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Journal of Nucleic Acids

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https://www.readbyqxmd.com/read/29862069/effects-of-5-hydroxymethylcytosine-epigenetic-modification-on-the-stability-and-molecular-recognition-of-vegf-i-motif-and-g-quadruplex-structures
#1
Rhianna K Morgan, Michael M Molnar, Harshul Batra, Bethany Summerford, Randy M Wadkins, Tracy A Brooks
Promoters often contain asymmetric G- and C-rich strands, in which the cytosines are prone to epigenetic modification via methylation (5-mC) and 5-hydroxymethylation (5-hmC). These sequences can also form four-stranded G-quadruplex (G4) or i-motif (iM) secondary structures. Although the requisite sequences for epigenetic modulation and iM/G4 formation are similar and can overlap, they are unlikely to coexist. Despite 5-hmC being an oxidization product of 5-mC, the two modified bases cluster at distinct loci...
2018: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/29854431/g-quadruplexes-gqu
#2
EDITORIAL
Shozeb Haider, Gary N Parkinson, Thomas C Marsh
No abstract text is available yet for this article.
2018: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/29666699/electrochemical-and-afm-characterization-of-g-quadruplex-electrochemical-biosensors-and-applications
#3
REVIEW
Ana-Maria Chiorcea-Paquim, Ramon Eritja, Ana Maria Oliveira-Brett
Guanine-rich DNA sequences are able to form G-quadruplexes, being involved in important biological processes and representing smart self-assembling nanomaterials that are increasingly used in DNA nanotechnology and biosensor technology. G-quadruplex electrochemical biosensors have received particular attention, since the electrochemical response is particularly sensitive to the DNA structural changes from single-stranded, double-stranded, or hairpin into a G-quadruplex configuration. Furthermore, the development of an increased number of G-quadruplex aptamers that combine the G-quadruplex stiffness and self-assembling versatility with the aptamer high specificity of binding to a variety of molecular targets allowed the construction of biosensors with increased selectivity and sensitivity...
2018: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/29657864/a-sequence-dependent-dna-condensation-induced-by-prion-protein
#4
Alakesh Bera, Sajal Biring
Different studies indicated that the prion protein induces hybridization of complementary DNA strands. Cell culture studies showed that the scrapie isoform of prion protein remained bound with the chromosome. In present work, we used an oxazole dye, YOYO, as a reporter to quantitative characterization of the DNA condensation by prion protein. We observe that the prion protein induces greater fluorescence quenching of YOYO intercalated in DNA containing only GC bases compared to the DNA containing four bases whereas the effect of dye bound to DNA containing only AT bases is marginal...
2018: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/29464116/putative-hiv-and-siv-g-quadruplex-sequences-in-coding-and-noncoding-regions-can-form-g-quadruplexes
#5
Petra Krafčíková, Erika Demkovičová, Andrea Halaganová, Viktor Víglaský
The HIV virus is one of the most studied viruses in the world. This is especially true in terms of gene sequencing, and to date more than 9 thousand genomic sequences of HIV isolates have been sequenced and analyzed. In this study, a series of DNA sequences, which have the potential to form G-quadruplex structures, is analyzed. Several such sequences were found in various coding and noncoding virus domains, including the U3 LTR, tat, rev, env, and vpx regions. Interestingly, a homological sequence to the already well-known HIV integrase aptamer was identified in the minus-strand...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/29445544/telomeric-g-quadruplexes-from-human-to-tetrahymena-repeats
#6
Erika Demkovičová, Ľuboš Bauer, Petra Krafčíková, Katarína Tlučková, Petra Tóthova, Andrea Halaganová, Eva Valušová, Viktor Víglaský
The human telomeric and protozoal telomeric sequences differ only in one purine base in their repeats; TTAGGG in telomeric sequences; and TTGGGG in protozoal sequences. In this study, the relationship between G-quadruplexes formed from these repeats and their derivatives is analyzed and compared. The human telomeric DNA sequence G3 (T2 AG3 )3 and related sequences in which each adenine base has been systematically replaced by a guanine were investigated; the result is Tetrahymena repeats. The substitution does not affect the formation of G-quadruplexes but may cause differences in topology...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/29250441/on-characterizing-the-interactions-between-proteins-and-guanine-quadruplex-structures-of-nucleic-acids
#7
REVIEW
Ewan K S McRae, Evan P Booy, Gay Pauline Padilla-Meier, Sean A McKenna
Guanine quadruplexes (G4s) are four-stranded secondary structures of nucleic acids which are stabilized by noncanonical hydrogen bonding systems between the nitrogenous bases as well as extensive base stacking, or pi-pi, interactions. Formation of these structures in either genomic DNA or cellular RNA has the potential to affect cell biology in many facets including telomere maintenance, transcription, alternate splicing, and translation. Consequently, G4s have become therapeutic targets and several small molecule compounds have been developed which can bind such structures, yet little is known about how G4s interact with their native protein binding partners...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/29230324/on-the-helical-structure-of-guanosine-5-monophosphate-formed-at-ph-5-is-it-left-or-right-handed
#8
Gang Wu, Irene C M Kwan, Zhimin Yan, Yining Huang, Eric Ye
Early X-ray fiber diffraction studies have established that the spontaneous gel formation of guanosine 5'-monophosphate (5'-GMP) under slightly acidic conditions (e.g., pH 5) results from self-assembly of 5'-GMP into a helical structure in which hydrogen-bonded guanine bases form a continuous helix with 15 nucleotides per 4 turns. For more than five decades, the sense of this helix is believed to be left-handed. Using multinuclear solid-state NMR and IR spectroscopic methods, we have finally determined the long-missing structural details of this helix...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/29225967/aptamers-as-the-agent-in-decontamination-assays-apta-decontamination-assays-from-the-environment-to-the-potential-application-in-vivo
#9
REVIEW
Mawethu Pascoe Bilibana, Marimuthu Citartan, Tzi Shien Yeoh, Timofey S Rozhdestvensky, Thean-Hock Tang
The binding specificity and affinity of aptamers have long been harnessed as the key elements in the development of aptamer-based assays, particularly aptasensing application. One promising avenue that is currently explored based on the specificity and affinity of aptamers is the application of aptamers in the decontamination assays. Aptamers have been successfully harnessed as the decontamination agents to remove contaminants from the environment and to decontaminate infectious elements. The reversible denaturation property inherent in aptamers enables the repeated usage of aptamers, which can immensely save the cost of decontamination...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/29204294/corrigendum-to-plant-microrna-prediction-by-supervised-machine-learning-using-c5-0-decision-trees
#10
Philip H Williams, Rodney P Eyles, Georg Weiller
[This corrects the article DOI: 10.1155/2012/652979.].
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/29181194/physiological-roles-of-dna-double-strand-breaks
#11
REVIEW
Farhaan A Khan, Syed O Ali
Genomic integrity is constantly threatened by sources of DNA damage, internal and external alike. Among the most cytotoxic lesions is the DNA double-strand break (DSB) which arises from the cleavage of both strands of the double helix. Cells boast a considerable set of defences to both prevent and repair these breaks and drugs which derail these processes represent an important category of anticancer therapeutics. And yet, bizarrely, cells deploy this very machinery for the intentional and calculated disruption of genomic integrity, harnessing potentially destructive DSBs in delicate genetic transactions...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/29181193/in-what-ways-do-synthetic-nucleotides-and-natural-base-lesions-alter-the-structural-stability-of-g-quadruplex-nucleic-acids
#12
REVIEW
Janos Sagi
Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/29129999/expression-of-genes-and-their-polymorphism-influences-the-risk-of-knee-osteoarthritis
#13
Abhishek Mishra, Rajeshwar Nath Srivastava, Sachin Awasthi, Devendra Parmar, Priya Mishra
Introduction: Genetic factors including the level of expression of the fingerprint of genes involved in the development of bones and cartilage such as GDF-5 or ESR- α or CALM-1 are known to be strong determinants of the osteoarthritis (OA) in Caucasian and Oriental populations. Because of high prevalence of OA in Indian population and availability of limited genetic data, we determined whether similar genetic factors are involved in Indians as well. Methods: A case control study was carried out involving 500 patients of knee OA and equal number of healthy controls...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/28698807/the-2d-structure-of-the-t-brucei-preedited-rps12-mrna-is-not-affected-by-macromolecular-crowding
#14
W-Matthias Leeder, Stephan Voskuhl, H Ulrich Göringer
Mitochondrial transcript maturation in African trypanosomes requires RNA editing to convert sequence-deficient pre-mRNAs into translatable mRNAs. The different pre-mRNAs have been shown to adopt highly stable 2D folds; however, it is not known whether these structures resemble the in vivo folds given the extreme "crowding" conditions within the mitochondrion. Here, we analyze the effects of macromolecular crowding on the structure of the mitochondrial RPS12 pre-mRNA. We use high molecular mass polyethylene glycol as a macromolecular cosolute and monitor the structure of the RNA globally and with nucleotide resolution...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/28280637/selection-of-dna-aptamers-for-ovarian-cancer-biomarker-ca125-using-one-pot-selex-and-high-throughput-sequencing
#15
Delia J Scoville, Tae Kyu Brian Uhm, Jamie A Shallcross, Rebecca J Whelan
CA125 is a mucin glycoprotein whose concentration in serum correlates with a woman's risk of developing ovarian cancer and also indicates response to therapy in diagnosed patients. Accurate detection of this large, complex protein in patient samples is of great clinical relevance. We suggest that powerful new diagnostic tools may be enabled by the development of nucleic acid aptamers with affinity for CA125. Here, we report on our use of One-Pot SELEX to isolate single-stranded DNA aptamers with affinity for CA125, followed by high-throughput sequencing of the selected oligonucleotides...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/28232872/systemic-identification-of-hevea-brasiliensis-est-ssr-markers-and-primer-screening
#16
Benjun Hou, Suping Feng, Yaoting Wu
This research aimed to systematically identify and preliminarily validate the Hevea brasiliensis expressed sequence tag (EST) information using Simple Sequence Repeat (SSR) and provide evidence for further development of SSR molecular marker. The definition of general SSR features of Hevea EST splicing sequences and development of SSR primers founded the basis of diversity analysis and variety identification for Hevea tree resource. 1134 SSR loci were identified in the EST splicing sequence and distributed in 840 Unigene...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/28194280/cell-selex-identifies-a-sticky-rna-aptamer-sequence
#17
Partha Ray, Rebekah R White
Cell-SELEX is performed to select for cell binding aptamers. We employed an additional selection pressure by using RNAse to remove surface-binding aptamers and select for cell-internalizing aptamers. A common RNA sequence was identified from independent cell-SELEX procedures against two different pancreatic cancer cell lines, indicating a strong selection pressure towards this sequence from the large pool of other available sequences present in the aptamer library. The aptamer is not specific for the pancreatic cancer cell lines, and a similar sequence motif is present in previously published internalizing aptamers...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/28116145/overexpression-of-pcna-attenuates-oxidative-stress-caused-delay-of-gap-filling-during-repair-of-uv-induced-dna-damage
#18
Yi-Chih Tsai, Yi-Hsiang Wang, Yin-Chang Liu
UVC irradiation-caused DNA lesions are repaired in mammalian cells solely by nucleotide excision repair (NER), which consists of sequential events including initial damage recognition, dual incision of damage site, gap-filling, and ligation. We have previously shown that gap-filling during the repair of UV-induced DNA lesions may be delayed by a subsequent treatment of oxidants or prooxidants such as hydrogen peroxide, flavonoids, and colcemid. We considered the delay as a result of competition for limiting protein/enzyme factor(s) during repair synthesis between NER and base excision repair (BER) induced by the oxidative chemicals...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/28083147/role-of-eukaryotic-initiation-factors-during-cellular-stress-and-cancer-progression
#19
REVIEW
Divya Khandige Sharma, Kamiko Bressler, Harshil Patel, Nirujah Balasingam, Nehal Thakor
Protein synthesis can be segmented into distinct phases comprising mRNA translation initiation, elongation, and termination. Translation initiation is a highly regulated and rate-limiting step of protein synthesis that requires more than 12 eukaryotic initiation factors (eIFs). Extensive evidence shows that the transcriptome and corresponding proteome do not invariably correlate with each other in a variety of contexts. In particular, translation of mRNAs specific to angiogenesis, tumor development, and apoptosis is altered during physiological and pathophysiological stress conditions...
2016: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/27092269/copy-number-variation-of-ugt-2b-genes-in-indian-families-using-whole-genome-scans
#20
Avinash M Veerappa, Prakash Padakannaya, Nallur B Ramachandra
Background and Objectives. Uridine diphospho-glucuronosyltransferase 2B (UGT2B) is a family of genes involved in metabolizing steroid hormones and several other xenobiotics. These UGT2B genes are highly polymorphic in nature and have distinct polymorphisms associated with specific regions around the globe. Copy number variations (CNVs) status of UGT2B17 in Indian population is not known and their disease associations have been inconclusive. It was therefore of interest to investigate the CNV profile of UGT2B genes...
2016: Journal of Nucleic Acids
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