Prediction of secondary and tertiary structures of human BC200 RNA (BCYRN1) based on experimental and bioinformatic cross-validation

2018 ◽  
Vol 475 (17) ◽  
pp. 2727-2748
Author(s):  
Patrycja Sosińska-Zawierucha ◽  
Piotr Zawierucha ◽  
Andrzej Bręborowicz ◽  
Jan Barciszewski
Keyword(s):  
Secondary Structure ◽  
Messenger Rna ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Rnase H ◽  
Partial Hydrolysis ◽  
Tertiary Structures ◽  
Phylogenetic Model ◽  
Bioinformatic Approaches

Based on experimental and bioinformatic approaches, we present the first empirically established complete secondary structure of human BC200 RNA. BC200 RNA is a brain-specific non-messenger RNA with a confirmed regulatory role in dendritic translation in neurons. Although the involvement of human BC200 RNA in various types of tumour and Alzheimer's disease has been repeatedly confirmed, the exact secondary structure remains not fully elucidated. To determine the secondary structure of BC200 RNA in vitro, we performed partial hydrolysis with sequence-specific nucleases and lead-induced cleavage. We also examined the availabilities of putative single-stranded regions and base-pairing interactions via specific DNAzymes and RNase H assay. To determine the complete spatial folding of BC200 RNA, we used experimental data as constraints in structure prediction programs and performed a comparison of results obtained by several algorithms using different criteria. Based on the experimental-derived secondary structure of BC200 RNA, we also predicted the tertiary structure of BC200 RNA. The presented combination of experimental and bioinformatic approaches not only enabled the determination of the most reliable secondary and tertiary structures of human BC200 RNA (largely in agreement with the previous phylogenetic model), but also verified the compatibility and potential disadvantages of utilizing in silico structure prediction programs.

Torus Circumference and Thickness Parameters From a Linear DNA Size Series Suggest How Toruses Self-Assemble

1985 ◽  
Vol 43 ◽  
pp. 522-523
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx
Keyword(s):  
Tertiary Structure ◽  
Dna Complexes ◽  
Tertiary Structures ◽  
Self Assembling ◽  
Double Stranded Dna ◽  
Calf Thymus ◽  
Dna Organization ◽  
Condensed Dna ◽  
Dna Size

Certain double stranded DNA bacteriophage and viruses are thought to have their DNA organized into large torus shaped structures. Morphologically, these poorly understood biological DNA tertiary structures resemble spermidine-condensed DNA complexes formed in vitro in the total absence of other macromolecules normally synthesized by the pathogens for the purpose of their own DNA packaging. Therefore, we have studied the tertiary structure of these self-assembling torus shaped spermidine- DNA complexes in a series of reports. Using freeze-etch, low Pt-C metal (10-15Å) replicas, we have visualized the microscopic DNA organization of both calf Thymus( CT) and linear 0X-174 RFII DNA toruses. In these structures DNA is circumferentially wound, continuously, around the torus into a semi-crystalline, hexagonal packed array of parallel DNA helix sections.

In Silico Study of Potential Cross-Kingdom Plant MicroRNA Based Regulation in Chronic Myeloid Leukemia

2020 ◽  
Vol 17 (2) ◽  
pp. 125-132
Author(s):  
Marjanu Hikmah Elias ◽  
Noraziah Nordin ◽  
Nazefah Abdul Hamid
Keyword(s):  
Targeted Therapy ◽  
In Silico ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Target Prediction ◽  
In Silico Analysis ◽  
Microrna Target ◽  
Good Target

Background: Chronic Myeloid Leukaemia (CML) is associated with the BCRABL1 gene, which plays a central role in the pathogenesis of CML. Thus, it is crucial to suppress the expression of BCR-ABL1 in the treatment of CML. MicroRNA is known to be a gene expression regulator and is thus a good candidate for molecularly targeted therapy for CML. Objective: This study aims to identify the microRNAs from edible plants targeting the 3’ Untranslated Region (3’UTR) of BCR-ABL1. Methods: In this in silico analysis, the sequence of 3’UTR of BCR-ABL1 was obtained from Ensembl Genome Browser. PsRNATarget Analysis Server and MicroRNA Target Prediction (miRTar) Server were used to identify miRNAs that have binding conformity with 3’UTR of BCR-ABL1. The MiRBase database was used to validate the species of plants expressing the miRNAs. The RNAfold web server and RNA COMPOSER were used for secondary and tertiary structure prediction, respectively. Results: In silico analyses revealed that cpa-miR8154, csi-miR3952, gma-miR4414-5p, mdm-miR482c, osa-miR1858a and osa-miR1858b show binding conformity with strong molecular interaction towards 3’UTR region of BCR-ABL1. However, only cpa-miR- 8154, osa-miR-1858a and osa-miR-1858b showed good target site accessibility. Conclusion: It is predicted that these microRNAs post-transcriptionally inhibit the BCRABL1 gene and thus could be a potential molecular targeted therapy for CML. However, further studies involving in vitro, in vivo and functional analyses need to be carried out to determine the ability of these miRNAs to form the basis for targeted therapy for CML.

In Silico Study of Secondary Structure of Hemoglobin Protein

2021 ◽  
pp. 6245-6249
Author(s):  
Roma Chandra
Keyword(s):  
Secondary Structure ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Alpha Helix ◽  
Prediction Methods ◽  
Protein Secondary Structures

Protein structure prediction is one of the important goals in the area of bioinformatics and biotechnology. Prediction methods include structure prediction of both secondary and tertiary structures of protein. Protein secondary structure prediction infers knowledge related to presence of helixes, sheets and coils in a polypeptide chain whereas protein tertiary structure prediction infers knowledge related to three dimensional structures of proteins. Protein secondary structures represent the possible motifs or regular expressions represented as patterns that are predicted from primary protein sequence in the form of alpha helix, betastr and and coils. The secondary structure prediction is useful as it infers information related to the structure and function of unknown protein sequence. There are various secondary structure prediction methods used to predict about helixes, sheets and coils. Based on these methods there are various prediction tools under study. This study includes prediction of hemoglobin using various tools. The results produced inferred knowledge with reference to percentage of amino acids participating to produce helices, sheets and coils. PHD and DSC produced the best of the results out of all the tools used.

scholarly journals TMBpro: secondary structure, β-contact and tertiary structure prediction of transmembrane β-barrel proteins

2007 ◽  
Vol 24 (4) ◽  
pp. 513-520 ◽  
Author(s):  
Arlo Randall ◽  
Jianlin Cheng ◽  
Michael Sweredoski ◽  
Pierre Baldi
Keyword(s):  
Secondary Structure ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Tertiary Structure Prediction

Protamine messenger RNA: partial purification and characterization of a heterogeneous family of polyadenylated messenger components

1979 ◽  
Vol 57 (6) ◽  
pp. 945-958 ◽  
Author(s):  
Kostas Iatrou ◽  
Lashitew Gedamu ◽  
Gordon H. Dixon
Keyword(s):  
Nucleotide Sequence ◽  
Messenger Rna ◽  
Rnase H ◽  
Partial Purification ◽  
Polyacrylamide Gels ◽  
Purification And Characterization ◽  
Sequence Variations ◽  
Duplex Formation

Poly(A)+ protamine mRNA (pmRNA) components were isolated after separation on denaturing preparative polyacrylamide gels. The four size classes of protamine mRNA described previously were found to contain poly(A) tracts of different lengths. The pmRNA1 was found to be associated with (A)110, pmRNA2 with (A)90, pmRNA3 with (A)85, and pmRNA4 with (A)69. Following deadenylation with RNase H after duplex formation with oligo-dT, the isolated mRNAs were found to be still heterogeneous, although highly enriched in certain of the deadenylated components. DNA complementary to the isolated mRNAs (cDNA) was synthesized in vitro. Following depurination, the oligopyrimidine maps indicated that C7T4, corresponding to an Arg-Arg-Gly-Gly sequence in protamine and originally thought to be characteristic of all mRNA components, is present in only one or possibly two of the components. Cross-hybridizations between the cDNAs and the four poly(A)+ pmRNAs indicated that a basic polynucleotide unit of substantial length is common to all four mRNAs and that the existing nucleotide sequence variations probably originate from one or both of the non-coding portions of the mRNA molecules.

PROTEIN SECONDARY STRUCTURE PREDICTION USING NMR CHEMICAL SHIFT DATA

2010 ◽  
Vol 08 (05) ◽  
pp. 867-884 ◽  
Author(s):  
YUZHONG ZHAO ◽  
BABAK ALIPANAHI ◽  
SHUAI CHENG LI ◽  
MING LI
Keyword(s):  
Chemical Shift ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Nearest Neighbor ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Accurate Determination ◽  
Protein Secondary Structure ◽  
Sequence Information ◽  
K Nearest Neighbor

Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b) easily extendable to (the dynamic) new databases; and (c) approaching to the limit of accuracy. We introduce new approaches using k-nearest neighbor algorithm to do the basic prediction and use the BCJR algorithm to smooth the predictions and combine different predictions from chemical shifts and based on sequence information only. Our new system, SUCCES, improves the accuracy of all existing methods on a large dataset of 805 proteins (at 86% Q3 accuracy and at 92.6% accuracy when the boundary residues are ignored), and it is easily extendable to any new dataset without requiring any new training. The software is publicly available at .

scholarly journals Secondary Structure and Hybridization Accessibility of Hepatitis C Virus 3′-Terminal Sequences

2002 ◽  
Vol 76 (19) ◽  
pp. 9563-9574 ◽  
Author(s):  
Robert M. Smith ◽  
Cherie M. Walton ◽  
Catherine H. Wu ◽  
George Y. Wu
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Secondary Structure ◽  
Rna Structure ◽  
Genome Stability ◽  
Rnase H ◽  
Hcv Rna ◽  
Positive Strand ◽  
Negative Strand

ABSTRACT The 3′-terminal sequences of hepatitis C virus (HCV) positive- and negative-strand RNAs contribute cis-acting functions essential for viral replication. The secondary structure and protein-binding properties of these highly conserved regions are of interest not only for the further elucidation of HCV molecular biology, but also for the design of antisense therapeutic constructs. The RNA structure of the positive-strand 3′ untranslated region has been shown previously to influence binding by various host and viral proteins and is thus thought to promote HCV RNA synthesis and genome stability. Recent studies have attributed analogous functions to the negative-strand 3′ terminus. We evaluated the HCV negative-strand secondary structure by enzymatic probing with single-strand-specific RNases and thermodynamic modeling of RNA folding. The accessibility of both 3′-terminal sequences to hybridization by antisense constructs was evaluated by RNase H cleavage mapping in the presence of combinatorial oligodeoxynucleotide libraries. The mapping results facilitated identification of antisense oligodeoxynucleotides and a 10-23 deoxyribozyme active against the positive-strand 3′-X region RNA in vitro.

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