Telomeric Repeat Sequences Research Articles

Metagenomic discovery of a distinct inflammatory subtype of human angiosarcoma associated with human herpesvirus 7.

11047 Background: Angiosarcomas are rare, clinically-aggressive endothelial tumors with remarkable heterogeneity in terms of anatomical and etiological origins, amongst which UV-radiation and oncogenic viruses have been implicated. Methods: The genomic and transcriptomic landscapes of human angiosarcomas were examined using whole genome sequencing (n = 18) and RNAseq (n = 14). Results were validated in an extended cohort of FFPE tissue (n = 57) on various platforms. Results: We observed recurrent mutations in known angiosarcoma-associated genes including TP53, KDR, POT1 and PTPRB. The median tumor mutation burden (TMB) was 1.95 mutations per megabase and was highest in a subset of head and neck angiosarcomas (HN-AS, n = 6) harboring UV signatures. The remaining cases, including seven HN-AS, contained a significantly lower TMB (5.04 vs 0.91, p= 0.0007). In corroboration, UV exposures were validated by cyclobutane pyrimidine dimer immunohistochemistry in 15 of 35 (42.9%) HN-AS and cutaneous angiosarcomas, but not in visceral or breast angiosarcomas. Gene set enrichment analysis (GSEA) revealed upregulation of “cell cycle” and “inflammation” pathways in angiosarcomas. Notably, drug inhibition of overexpressed kinases including aurora kinase, polo-like kinase and checkpoint kinase-1 potently reduced viability in two angiosarcoma cell lines, achieving IC50s of < 1µM. Metagenomic analysis detected viral reads mapping to the human herpesvirus-7 (HHV-7) genome, which were verified by PCR and immunohistochemistry. Genomic integration of HHV-7 was demonstrated at its flanking DRR telomeric repeat sequence adjoining the subtelomeric region of chromosome 17p. Overall, HHV-7 was detected in 38 of 57 (66.7%) angiosarcomas and inversely correlated with UV exposure ( p= 0.01). GSEA and Nanostring IO360 profiling showed that “inflammation” pathways were enriched in viral-positive angiosarcomas, while “cell cycle” pathways were enriched in viral-negative cases. Compared with HHV-7 negative cases, HHV-7 positive angiosarcomas were associated with high tumor inflammation scores (TIS ≥ median 6.74) (73.3% vs 25.0%, p = 0.02). Conclusions: We identified distinct subtypes of angiosarcoma characterized by HHV7-positive “inflammation” and UV-associated “cell cycle” phenotypes.

Cancer therapy with a CRISPR-assisted telomerase-activating gene expression system.

Cancer is caused by a series of alterations in genome and epigenome and exists in multiple complex forms, making it difficult to be prevented and/or treated. Telomerase, an enzyme responsible for the maintenance of telomere, is silent in most normal somatic cells but activated in 90% of cancer cells, making it an excellent target for cancer therapy. Therefore, various telomerase activity inhibitors have been developed to treat cancer but all failed due to side effects. Here we acted oppositely to develop a cancer gene therapy named telomerase-activating gene expression (Tage) system by utilizing the telomerase activity in cancer cells. The Tage system consisted of an effector gene expression vector that carried a 3' telomerase-recognizable stick end and an artificial transcription factor expression vector that could express dCas9-VP64 and an sgRNA targeting telomere repeat sequences. By using Cas9 as an effector gene, the Tage system effectively killed various cancer cells, including HepG2, HeLa, PANC-1, MDA-MB-453, A549, HT-29, SKOV-3, Hepa1-6, and RAW264.7, without affecting normal cells MRC-5, HL7702, and bone marrow mesenchymal stem cell (BMSC). More importantly, a four-base 3' stick end produced by the homothallic switching endonuclease in cells could be recognized by telomerase, allowing the Tage system to effectively kill cancer cells in vivo. The Tage system could effectively and safely realize its in vivo application by using adeno-associated virus (AAV) as gene vector. The virus-loaded Tage system could significantly and specifically kill cancer cells in mice by intravenous drug administration without side effects or toxicity.

The interactions of novel mononuclear platinum-based complexes with DNA

BackgroundCisplatin has been widely used for the treatment of cancer and its antitumour activity is attributed to its capacity to form DNA adducts, predominantly at guanine residues, which impede cellular processes such as DNA replication and transcription. However, there are associated toxicity and drug resistance issues which plague its use. This has prompted the development and screening of a range of chemotherapeutic drug analogues towards improved efficacy. The biological properties of three novel platinum-based compounds consisting of varying cis-configured ligand groups, as well as a commercially supplied compound, were characterised in this study to determine their potential as anticancer agents.MethodsThe linear amplification reaction was employed, in conjunction with capillary electrophoresis, to quantify the sequence specificity of DNA adducts induced by these compounds using a DNA template containing telomeric repeat sequences. Additionally, the DNA interstrand cross-linking and unwinding efficiency of these compounds were assessed through the application of denaturing and native agarose gel electrophoresis techniques, respectively. Their cytotoxicity was determined in HeLa cells using a colorimetric cell viability assay.ResultsAll three novel platinum-based compounds were found to induce DNA adduct formation at the tandem telomeric repeat sequences. The sequence specificity profile at these sites was characterised and these were distinct from that of cisplatin. Two of these compounds with the enantiomeric 1,2-diaminocyclopentane ligand (SS and RR-DACP) were found to induce a greater degree of DNA unwinding than cisplatin, but exhibited marginally lower DNA cross-linking efficiencies. Furthermore, the RR-isomer was more cytotoxic in HeLa cells than cisplatin.ConclusionsThe biological characteristics of these compounds were assessed relative to cisplatin, and a variation in the sequence specificity and a greater capacity to induce DNA unwinding was observed. These compounds warrant further investigations towards developing more efficient chemotherapeutic drugs.

Multivalent Self-Assembled DNA Polymer for Tumor-Targeted Delivery and Live Cell Imaging of Telomerase Activity.

The efficient detection and in situ monitoring of telomerase activity is of great importance for cancer diagnosis and biomedical research. Here we report for the first time that the development of a novel multivalent self-assembled DNA polymer, constructed through telomerase primer sequence (ITS) triggered hybridization chain assembly using two functional hairpin probes (tumor-trageting aptamer modified H1 and signal probe modified H2), for sensitive detection and imaging of telomerase activity in living cells. After internalizing into the tumor cells by multivalent aptamer targeting, the ITS on DNA polymers can be elongated by intracellular telomerase to generate telomere repeat sequences that are complementary with the signal probe, which can proceed along the DNA polymers, and gradually light up the whole DNA polymers, leading to an enhanced fluorescence signal directly correlated with the activity of telomerase. Our results demonstrated that the developed DNA polymer show excellent performance for specifically detecting telomerase activity in cancer cells, dynamically monitoring the activity change of telomerase in response to telomerase-based drugs, and efficiently distinguishing cancer cells from normal cells. The proposed strategy may afford a valuable tool for the monitoring of telomerase activity in living cells and have great implications for biological and diagnostic applications.

Holliday Junctions Formed from Human Telomeric DNA.

Cells have evolved inherent mechanisms, like homologous recombination (HR), to repair damaged DNA. However, repairs at telomeres can lead to genomic instability, often associated with cancer. While most rapidly dividing cells employ telomerase, the others maintain telomere length through HR-dependent alternative lengthening of telomeres (ALT) pathways. Here we describe the crystal structures of Holliday junction intermediates of the HR-dependent ALT mechanism. Using an extended human telomeric repeat, we also report the crystal structure of two Holliday junctions in close proximity, which associate together through strand exchange to form a hemicatenated double Holliday junction. Our combined structural results demonstrate that ACC nucleotides in the C-rich lagging strand (5'-CTAACCCTAA-3') at the telomere repeat sequence constitute a conserved structural feature that constrains crossover geometry and is a preferred site for Holliday junction formation in telomeres.

Relationship Between Sequence Homology, Genome Architecture, and Meiotic Behavior of the Sex Chromosomes in North American Voles.

In most mammals, the X and Y chromosomes synapse and recombine along a conserved region of homology known as the pseudoautosomal region (PAR). These homology-driven interactions are required for meiotic progression and are essential for male fertility. Although the PAR fulfills key meiotic functions in most mammals, several exceptional species lack PAR-mediated sex chromosome associations at meiosis. Here, we leveraged the natural variation in meiotic sex chromosome programs present in North American voles (Microtus) to investigate the relationship between meiotic sex chromosome dynamics and X/Y sequence homology. To this end, we developed a novel, reference-blind computational method to analyze sparse sequencing data from flow-sorted X and Y chromosomes isolated from vole species with sex chromosomes that always (Microtus montanus), never (Microtus mogollonensis), and occasionally synapse (Microtus ochrogaster) at meiosis. Unexpectedly, we find more shared X/Y homology in the two vole species with no and sporadic X/Y synapsis compared to the species with obligate synapsis. Sex chromosome homology in the asynaptic and occasionally synaptic species is interspersed along chromosomes and largely restricted to low-complexity sequences, including a striking enrichment for the telomeric repeat sequence, TTAGGG. In contrast, homology is concentrated in high complexity, and presumably euchromatic, sequence on the X and Y chromosomes of the synaptic vole species, M. montanus Taken together, our findings suggest key conditions required to sustain the standard program of X/Y synapsis at meiosis and reveal an intriguing connection between heterochromatic repeat architecture and noncanonical, asynaptic mechanisms of sex chromosome segregation in voles.

Characterization of Chromosome-Specific Microsatellite Repeats and Telomere Repeats Based on Low Coverage Whole Genome Sequence Reads in Panax ginseng

Repetitive DNA elements are ubiquitous in plant genomes. Although repeats provide relevant information for cytogenetic, evolutionary, and genomic studies, identifying and characterizing their sequence and chromosomal distribution are not always easily achieved through conventional methods. However, a high-throughput identification of genomic repeats can be obtained with short reads from next-generation sequencing data. Here, we identified the telomeric and two chromosome-specific repeats in Panax ginseng using low-coverage whole genome sequence data. The telomeric repeat sequence is same with the canonical angiosperm sequence, (TTTAGGG)n, and localized mostly in every chromosome termini, except for an additional interstitial location in chromosome 10. A dinucleotide (GA) microsatellite, PgGA15, with total genome representation (GR) of more than 33 kb localized in the long arm of chromosome 20. An 11-bp minisatellite, Pgms1, with more than 58 kb of GR localized in the long arm of chromosome 1. This study provides chromosome-specific markers for cytogenetic studies in P. ginseng.

Telomeres and genomic evolution.

The terminal regions of eukaryotic chromosomes, composed of telomere repeat sequences and sub-telomeric sequences, represent some of the most variable and rapidly evolving regions of the genome. The sub-telomeric regions are characterized by segmentally duplicated repetitive DNA elements, interstitial telomere repeat sequences and families of variable genes. Sub-telomeric repeat sequence families are shared among multiple chromosome ends, often rendering detailed sequence characterization difficult. These regions are composed of constitutive heterochromatin and are subjected to high levels of meiotic recombination. Dysfunction within telomere repeat arrays, either due to disruption in the chromatin structure or because of telomere shortening, can lead to chromosomal fusion and the generation of large-scale genomic rearrangements across the genome. The dynamic nature of telomeric regions, therefore, provides functionally useful variation to create genetic diversity, but also provides a mechanism for rapid genomic evolution that can lead to reproductive isolation and speciation. This article is part of the theme issue 'Understanding diversity in telomere dynamics'.This article is part of the theme issue 'Understanding diversity in telomere dynamics'.

The mechanisms of K. lactis Cdc13 in telomere DNA-binding and telomerase regulation

Eukaryotic chromosome ends, or telomeres, are essential for genome stability and are protected by an intricate nucleoprotein assembly. Cdc13, the major single-strand telomere-binding protein in budding yeasts, mediates critical functions in both telomere protection and telomere elongation by telomerase. In particular, the interaction between S. cerevisiae Cdc13 and telomerase subunit Est1 has long served as a paradigm for telomerase regulation. However, despite extensive investigations, the role of this interaction in regulating telomerase recruitment or activation remains controversial. In addition, budding yeast telomere repeat sequences are extraordinarily variable and how Cdc13 orthologs recognize diverse repeats is not well understood. In this report, we examined these issues using an alternative model, K. lactis. We reconstituted a direct physical interaction between purified K. lactis Cdc13 and Est1, and by analyzing point mutations, we demonstrated a close correspondence between telomere maintenance defects in vivo and Cdc13-Est1 binding defects in vitro, thus supporting a purely recruitment function for this interaction in K. lactis. Because mutations in well aligned residues of Cdc13 and Est1 in S. cerevisiae and K. lactis do not cause identical defects, our results also point to significant evolutionary divergence in the Cdc13-Est1 interface. In addition, we found that K. lactic Cdc13, unlike previously characterized orthologs, recognizes an unusually long and non-G-rich target sequence, underscoring the flexibility of the Cdc13 DNA-binding domain. Analysis of K. lactis Cdc13 and Est1 thus broadens understanding of telomere and telomerase regulation in budding yeast.

Expression and clinical significance of relative telomere length and telomerase activity in CD34+ CD38+ acute myeloid leukemia

Objective To discuss the clinical and guiding signification of relative telomere length and telomerase activity in diagnosis, prognosis and treatment of CD34+ CD38+ acute myeloid leukemia (AML). Methods From April to July 2015, a total of 20 cases of newly diagnosed CD34+ CD38+ AML patients who were hospitalized in Department of Hematology, Xiangya Hospital, Central South University were selected randomly as study subjects and enrolled in study group (n=20). And 10 cases of participants who were conducted bone marrow puncture due to suspected blood system malignant diseases were selected as control group, randomly (n=10). Relative quantitative PCR was conducted to detect relative telomere length of participants′ bone marrow specimens in two groups, and telomere repeat sequence amplification method (TRAP)-argentation and absolute quantitative PCR were conducted to detect telomerase activity; rate of complete remission (CR) after chemotherapy was collected in study group. MRD was obtained by flow cytometry. Relative telomere length, telomerase activity of two groups, relationship between relative telomere lengths, telomerase activity and clinical data, curative effect, MRD and prognosis of study group were analyzed retrospectively and compared statistically. The study protocol was approved by the Ethical Review Board of Investigation in Human at Xiangya Hospital, Central South University. Informed consent was obtained from all participants. There were no significant differences in average age and constituent ratio of gender between two groups (P>0.05). Results ① As TRAP-argentation showed, the telomerase activity of CD34+ CD38+ AML patient in study group was higher than that of control group. Relative quantitative PCR of telomere and absolute quantitative PCR of telomerase showed, relative telomere length of study group was 1.72±0.42, and significantly shorter than that of control group which was 4.68±1.89 (t=-6.906, P=0.002 0). Telomerase activity of study group was (405 242.01±357 412.39) copies/μL, and significantly higher than that of control group which was (17 956.53±6 952.03) copies/μL (t=3.357, P=0.002). There was a negative correlation between relative telomere length and telomerase activity in study group (r=-0.508, P 0.05). Compared with CD7- patients and patients with hemoglobin (Hb) level≤50 g/L, relative telomere length of CD7+ patients and patients with Hb level within (>50-120) g/L were significantly shorter(t=-2.217, -3.011; P=0.040, 0.008), and their telomerase activity were significantly higher (t=3.253, 2.255; P=0.010, 0.037). Compared with patients with immature cells ratio>50%, white blood cell count>50×109/L, relative telomere length and telomerase activity of patients with immature cells ratio≤50%, white blood cell count≤50×109/L were significantly longer (t=4.218, 2.637; P=0.001, 0.018), their telomerase activity were significantly lower (t=-3.052, -3.281; P=0.009, 0.008). ③ In study group, relative telomere length of CD34+ CD38+ AML patients who achieved CR was 1.95±0.19, and significantly longer than that of patients who didn′t achieve CR, which was 1.28±0.38 (t=5.336, P 1.95, MRD of 1 case was positive, and 5 cases were negative. Among 7 cases with telomerase activity≤197 670.43 copies/μL, MRD of 1 case was positive, and 6 cases were negative. Among the 6 cases with telomerase activity>197 670.43 copies/μL, MRD of 5 cases were positive, 1 case was negative. From August 2015 and March 2016, follow-up of 5 patients who achieved CR showed, relative telomere length and telomerase activity of the 3 cases with long-term in CR were similar to these of control group. Relative telomere length shortened, and telomerase activity elevated again in 2 cases with recurrence. Conclusions The relative telomere length and telomerase activity can be used as one of the diagnostic, prognostic and recurrent criteria of CD34+ CD38+ AML, and provide some theoretical basis for the determination of treatment options. Key words: Leukemia, myeloid, acute; Telomere; Telomerase; Polymerase chain reaction

Rap1 and Cdc13 have complementary roles in preventing exonucleolytic degradation of telomere 5\u2032 ends

Telomere DNA ends with a single-stranded 3′ overhang. Long 3′ overhangs may cause aberrant DNA damage responses and accelerate telomere attrition, which is associated with cancer and aging, respectively. Genetic studies have indicated several important players in preventing 5′ end hyper-resection, yet detailed knowledge about the molecular mechanism in which they act is still lacking. Here, we use an in vitro DNA 5′ end protection assay, to study how N. castellii Cdc13 and Rap1 protect against 5′ exonucleolytic degradation by λ-exonuclease. The homogeneous telomeric repeat sequence of N. castellii allows us to study their protection ability at exact binding sites relative to the 5′ end. We find efficient protection by both Cdc13 and Rap1 when bound close to the 5′ end. Notably, Rap1 provides protection when binding dsDNA at a distance from the 5′ end. The DNA binding domain of Rap1 is sufficient for 5′ end protection, and its wrapping loop region is essential. Intriguingly, Rap1 facilitates protection also when its binding site contains 2 nt of ssDNA, thus spanning across the ds-ss junction. These results highlight a role of Rap1 in 5′ end protection and indicate that Cdc13 and Rap1 have complementary roles in maintaining proper 3′ overhang length.

Human CST Prefers G-Rich but Not Necessarily Telomeric Sequences.

The human CST (CTC1-STN1-TEN1) heterotrimeric complex plays roles in both telomere maintenance and DNA replication through its ability to interact with single-stranded DNA (ssDNA) of a variety of sequences. The precise sequence specificity required to execute these functions is unknown. Telomere-binding proteins have been shown to specifically recognize key telomeric sequence motifs within ssDNA while accommodating nonspecifically recognized sequences through conformationally plastic interfaces. To better understand the role CST plays in these processes, we have produced a highly purified heterotrimer and elucidated the sequence requirements for CST recognition of ssDNA in vitro. CST discriminates against random sequence and binds a minimal ssDNA comprised of three repeats of telomeric sequence. Replacement of individual nucleotides with their complement reveals that guanines are specifically recognized in a largely additive fashion and that specificity is distributed uniformly throughout the ligand. Unexpectedly, adenosines are also well tolerated at these sites, but cytosines are disfavored. Furthermore, sequences unrelated to the telomere repeat, yet still G-rich, bind CST well. Thus, CST is not inherently telomere-specific, but rather is a G-rich sequence binder. This biochemical activity is reminiscent of the yeast t-RPA and Tetrahymena thermophila CST complexes and is consistent with roles at G-rich sites throughout the genome.

Single-molecule analysis in an electrochemical confined space

Electrochemical analysis of single molecules is a method with the strong ability of the enhanced efficiency and ultra-sensitivity. Here, we demonstrate that the electrochemical confined space could efficiently convert single molecule characteristics into measurable electrochemical signatures with high temporal resolution. The human telomere repeat sequence T8 was used as a probe to determine the electrochemical confined effect in a nanopore. Our results show that the nanopore with comparable confined space of the telomere repeat sequence exhibits the most distinguishable single-molecule signals which suggest the folded conformation of T8. This method will greatly extend the lifetime of a metastable conformation for a single biomolecule by strong analyte-nanopore interactions, which brings the new insight into the understanding of the biomolecule’s function at single-molecule level.

Proteomic identification of proteins differentially expressed following overexpression of hTERT (human telomerase reverse transcriptase) in cancer cells.

Reverse transcriptase activity of telomerase adds telomeric repeat sequences at extreme ends of the newly replicated chromosome in actively dividing cells. Telomerase expression is not detected in terminally differentiated cells but is noticeable in 90% of the cancer cells. hTERT (human telomerase reverse transcriptase) expression seems to promote invasiveness of cancer cells. We here present proteomic profiles of cells overexpressing or knocked down for hTERT. This study also attempts to find out the potential interacting partners of hTERT in cancer cell lines. Two-dimensional gel electrophoresis (2-DE) of two different cell lines U2OS (a naturally hTERT negative cell line) and HeLa revealed differential expression of proteins in hTERT over-expressing cells. In U2OS cell line 28 spots were picked among which 23 spots represented upregulated and 5 represented down regulated proteins. In HeLa cells 21 were upregulated and 2 were down regulated out of 23 selected spots under otherwise identical experimental conditions. Some heat shock proteins viz. Hsp60 and Hsp70 and GAPDH, which is a housekeeping gene, were found similarly upregulated in both the cell lines. The upregulation of these proteins were further confirmed at RNA and protein level by real-time PCR and western blotting respectively.

Analysis of the origin of inherited chromosomally integrated human herpesvirus 6 in the Japanese population.

Integration of the complete human herpesvirus 6 (HHV-6) genome into the telomere of a chromosome has been reported in some individuals (inherited chromosomally integrated HHV-6; iciHHV-6). Since the proportion of iciHHV-6-positive individuals with integration in chromosome 22 is high in Japan, we hypothesized a founder effect. In this study, we sought to elucidate the reason for the high proportion of viral integrations into chromosome 22. We analyzed six cases of iciHHV-6A and two cases of iciHHV-6B, including one iciHHV-6A case with a matched sample from a father and one iciHHV-6B case with a matched sample from a mother. In iciHHV-6A, the same copy numbers of viral telomeric repeat sequences (TRS) and the same five microsatellite markers were detected in both the index case and paternal sample. Moreover, the same five microsatellite markers were demonstrated in four cases and the same copy numbers of viral TRS were demonstrated in two pairs of two cases. The present microsatellite analysis suggested that the viral genomes detected in some iciHHV-6A patients were derived from a common ancestral integration.

Yeast Hrq1 shares structural and functional homology with the disease-linked human RecQ4 helicase.

The five human RecQ helicases participate in multiple processes required to maintain genome integrity. Of these, the disease-linked RecQ4 is the least studied because it poses many technical challenges. We previously demonstrated that the yeast Hrq1 helicase displays similar functions to RecQ4 in vivo, and here, we report the biochemical and structural characterization of these enzymes. In vitro, Hrq1 and RecQ4 are DNA-stimulated ATPases and robust helicases. Further, these activities were sensitive to DNA sequence and structure, with the helicases preferentially unwinding D-loops. Consistent with their roles at telomeres, telomeric repeat sequence DNA also stimulated binding and unwinding by these enzymes. Finally, electron microscopy revealed that Hrq1 and RecQ4 share similar structural features. These results solidify Hrq1 as a true RecQ4 homolog and position it as the premier model to determine how RecQ4 mutations lead to genomic instability and disease.

Possible chromosomal and germline integration of human herpesvirus 7.

Human herpesvirus 7 (HHV-7) is a betaherpesvirus, and is phylogenetically related to both HHV-6A and HHV-6B. The presence of telomeric repeat sequences at both ends of its genome should make it equally likely to integrate into the human telomere as HHV-6. However, numerous studies have failed to detect germline integration of HHV-7, suggesting an important difference between the HHV-6A/-6B and HHV-7 genomes. In search of possible germline integrated HHV-7, we developed a sensitive and quantitative real-time PCR assay and discovered that primers designed against some parts of the HHV-7 genome can frequently miss HHV-7 positive clinical samples even though they work efficiently in cell-culture-derived HHV-7 positive materials. Using a primer pair against the U90 ORF of HHV-7, we identified a possible case of germline integration of HHV-7 with one copy of viral genome per cell in both peripheral blood cells and hair follicles. Chromosomal integration of HHV-7 in these individuals was confirmed by fluorescence in situ hybridization analysis. Germline integration of HHV-7 was further confirmed by detection of ~2.6 copies of HHV-7 in the hair follicles of one of the parents. Our results shed light on the complex nature of the HHV-7 genome in human-derived materials in comparison to cell-culture-derived materials and show the need for stringent criteria in the selection of primers for epidemiological HHV-7 studies.

Telomere Length Analysis by Quantitative Fluorescent in Situ Hybridization (Q-FISH).

Length is a functional parameter of telomeres, the nucleoprotein structures that protect chromosome ends. The availability of highly specific, high affinity probes for telomeric repeat sequences allowed the development of quantitative approaches aimed at measuring telomere length directly on chromosomes or in interphase nuclei. Here, we describe a general method for telomere quantitative FISH on metaphase chromosomes and discuss its most common applications in research.

An optimization algorithm for single-molecule fluorescence resonance (smFRET) data processing

The single-molecule fluorescence resonance energy transfer (smFRET) technique plays an important role in the development of biophysics. Measuring the changes of the fluorescence intensities of donor and acceptor and of the FRET efficiency can reveal the changes of distance between the labeling positions. The smFRET may be used to study conformational changes of DNA, proteins and other biomolecules. Traditional algorithm for smFRET data processing is highly dependent on manual operation, leading to high noise, low efficiency and low reliability of the outputs. In the present work, we propose an automatic and more accurate algorithm for smFRET data processing. It consists of three parts: algorithm for automatic pairing of donor and acceptor fluorescence spots based on negative correlation between their intensities; algorithm for data screening by eliminating invalid fluorescence spots sections; algorithm for global data fitting based on Baum-Welch algorithm of hidden Markov model (HMM). Based on the law of energy conservation, the light intensity of one pair of donor and acceptor shows a negative correlation. We can use this feature to find the active smFRET pairs automatically. The algorithm will first find out three active smFRET pairs with correlation coefficient lower than the threshold we set. This three active smFRET pairs will provide enough coordinate data for the algorithm to calculate the pairing matrix in the rest of automatic pairing work. After obtaining all the smFRET pairs, the algorithm for data screening will check the correlation coefficient for each pair. The invalid pairs with correlation coefficient higher than the threshold value will be eliminated. The rest of smFRET pairs will be analyzed by the data fitting algorithm. The Baum-Welch algorithm can be used for learning the global parameters. The global parameters we obtained will then be used to fit each FRET-time curve with Viterbi algorithm. The global parameter learning part will help us find the specific FRET efficiency for each state and the curve fitting part will provide more kinetic parameters. The optimization algorithm significantly simplifies the procedures of manual operation in the traditional algorithm and eliminate several types of noises from the experimental data automatically. We apply the new optimization algorithm to the analyses of folding kinetics data for human telomere repeat sequence, the G-quadruplex DNA. It is demonstrated that the optimization algorithm is more efficient to produce data with higher S/N ratio than the traditional algorithm. The final results reveal clearly the folding of G-quadruplex DNA in multiple states that are influenced by the K+ concentration.

NMR based model of human telomeric repeat G-quadruplex in complex with 2,4,6-triarylpyridine family ligand.

G-quadruplexes (G4) are one of the several different forms of non-canonical DNA structures that can occur in our genome. Their existence is thought to be implicated in important biological functions such as positive and negative transcription regulation or telomeric extension. The human telomeric sequence G4 formed by repetitive nucleotide sequences (T2AG3) at each chromosome end is an important example of intramolecular G4. Knowing the atomic details for different families of ligands targeting G-quadruplex structures hypothetically found in the telomeric repeat it is an important step for rational drug design. Especially if the aim is to prevent or interfere with telomerase extending the 3' end of telomeres. In this study, we report the structure of the complex formed between the telomeric repeat sequence (d[AG3(T2AG3)3]) intramolecular G-quadruplex and the 2,4,6-Triarylpyridine compound. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.