistic knowledge is utilized for such a design process.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Rakesh Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sanchita Mukherjee
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | | |
Collapse
|
3
|
Mishra RK, Maganti L. Antitumor drugs effect on the stability of double-stranded DNA: steered molecular dynamics analysis. J Biomol Struct Dyn 2022; 40:11373-11382. [PMID: 34355668 DOI: 10.1080/07391102.2021.1960193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Denaturation of the DNA double helix inside the cell is essential for cellular processes such as replication and transcription for the growth of the cells. However, the growth of unwanted cells, which are responsible for cancerous kind of disease, is one of the biggest challenges of modern therapeutics. DNA cross-linking agents may kill cancer cells by damaging their DNA and stopping them from dividing. In the present study, we have carried out steered molecular dynamics simulations to study the effects of rupture and unzipping forces on the stability of dsDNA in the absence and presence of covalently bonded drugs. We have found that the stability of dsDNA increases strongly in the presence of covalently bonded drugs. The microscopic study of disruption of hydrogen-bonds associated with base-pairs of the dsDNA and the study of the variation of stacking overlap parameters gives evidence of symmetry during the rupture and asymmetry in the unzip event. The significance of the mechanism of force-induced melting study of the dsDNA in the absence and presence of antitumor drugs might have a biological relevance as it provides a pathway to open the double helix in a specific position and may help for the pharmaceutical design of drugs.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Rakesh Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Lakshmi Maganti
- Computational Science Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
| |
Collapse
|
4
|
Mukherjee D, Maiti S, Gouda PK, Sharma R, Roy P, Bhattacharyya D. RNABPDB: Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction. Interdiscip Sci 2022; 14:759-774. [PMID: 35705797 DOI: 10.1007/s12539-022-00528-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The stable three-dimensional structure of RNA is known to play several important biochemical roles, from post-transcriptional gene regulation to enzymatic action. These structures contain double-helical regions, which often have different types of non-canonical base pairs in addition to Watson-Crick base pairs. Hence, it is important to study their structures from experimentally obtained or even predicted ones, to understand their role, or to develop a drug against the potential targets. Molecular Modeling of RNA double helices containing non-canonical base pairs is a difficult process, particularly due to the unavailability of structural features of non-Watson-Crick base pairs. Here we show a composite web-server with an associated database that allows one to generate the structure of RNA double helix containing non-canonical base pairs using consensus parameters obtained from the database. The database classification is followed by an evaluation of the central tendency of the structural parameters as well as a quantitative estimation of interaction strengths. These parameters are used to construct three-dimensional structures of double helices composed of Watson-Crick and/or non-canonical base pairs. Our benchmark study to regenerate double-helical fragments of many experimentally derived RNA structures indicate very high accuracy. This composite server is expected to be highly useful in understanding functions of various pre-miRNA by modeling structures of the molecules and estimating binding efficiency. The database can be accessed from http://hdrnas.saha.ac.in/rnabpdb .
Collapse
Affiliation(s)
- Debasish Mukherjee
- Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India.
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Satyabrata Maiti
- Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhaba National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Prasanta Kumar Gouda
- Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Richa Sharma
- Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Parthajit Roy
- Department of Computer Science, The University of Burdwan, Golapbag, Burdwan, 713104, India
| | - Dhananjay Bhattacharyya
- Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhaba National Institute, Anushaktinagar, Mumbai, 400094, India
| |
Collapse
|
5
|
Structural switching/polymorphism by sequential base substitution at quasi-palindromic SNP site (G → A) in LCR of human β-globin gene cluster. Int J Biol Macromol 2021; 201:216-225. [PMID: 34973267 DOI: 10.1016/j.ijbiomac.2021.12.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/20/2022]
Abstract
The human β-globin gene Locus Control Region (LCR), a dominant regulator of globin gene expression contains five tissue-specific DNase I-hypersensitive sites (HSs). A single nucleotide polymorphism (SNP) (A → G) present in HS4 region of locus control region (LCR), have shown a notable association between the G allele and the occurrence of β-thalassemia. This SNP site exhibiting a hairpin - duplex equilibrium manifested in A → B like DNA transition has previously been reported from this laboratory. Since, DNA is a dynamic and adaptable molecule, so any change of a single base within a primary DNA sequence can produce major biological consequences commonly manifested in genetic disorders such as sickle cell anemia and β-thalassemia. Herein, the differential behavior of sequential single base substitutions G → A on the quasi-palindromic sequence (d-TGGGGGCCCCA; HPG11) has been explored. A combination of native gel electrophoresis, circular dichroism (CD), and UV-thermal denaturation (Tm) techniques have been used to investigate the structural polymorphism associated with various variants of HPG11 i.e. HPG11A2 to HPG11A5. The CD spectra confirmed that all the HPG11 variants exhibit a hairpin - duplex equilibrium. Oligomer concentration dependence on CD spectra has been correlated with A → B DNA conformational transition. However, as revealed in gel electrophoresis, HPG11A2 → A5 exhibit the formation of a tetramolecular structure (four-way junction) at higher oligomer concentration. UV-melting studies also supported the melting of hairpin, duplex and four-way junction structure. This polymorphism pattern may possibly be significant for DNA-protein recognition, in the process of regulation of LCR in the β-globin gene.
Collapse
|
6
|
Wang Y, Li G, Meng T, Qi L, Yan H, Wang Z. Molecular insights into the selective binding mechanism targeting parallel human telomeric G-quadruplex. J Mol Graph Model 2021; 110:108058. [PMID: 34736054 DOI: 10.1016/j.jmgm.2021.108058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/15/2022]
Abstract
Stabilizing human telomere DNA G-quadruplex (G4) proves a promising anti-cancer strategy. Though plenty of G4 stabilizing molecules have been reported, little is known about their selective binding mechanism among various G4s. Recently, a designed monohydrazone derivative (compound 15) was reported to display specific preference in binding and stabilizing parallel human telomeric G4. To reveal the selective binding mechanism, a comparative theoretical investigation was performed on two monohydrazone derivatives (compounds 1 and 15) and three telomeric G4s showing parallel, hybrid-I, and hybrid-II conformations. Two probable binding modes, i.e. the end-stacking binding and the groove binding, were predicted by molecular dockings for each monohydrazone in its binding with the telomeric G4s. Further long-timescale molecular dynamics simulations reveal the conversion from the groove binding to the end-stacking binding for both compounds, indicating the preference of the end-stacking binding mode. Structural analysis together with binding free energy calculations show that the van der Waals interaction plays a leading role in ranking the binding affinity. By forming extensive van der Waals interactions, the parallel G4-15 binding complex shows the highest binding affinity, and the corresponding compound 15 exhibits the strongest stabilizing effect to the telomeric G4. These findings agree well with the experimental observations. Through characterizing the selective binding between monohydrazones and telomeric G4s at the atomic level, the current study provides support to the design of novel selective stabilizers targeting telomeric G4s.
Collapse
Affiliation(s)
- Yue Wang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong Province, 252059, China
| | - Guo Li
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, Hainan Province, 571199, China
| | - Tong Meng
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong Province, 252059, China
| | - Lin Qi
- Railway Police College, Zhengzhou, Henan Province, 450053, China
| | - Hui Yan
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong Province, 252059, China.
| | - Zhiguo Wang
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, China.
| |
Collapse
|
7
|
Stacking geometry between two sheared Watson-Crick basepairs: Computational chemistry and bioinformatics based prediction. Biochim Biophys Acta Gen Subj 2020; 1864:129600. [PMID: 32179130 DOI: 10.1016/j.bbagen.2020.129600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 03/05/2020] [Accepted: 03/11/2020] [Indexed: 11/21/2022]
Abstract
BACKGROUND Molecular modeling of RNA double helices is possible using most probable values of basepair parameters obtained from crystal structure database. The A:A w:wC non-canonical basepair, involving Watson-Crick edges of two Adenines in cis orientation, appears quite frequently in database. Bimodal distribution of its Shear, due to two different H-bonding schemes, introduces the confusion in assigning most the probable value. Its effect is pronounced when the A:A w:wC basepair stacks on Sheared wobble G:U W:WC basepairs. METHODS We employed molecular dynamics simulations of three possible double helices with GAG, UAG and GAU sequence motifs at their centers and quantum chemical calculation for non-canonical A:A w:wC basepair stacked on G:U W:WC basepair. RESULTS We noticed stable structures of GAG motif with specifically negative Shear of the A:A basepair but stabilities of the other motifs were not found with A:A w:wC basepairing. Hybrid DFT-D and MP2 stacking energy analyses on dinucleotide step sequences, A:A w:wC::G:U W:WC and A:A w:wC::U:G W:WC reveal that viable orientation of A:A::G:U prefers one of the H-bonding modes with negative Shear, supported by crystal structure database. The A:A::U:G dinucleotide, however, prefers structure with only positive Shear. CONCLUSIONS The quantum chemical calculations explain why MD simulations of GAG sequence motif only appear stable. In the cases of the GAU and UAG motifs "tug of war" situation between positive and negative Shears of A:A w:wC basepair induces conformational plasticity. GENERAL SIGNIFICANCE We have projected comprehensive reason behind the promiscuous nature of A:A w:wC basepair which brings occasional structural plasticity.
Collapse
|
8
|
Maganti L, Bhattacharyya D. Sequence specificity in DNA–drug intercalation: MD simulation and density functional theory approaches. J Comput Aided Mol Des 2019; 34:83-95. [DOI: 10.1007/s10822-019-00268-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/29/2019] [Indexed: 12/14/2022]
|
9
|
Biswas A, Chakraborty K, Dutta C, Mukherjee S, Gayen P, Jan S, Mallick AM, Bhattacharyya D, Sinha Roy R. Engineered Histidine-Enriched Facial Lipopeptides for Enhanced Intracellular Delivery of Functional siRNA to Triple Negative Breast Cancer Cells. ACS APPLIED MATERIALS & INTERFACES 2019; 11:4719-4736. [PMID: 30628773 DOI: 10.1021/acsami.8b13794] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cytosolic delivery of functional siRNA remains the major challenge to develop siRNA-based therapeutics. Designing clinically safe and effective siRNA transporter to deliver functional siRNA across the plasma and endosomal membrane remains a key hurdle. With the aim of improving endosomal release, we have designed cyclic and linear peptide-based transporters having an Arg-DHis-Arg template. Computational studies show that the Arg-DHis-Arg template is also stabilized by the Arg-His side-chain hydrogen bonding interaction at physiological pH, which dissociates at lower pH. The overall atomistic interactions were examined by molecular dynamics simulations, which indicate that the extent of peptide_siRNA assembly formation depends greatly on physicochemical properties of the peptides. Our designed peptides having the Arg-DHis-Arg template and two lipidic moieties facilitate high yield of intracellular delivery of siRNA. Additionally, unsaturated lipid, linoleic acid moieties were introduced to promote fusogenicity and facilitate endosomal release and cytosolic delivery. Interestingly, such protease-resistant peptides provide serum stability to siRNA and exhibit high efficacy of erk1 and erk2 gene silencing in the triple negative breast cancer (TNBC) cell line. The peptide having two linoleyl moieties demonstrated comparable efficacy with commercial transfection reagent HiPerFect, as evidenced by the erk1 and erk2 gene knockdown experiment. Additionally, our study shows that ERK1/2 silencing siRNA and doxorubicin-loaded gramicidin-mediated combination therapy is more effective than siRNA-mediated gene silencing-based monotherapy for TNBC treatment.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Dhananjay Bhattacharyya
- Computational Science Division , Saha Institute of Nuclear Physics, Kolkata , 1/AF Bidhannagar , Kolkata 700064 , India
| | | |
Collapse
|
10
|
Chaudhary S, Kaushik M, Ahmed S, Kukreti R, Kukreti S. Structural Switch from Hairpin to Duplex/Antiparallel G-Quadruplex at Single-Nucleotide Polymorphism (SNP) Site of Human Apolipoprotein E ( APOE) Gene Coding Region. ACS OMEGA 2018; 3:3173-3182. [PMID: 30023863 PMCID: PMC6045395 DOI: 10.1021/acsomega.7b01654] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/19/2018] [Indexed: 05/25/2023]
Abstract
A gradual dementia, which leads to the loss of memory and intellectual abilities, is the main characteristics of Alzheimer's disease. Amyloid-β (Aβ) plaques are the main components that accumulate and form clumps in the brains of people suffering from Alzheimer's disease. Apolipoprotein E (APOE), an amyloid-binding protein is considered as one of the main genetic risk factor of the late-onset Alzheimer's disease. Different isoforms of APOE gene named APOE2, APOE3, and APOE4 are known to exist, which differ from each other at certain positions involving single-nucleotide polymorphisms (SNPs). Out of these isoforms, APOE4 increases the risk of developing late-onset Alzheimer's disease, whereas APOE3 is the most common among the general population. APOE4 differs from the common APOE3 by only one nucleotide at position +2985 (T to C), which results in immense alteration in the structure and function of the APOE gene. A combination of gel electrophoresis (polyacrylamide gel electrophoresis, PAGE), circular dichroism (CD), CD melting, thermal difference spectra and UV-thermal denaturation (TM) techniques was used to investigate the structural polymorphism associated with T → C single-nucleotide polymorphism (SNP) at the GC-rich sequence (d-TGGAGGACGTGTGCGGCCGCCT; APOE22T). Herein, we report that APOE22T DNA sequence switches between hairpin to antiparallel quadruplex from low to high oligomer concentration. On the contrary, its C-counterpart (APOE22C) forms hairpin as well as intermolecular antiparallel duplex structure. This structural change may possibly contribute to the protein recognition pattern, which, in turn, might control the APOE gene expression.
Collapse
Affiliation(s)
- Swati Chaudhary
- Nucleic
Acids Research Lab, Department of Chemistry and Cluster Innovation Center, University of Delhi, Delhi 110007, India
| | - Mahima Kaushik
- Nucleic
Acids Research Lab, Department of Chemistry and Cluster Innovation Center, University of Delhi, Delhi 110007, India
| | - Saami Ahmed
- Nucleic
Acids Research Lab, Department of Chemistry and Cluster Innovation Center, University of Delhi, Delhi 110007, India
| | - Ritushree Kukreti
- CSIR-Institute
of genomics and Integrative Biology, Delhi 110007, India
| | - Shrikant Kukreti
- Nucleic
Acids Research Lab, Department of Chemistry and Cluster Innovation Center, University of Delhi, Delhi 110007, India
| |
Collapse
|
11
|
Effect of single-residue bulges on RNA double-helical structures: crystallographic database analysis and molecular dynamics simulation studies. J Mol Model 2017; 23:311. [DOI: 10.1007/s00894-017-3480-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/19/2017] [Indexed: 11/26/2022]
|
12
|
Mukherjee D, Bhattacharyya D. Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation. J Mol Model 2017; 23:300. [DOI: 10.1007/s00894-017-3470-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/10/2017] [Indexed: 10/18/2022]
|
13
|
Kundu S, Mukherjee S, Bhattacharyya D. Melting of polymeric DNA double helix at elevated temperature: a molecular dynamics approach. J Mol Model 2017; 23:226. [DOI: 10.1007/s00894-017-3398-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 06/25/2017] [Indexed: 01/27/2023]
|
14
|
Warden MS, Tonelli M, Cornilescu G, Liu D, Hopersberger LJ, Ponniah K, Pascal SM. Structure of RNA Stem Loop B from the Picornavirus Replication Platform. Biochemistry 2017; 56:2549-2557. [PMID: 28459542 DOI: 10.1021/acs.biochem.7b00141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The presumptive RNA cloverleaf at the start of the 5'-untranslated region of the picornavirus genome is an essential element in replication. Stem loop B (SLB) of the cloverleaf is a recognition site for the host polyC-binding protein, which initiates a switch from translation to replication. Here we present the solution structure of human rhinovirus isotype 14 SLB using nuclear magnetic resonance spectroscopy. SLB adopts a predominantly A-form helical structure. The stem contains five Watson-Crick base pairs and one wobble base pair and is capped by an eight-nucleotide loop. The wobble base pair introduces perturbations into the helical parameters but does not appear to introduce flexibility. However, the helix major groove appears to be accessible. Flexibility is seen throughout the loop and in the terminal nucleotides. The pyrimidine-rich region of the loop, the apparent recognition site for the polyC-binding protein, is the most disordered region of the structure.
Collapse
Affiliation(s)
- Meghan S Warden
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Dong Liu
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Lorelei J Hopersberger
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Komala Ponniah
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Steven M Pascal
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| |
Collapse
|
15
|
Maiti S, Bhattacharyya D. Stacking interactions involving non-Watson–Crick basepairs: dispersion corrected density functional theory studies. Phys Chem Chem Phys 2017; 19:28718-28730. [DOI: 10.1039/c7cp04904h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stacking interactions between a non Watson–Crick G:A S:HT basepair and C:G basepair is predicted in terms of roll, twist and slide basepair step parameters using DFT-D augmented with coarse-grain energy penalty for sugar–phosphate backbone.
Collapse
Affiliation(s)
- Satyabrata Maiti
- Computational Science Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
- Homi Bhaba National Institute
| | - Dhananjay Bhattacharyya
- Computational Science Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
- Homi Bhaba National Institute
| |
Collapse
|
16
|
Mukherjee S, Kailasam S, Bansal M, Bhattacharyya D. Stacking interactions in RNA and DNA: Roll-slide energy hyperspace for ten unique dinucleotide steps. Biopolymers 2016; 103:134-47. [PMID: 25257334 DOI: 10.1002/bip.22566] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 12/15/2022]
Abstract
Understanding dinucleotide sequence directed structures of nuleic acids and their variability from experimental observation remained ineffective due to unavailability of statistically meaningful data. We have attempted to understand this from energy scan along twist, roll, and slide degrees of freedom which are mostly dependent on dinucleotide sequence using ab initio density functional theory. We have carried out stacking energy analysis in these dinucleotide parameter phase space for all ten unique dinucleotide steps in DNA and RNA using DFT-D by ωB97X-D/6-31G(2d,2p), which appears to satisfactorily explain conformational preferences for AU/AU step in our recent study. We show that values of roll, slide, and twist of most of the dinucleotide sequences in crystal structures fall in the low energy region. The minimum energy regions with large twist values are associated with the roll and slide values of B-DNA, whereas, smaller twist values correspond to higher stability to RNA and A-DNA like conformations. Incorporation of solvent effect by CPCM method could explain the preference shown by some sequences to occur in B-DNA or A-DNA conformations. Conformational preference of BII sub-state in B-DNA is preferentially displayed mainly by pyrimidine-purine steps and partly by purine-purine steps. The purine-pyrimidine steps show largest effect of 5-methyl group of thymine in stacking energy and the introduction of solvent reduces this effect significantly. These predicted structures and variabilities can explain the effect of sequence on DNA and RNA functionality.
Collapse
Affiliation(s)
- Sanchita Mukherjee
- Computational Science Division, Saha Institute of Nuclear Physics, Kolkata, 700064, West Bengal, India
| | | | | | | |
Collapse
|
17
|
Mondal M, Halder S, Chakrabarti J, Bhattacharyya D. Hybrid simulation approach incorporating microscopic interaction along with rigid body degrees of freedom for stacking between base pairs. Biopolymers 2015; 105:212-26. [PMID: 26600167 DOI: 10.1002/bip.22787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/19/2015] [Accepted: 11/17/2015] [Indexed: 11/07/2022]
Abstract
Stacking interaction between the aromatic heterocyclic bases plays an important role in the double helical structures of nucleic acids. Considering the base as rigid body, there are total of 18 degrees of freedom of a dinucleotide step. Some of these parameters show sequence preferences, indicating that the detailed atomic interactions are important in the stacking. Large variants of non-canonical base pairs have been seen in the crystallographic structures of RNA. However, their stacking preferences are not thoroughly deciphered yet from experimental results. The current theoretical approaches use either the rigid body degrees of freedom where the atomic information are lost or computationally expensive all atom simulations. We have used a hybrid simulation approach incorporating Monte-Carlo Metropolis sampling in the hyperspace of 18 stacking parameters where the interaction energies using AMBER-parm99bsc0 and CHARMM-36 force-fields were calculated from atomic positions. We have also performed stacking energy calculations for structures from Monte-Carlo ensemble by Dispersion corrected density functional theory. The available experimental data with Watson-Crick base pairs are compared to establish the validity of the method. Stacking interaction involving A:U and G:C base pairs with non-canonical G:U base pairs also were calculated and showed that these structures were also sequence dependent. This approach could be useful to generate multiscale modeling of nucleic acids in terms of coarse-grained parameters where the atomic interactions are preserved. This method would also be useful to predict structure and dynamics of different base pair steps containing non Watson-Crick base pairs, as found often in the non-coding RNA structures. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 212-226, 2016.
Collapse
Affiliation(s)
- Manas Mondal
- Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700 064, India
| | - Sukanya Halder
- Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700 064, India
| | - Jaydeb Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Center for Basic Sciences, Sector III, Salt Lake, Kolkata, 700 098, India
| | - Dhananjay Bhattacharyya
- Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700 064, India
| |
Collapse
|
18
|
Mondal P, Biswas M, Goldau T, Heckel A, Burghardt I. In Search of an Efficient Photoswitch for Functional RNA: Design Principles from a Microscopic Analysis of Azobenzene-linker-RNA Dynamics with Different Linkers. J Phys Chem B 2015; 119:11275-86. [PMID: 26125118 DOI: 10.1021/acs.jpcb.5b03118] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The design of optimal photoswitches to regulate nucleic acid functionality is a considerable challenge. Azobenzene switches that are covalently bound to the nucleic acid backbone are a paradigm example that has been studied using different types of linker species connecting the chromophore to the backbone. To support experimental efforts to construct optimal azobenzene-linker-RNA combinations, we introduce here a systematic approach for theoretical analysis, which provides criteria for the local embedding of the chromophore via a chosen linker. Using a local reference frame adapted to the chromophore, quantitative measures are provided for (i) the propensity of stacking in competition with a drift toward the minor or major groove, (ii) the tendency to disrupt the native hydrogen bond network, (iii) the structural flexibility of the chromophore-linker combination, and (iv) the correlations with the presence of a base in the opposite strand. Large differences in structural stability between the trans and cis forms of the azobenzene chromophore, according to these criteria, indicate good functionality and lead to significant differences in melting temperatures. In particular, a recently synthesized deoxyribose linker proves optimal within the set of azobenzene-linker-RNA combinations considered.
Collapse
Affiliation(s)
- Padmabati Mondal
- Institute for Physical and Theoretical Chemistry and ‡Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Mithun Biswas
- Institute for Physical and Theoretical Chemistry and ‡Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Thomas Goldau
- Institute for Physical and Theoretical Chemistry and ‡Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Alexander Heckel
- Institute for Physical and Theoretical Chemistry and ‡Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Irene Burghardt
- Institute for Physical and Theoretical Chemistry and ‡Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| |
Collapse
|
19
|
Mondal M, Mukherjee S, Halder S, Bhattacharyya D. Stacking geometry for non-canonical G:U wobble base pair containing dinucleotide sequences in RNA: dispersion-corrected DFT-D study. Biopolymers 2015; 103:328-38. [DOI: 10.1002/bip.22616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 01/01/2015] [Accepted: 01/08/2015] [Indexed: 01/06/2023]
Affiliation(s)
- Manas Mondal
- Computational Science Division; Saha Institute of Nuclear Physics; 1/AF Bidhannagar Kolkata 700064 India
| | - Sanchita Mukherjee
- Computational Science Division; Saha Institute of Nuclear Physics; 1/AF Bidhannagar Kolkata 700064 India
| | - Sukanya Halder
- Computational Science Division; Saha Institute of Nuclear Physics; 1/AF Bidhannagar Kolkata 700064 India
| | - Dhananjay Bhattacharyya
- Computational Science Division; Saha Institute of Nuclear Physics; 1/AF Bidhannagar Kolkata 700064 India
| |
Collapse
|
20
|
Bhattacharya S, Mittal S, Panigrahi S, Sharma P, S P P, Paul R, Halder S, Halder A, Bhattacharyya D, Mitra A. RNABP COGEST: a resource for investigating functional RNAs. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav011. [PMID: 25776022 PMCID: PMC4360618 DOI: 10.1093/database/bav011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Structural bioinformatics of RNA has evolved mainly in response to the rapidly accumulating evidence that non-(protein)-coding RNAs (ncRNAs) play critical roles in gene regulation and development. The structures and functions of most ncRNAs are however still unknown. Most of the available RNA structural databases rely heavily on known 3D structures, and contextually correlate base pairing geometry with actual 3D RNA structures. None of the databases provide any direct information about stabilization energies. However, the intrinsic interaction energies of constituent base pairs can provide significant insights into their roles in the overall dynamics of RNA motifs and structures. Quantum mechanical (QM) computations provide the only approach toward their accurate quantification and characterization. ‘RNA Base Pair Count, Geometry and Stability’ (http://bioinf.iiit.ac.in/RNABPCOGEST) brings together information, extracted from literature data, regarding occurrence frequency, experimental and quantum chemically optimized geometries, and computed interaction energies, for non-canonical base pairs observed in a non-redundant dataset of functional RNA structures. The database is designed to enable the QM community, on the one hand, to identify appropriate biologically relevant model systems and also enable the biology community to easily sift through diverse computational results to gain theoretical insights which could promote hypothesis driven biological research. Database URL:http://bioinf.iiit.ac.in/RNABPCOGEST
Collapse
Affiliation(s)
- Sohini Bhattacharya
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Shriyaa Mittal
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Swati Panigrahi
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Purshotam Sharma
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Preethi S P
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Rahul Paul
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Sukanya Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Dhananjay Bhattacharyya
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| |
Collapse
|