Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes

2012 ◽  
Vol 14 (36) ◽  
pp. 12580 ◽  
Author(s):  
Claudio A. Morgado ◽  
Daniel Svozil ◽  
Douglas H. Turner ◽  
Jiří Šponer
Keyword(s):  
Nucleic Acids ◽  
Base Stacking ◽  
Base Pairs ◽  
Rna Duplexes

scholarly journals Role of Inosine–Uracil Base Pairs in the Canonical RNA Duplexes

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 324 ◽  
Author(s):  
Naďa Špačková ◽  
Kamila Réblová
Keyword(s):  
Base Pairs ◽  
Rna Duplexes ◽  
Uracil Base

scholarly journals Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor

2020 ◽  
Vol 48 (14) ◽  
pp. 7640-7652 ◽  
Author(s):  
Anna Wypijewska del Nogal ◽  
Anders F Füchtbauer ◽  
Mattias Bood ◽  
Jesper R Nilsson ◽  
Moa S Wranne ◽  
...  
Keyword(s):  
Quantum Yield ◽  
Nucleic Acids ◽  
Photophysical Properties ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Molar Absorptivity ◽  
Dna And Rna ◽  
Double Stranded Dna ◽  
Rna Duplexes

Abstract With the central role of nucleic acids there is a need for development of fluorophores that facilitate the visualization of processes involving nucleic acids without perturbing their natural properties and behaviour. Here, we incorporate a new analogue of adenine, 2CNqA, into both DNA and RNA, and evaluate its nucleobase-mimicking and internal fluorophore capacities. We find that 2CNqA displays excellent photophysical properties in both nucleic acids, is highly specific for thymine/uracil, and maintains and slightly stabilises the canonical conformations of DNA and RNA duplexes. Moreover, the 2CNqA fluorophore has a quantum yield in single-stranded and duplex DNA ranging from 10% to 44% and 22% to 32%, respectively, and a slightly lower one (average 12%) inside duplex RNA. In combination with a comparatively strong molar absorptivity for this class of compounds, the resulting brightness of 2CNqA inside double-stranded DNA is the highest reported for a fluorescent base analogue. The high, relatively sequence-independent quantum yield in duplexes makes 2CNqA promising as a nucleic acid label and as an interbase Förster resonance energy transfer (FRET) donor. Finally, we report its excellent spectral overlap with the interbase FRET acceptors qAnitro and tCnitro, and demonstrate that these FRET pairs enable conformation studies of DNA and RNA.

scholarly journals Role of the backbone of nucleic acids in the stability of Hg2+-mediated canonical base pairs and thymine–thymine mispair: a DFT study

RSC Advances ◽  
2020 ◽  
Vol 10 (67) ◽  
pp. 40969-40982
Author(s):  
Surjit Bhai ◽  
Bishwajit Ganguly
Keyword(s):  
Nucleic Acids ◽  
Dft Study ◽  
Base Pairs ◽  
Canonical Base ◽  
The Stability

Hg2+-mediated PNA–PNA mispair duplex (PTTTTP) is more energetically favoured compared to DNA–DNA mispair duplex (DTTTTD).

Evaluation of the 2 NH2A—T Pair in Hybridization, I Synthesis of the DNA/RNA Hybrid Oligomers Containing 2-Aminoadenosines

1988 ◽  
Vol 43 (5) ◽  
pp. 623-630 ◽  
Author(s):  
Kaeko Kikuchi ◽  
Yoshio Taniyama ◽  
Ryuji Marumoto
Keyword(s):  
Hydrogen Bonding ◽  
Dna Structure ◽  
Dna Duplexes ◽  
Cd Spectra ◽  
Base Pairing ◽  
Base Stacking ◽  
Base Pairs ◽  
Nuclease P1 ◽  
Rna Duplexes

Abstract DNA decamers containing 2-aminoadenosine were synthesized. Oligonucleotide duplexes including the 2 NH2A-T base pairs were prepared and their Tm profile examined. Contrary to expectation, elevation of the Tm value by the 2 NH2 group is very small in DNA/RNA duplexes. From the CD spectra measurement, we assume that the distortion of the B-DNA structure caused by scattered DNA/RNA base pairing diminishes the efficient hydrogen bonding and base stacking of the duplexes. It was also found that the DNA duplexes containing 2-aminoadenosine hybrids are considerably resistant to ribonuclease T2 or nuclease P1 digestion.

scholarly journals Role of pH in The Stability of Cytosine-Cytosine Mismatch and Canonical AT & GC Base Pairs Mediated With Silver Ion: A DFT Study

2021 ◽  
Author(s):  
Surjit Bhai ◽  
Bishwajit Ganguly
Keyword(s):  
Hydrogen Bonding ◽  
Nucleic Acids ◽  
Base Pair ◽  
Dna Duplexes ◽  
Base Pairs ◽  
Aim Analysis ◽  
C Complex ◽  
The Stability ◽  
Ph Range

Abstract Metallo-nucleic acids have been investigated for their applications in the field of nanodevices and genetic expansion. The cytosine-Ag+-cytosine mismatch base pair interactions and their stability in nucleic acids have attracted the attention of chemists. We report a systematic study of canonical, mismatch, Ag+ mediated system with CC, AT, and GC base pairs computationally. The stability of such mismatch base pairs is dependent on the pH range ~5 to 9 and the duplexes beyond this range are unstable. The DFT calculations performed with the model DNA duplexes comprising of such mismatch pairs reveal the stability trend while varying the pH conditions. The stability of canonical Watson-Crick ATGC base pairs was compared with the CCAT and CCGC mismatch base pairs and the calculated results at B3LYP-D3/6-31G* level of theory in the aqueous phase suggest that the base stacking and hydrogen bonding are well maintained in the former case, however, the larger perturbations in the geometry are observed with the mispair and relatively unstable. The calculated binding energy at B3LYP/6-31G* level of theory of ATGC is energetically more stable (~15 kcal/mol) than the mismatch base pairs. The Ag+ mediated mismatch base pairs i.e., C_CAT and C_CGC examined at the same level of theory suggest that the CC mismatch base pairs complexed with proper alignment to the Ag+ ion and the AT and GC bases maintained the hydrogen bonding interactions. The mismatched base pair duplex systems i.e., C_CAT and C_CGC are structurally similar to the canonical Watson-Crick base pairs and energetically stable by ~40 and ~50 kcal/mol compared to the canonical ATGC base pairs. The experimental report on the thermal transition profile in 5’-(A)10C(A)10-3’ and 5’ (T)10C(T)10-3’ duplexes showed remarkable stability and corroborate the calculated results.[1] The stability of Ag+ mediated mismatch bases at the higher pH 9 was also examined and the nucleobases such as guanine and thymine would be deprotonated under this condition. The calculated results suggest that the CCA_T and CCG_C duplexes are largely distorted with the complexation of Ag+ with the AT and GC base pairs and would in turn denature the duplex. The AIM analysis performed at B3LYP-D3/6-31G* level of theory for all the studied Ag+ mediated complexes reveals that the Ag+ interaction with the corresponding nucleobases was electrostatic in nature. The role of pH in governing the stability of C-Ag+-C complex formation in mismatch base nucleic acids is crucial for their application of genetic expansion and nucleic acid-based nanodevices.

scholarly journals OP0045 NLRP12 INVOLVES IN THE LUPUS WITH POSITIVE INTERFERON SIGNATURE

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 23.2-24
Author(s):  
Y. P. Tsao ◽  
F. Y. Tseng ◽  
C. W. Chao ◽  
M. H. Chen ◽  
S. T. Chen
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Animal Models ◽  
Nucleic Acids ◽  
Disease Activity ◽  
Interferon Signature ◽  
Healthy Donors ◽  
Healthy Control ◽  
Lupus Disease Activity

Background:Systemic lupus erythematous (SLE) is a systemic autoimmune disease with diverse etiological factors. It was recognized that interferon (IFN) signature involved in the progress of SLE. NLRP12 (NOD-like receptor family (NLR) pyrin domain containing 12) is a pyrin containing NLR protein that we had linked its new biological function to the cross-regulation of Toll like receptor (TLRs) and Rig-I like receptor (RIG-I) pathways. NLPR12 acts as an innate immune check-point in regulating type I IFNs expression during TLRs and RIG-I activation. The importance of NLRP12 in lupus disease activity remained to be elucidated.Objectives:To clarify the role of NLRP12 in regulating the interferon signature.Methods:Peripheral blood mononuclear cells (PBMCs) were collected from SLE patients and healthy donors for analysis of NLRP12 and IFN-α gene expression by RT-QPCR. PBMCs were applied for Chromatin immuneprecipitation (ChIP) assay and electrical mobility shift assay (EMSA) to determine the putative transcription factor that regulates NLRP12 expression. An involvement of epigenetic regulation of NLRP12 expression in SLE patients was also analyzed. Bone marrow derived dendritic cells (BMDCs) were collected from wild type mouse and Nlrp12 knocked-out mice. Another CD14+ monocytes were isolated from 10 cases of lupus patients and 8 cases of healthy control, following by stimulating different type of nucleic acids, and IFN-α and IL-6 were measured with ELISA assay. CD14+ monocytes in lupus patients were also pre-treated with IFNAR2 antibody for further nucleic acid stimulation. Two mice models were applied for evaluation the role of Nlrp12: intraperitoneal injection of TMPD (2,6,10,14-tetramethylpentadecane, or pristane) in C57BL/6 mice and Faslpr mice. Both models were conducted with and without Nlrp12 knockout.Results:NLRP12 expression was significantly lower in PBMC isolated from SLE patients compared to healthy donors. The inverse correlation was observed in NLRP12 and IFNA gene expression as well as NLRP12 expression and amount of double-stranded DNA autoantibody in SLE patients. NLRP12 expression showed negative correlations with IFN-α treatment, as well as herpes simplex virus-1 (HSV-1) infection. Results from ChIP and EMSA analysis indicated a potential transcription factor 1 (TF-1) regulating NLRP12 promoter activity. TF-1 lead to transcriptional suppression of NLRP12 in SLE PBMC, and it was gradually induced after IFN treatment. Recruitment of TF-1 to NLRP12 promoter in SLE PBMC compared to the healthy PBMC was detected, and increased when treating with IFN. Human CD14+ monocytes collected from lupus and healthy control stimulating with different type of nucleic acids revealing significant increasing level of IFN-α and IL-6 in lupus patients. Among animal models, both pristine induced mice and Faslpr mice revealed increasing autoantibodies production and severity of glomerulonephritis in Nlrp12-/- group in comparison with Nlrp12+/+ ones, indicating the role of NLRP12 in maintaining positive interferon signature as well as disease activity.Conclusion:Expression level of NLRP1.2 has been demonstrated to be a biomarker of disease activity in SLE patients. The NLRP12 was involved in the interferon signature, which was also negatively regulated by TF-1. Both clinical samples and animal models revealed NLRP12 in maintaining the positive interferon signature, indicating the possible role of exacerbating factor for lupus disease activity.Disclosure of Interests:None declared

scholarly journals Adaptation, Ecology, and Evolution of the Halophilic Stromatolite ArchaeonHalococcus hamelinensisInferred through Genome Analyses

Archaea ◽  
2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Reema K. Gudhka ◽  
Brett A. Neilan ◽  
Brendan P. Burns
Keyword(s):  
Unknown Function ◽  
Energy Production ◽  
Extreme Environment ◽  
Evolutionary Significance ◽  
Base Pairs ◽  
Protein Coding ◽  
Inorganic Ion ◽  
Damage Repair ◽  
Genome Analyses

Halococcus hamelinensiswas the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome ofH. hamelinensisconsisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of theH. hamelinensisgenome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome ofH. hamelinensisalso revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes ofH. hamelinensisagainst various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

Sign in / Sign up

Export Citation Format

Share Document