I Wayan Suardana

Erratum to &#x201C;Analysis of Nucleotide Sequences of the 16S rRNA Gene of Novel Escherichia coli Strains Isolated from Feces of Human and Bali Cattle&#x201D;

The nucleoside 2,2,4-triamino-5(2H)-oxazolone (Oz) can result from oxidative damage to guanine residues in DNA. Despite differences among the three polymerases (Pol &#x3b2;, KF exo&#x2212;, and Pol &#x3b7;) regarding nucleotide incorporation patterns opposite Oz, all three polymerases can incorporate guanine opposite Oz. Based on ab initio calculations, we proposed a structure for a stable Oz:G base pair. Here, to assess the stability of each Oz-containing base pair (Oz:G, Oz:A, Oz:C, and Oz:T) upon DNA replication, we determined the efficiency of Pol &#x3b2;-, KF exo&#x2212;-, or Pol &#x3b7;-catalyzed primer extension beyond each base pair. With each polymerase, extension beyond Oz:G was more efficient than that beyond Oz:A, Oz:C, or Oz:T. Moreover, thermal denaturation studies revealed that the <svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" style="vertical-align:-3.42778pt" id="M1" height="12.7657pt" version="1.1" viewBox="-0.0498162 -9.33792 15.7674 12.7657" width="15.7674pt"><g transform="matrix(.0135,0,0,-0.0135,0,0)"><path id="g113-85" d="M620 675H597C578 656 570 650 541 650H144C112 650 104 653 94 675H72C59 618 42 552 23 493L53 491C71 534 88 564 105 585C124 608 144 615 238 615H290L197 121C182 40 174 34 88 28L82 0H361L367 28C275 34 266 38 281 121L374 615H441C522 615 543 608 553 583C562 560 566 531 565 493L597 494C603 551 612 629 620 675Z"/></g><g transform="matrix(.0095,0,0,-0.0095,7.479,3.264)"><path id="g50-110" d="M781 91L765 118C733 86 702 70 693 70C686 70 685 77 692 106L738 297C772 439 736 451 712 451S675 445 647 431C605 410 526 356 452 257H450L459 294C491 426 459 451 429 451C403 451 386 445 361 431C312 404 239 343 170 253H168L188 333C208 411 205 451 175 451C148 451 85 417 24 346L39 318C57 338 100 374 112 374C120 374 122 372 115 339C91 226 62 112 28 -6L37 -12C59 -4 87 3 114 6C125 68 142 127 154 168C184 227 316 383 372 383C397 383 396 366 381 289C362 192 338 92 312 -6L317 -12C339 -5 367 3 396 6L434 170C468 234 598 383 650 383C668 383 676 369 664 319L609 90C593 23 600 -12 629 -12C654 -12 722 23 781 91Z"/></g></svg> value for the duplex containing Oz:G was significantly higher than those obtained for duplexes containing Oz:A, Oz:C, or Oz:T. Therefore, the results from ab initio calculations along with those from DNA replication assays and thermal denaturation experiments supported the conclusion that Oz:G is the most stable of the Oz-containing base pairs.

Masayo Suzuki

Kazuya Ohtsuki

Katsuhito Kino

Teruhiko Kobayashi

Masayuki Morikawa

Takanobu Kobayashi

Hiroshi Miyazawa

Effects of Stability of Base Pairs Containing an Oxazolone on DNA Elongation

Bromacil is a widely used herbicide that is known to contaminate environmental systems. Due to the hazards it presents and inefficient detection methods, it is necessary to create a rapid and efficient sensing device. Towards this end, we have utilized a stringent in vitro selection method to identify single-stranded DNA molecular recognition elements (MRE) specific for bromacil. We have identified one MRE with high affinity (<svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" style="vertical-align:-3.427751pt" id="M1" height="12.4257pt" version="1.1" viewBox="-0.0498162 -8.99795 47.3301 12.4257" width="47.3301pt"><g transform="matrix(.0135,0,0,-0.0135,0,0)"><path id="g113-76" d="M743 650H503L496 622L527 618C563 613 564 603 532 573C449 495 371 431 323 392C301 374 272 355 246 346L280 522C297 609 300 614 379 622L385 650H135L129 622C209 614 215 609 198 522L124 133C106 39 99 35 23 28L17 0H271L277 28C193 35 192 39 208 133L239 316C264 328 280 325 303 288C368 183 435 90 502 0H652L659 28C602 34 584 43 543 94C495 154 403 283 347 369L574 554C634 603 659 612 735 624L743 650Z"/></g><g transform="matrix(.0095,0,0,-0.0095,9.619,3.264)"><path id="g50-101" d="M538 684C542 703 539 710 529 710C512 710 455 682 363 674L361 644H396C444 644 448 642 438 594L405 438C373 450 347 451 336 451C288 451 200 416 147 374C69 312 24 207 24 113C24 29 60 -12 94 -12C126 -12 156 4 196 30C231 53 296 100 346 166H348L328 81C311 10 325 -12 348 -12C380 -12 450 24 512 98L495 125C466 97 431 70 417 70C408 70 408 80 411 98L538 684ZM390 373L361 240C336 196 210 56 145 56C132 56 113 73 113 131C113 216 156 338 220 379C243 394 266 402 303 402C331 402 375 388 390 373Z"/></g><g transform="matrix(.0135,0,0,-0.0135,19.271,0)"><path id="g117-34" d="M535 323V373H52V323H535ZM535 138V188H52V138H535Z"/></g><g transform="matrix(.0135,0,0,-0.0135,31.009,0)"><path id="g113-58" d="M244 635C114 635 38 519 38 422C38 317 111 240 217 240C236 240 255 244 277 256L345 292C311 140 203 39 59 15L64 -15C89 -15 150 -5 204 17C339 72 440 202 440 386C440 521 368 635 244 635ZM228 602C326 602 352 479 352 390C352 370 351 347 348 324C327 308 293 296 258 296C174 296 124 369 124 458C124 517 152 602 228 602Z"/></g><g transform="matrix(.0135,0,0,-0.0135,37.513,0)"><path id="g113-47" d="M113 -12C146 -12 170 11 170 46C170 78 146 103 114 103S58 78 58 46C58 11 82 -12 113 -12Z"/></g><g transform="matrix(.0135,0,0,-0.0135,40.602,0)"><path id="g113-55" d="M137 343C167 482 260 545 321 574C357 591 397 603 429 609L423 641C382 634 335 622 295 608C189 570 37 457 37 238C37 84 125 -12 242 -12C362 -12 447 89 447 209C447 311 374 393 267 393C247 393 226 386 204 376L137 343ZM227 337C318 337 361 256 361 173C361 105 336 22 258 22C176 22 126 120 126 240C126 266 127 291 132 310C155 323 189 337 227 337Z"/></g></svg>&#x2009;nM) and specificity for bromacil compared to negative targets of selection and other pesticides. The selected ssDNA MRE will be useful as the sensing element in a field-deployable bromacil detection device.

Ryan M. Williams

Amanda R. Kulick

Srilakshmi Yedlapalli

Louisa Battistella

Cyrus J. Hajiran

Letha J. Sooter

In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element Specific for Bromacil

Livestock especially cattle are known as a main reservoir of Escherichia coli O157:H7. This bacterium is considered as a pathogenic agent characterized by producing toxins, which are familiarly known as Shiga-like toxin-1 (Stx1) and Stx2. The aim of this work was to analyse the novel sequence of the 16S rRNA gene of strains isolated in this study in order to know the phylogenetic relationships between these sequences and those between the sequences of bacteria available in databanks. The results of this analysis showed that the strains KL-48(2) and SM25(1) that originated from human and cattle feces, respectively, are closely related among them and with respect to E. coli EDL 933, E. coli Sakai, E. coli ATCC 43894, E. coli O111:H-, E. coli O121:H19, E. coli O104:H4, and Shigella sonnei with more than 99&#x25; similarity values.

Analysis of Nucleotide Sequences of the 16S rRNA Gene of Novel Escherichia coli Strains Isolated from Feces of Human and Bali Cattle

MicroRNAs are endogenous small noncoding RNAs which play critical roles in gene regulation. Few wheat (Triticum aestivum L.) miRNA sequences are available in miRBase repertoire and knowledge of their biological functions related to biotic stress is limited. We identified 52 miRNAs, belonging to 19 families, from next-generation transcriptome sequence data based on homology search. One wheat specific novel miRNA was identified but could not be ascribed or assigned to any known miRNA family. Differentially expressed 22 miRNAs were found between susceptible and resistant wheat near-isogenic lines inoculated with leaf rust pathogen Puccinia triticina and compared with mock inoculated controls. Most miRNAs were more upregulated in susceptible NIL compared to resistant NIL. We identified 1306 potential target genes for these 52 miRNAs with vital roles in response to stimuli, signaling, and diverse metabolic and cellular processes. Gene ontology analysis showed 66, 20, and 35 target genes to be categorized into biological process, molecular function, and cellular component, respectively. A miRNA-mediated regulatory network revealed relationships among the components of the targetome. The present study provides insight into potential miRNAs with probable roles in leaf rust pathogenesis and their target genes in wheat which establish a foundation for future studies.

Dhananjay Kumar

Dharmendra Singh

Pulkit Kanodia

Kumble Vinod Prabhu

Manish Kumar

Kunal Mukhopadhyay

Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes

Infection with Shiga toxin- (Stx-) producing E. coli causes life threatening hemolytic uremic syndrome (HUS), a leading cause of acute renal failure in children. Of the two antigenically distinct toxins, Stx1 and Stx2, Stx2 is more firmly linked with the development of HUS. In the present study, selective evolution of ligands by exponential enrichment (SELEX) was used in an attempt to identify RNA aptamers against Stx1 and Stx2. After 5 rounds of selection, significant enrichment of aptamer pool was obtained against Stx2, but not against Stx1, using a RNA aptamer library containing 56 random nucleotides (N56). Characterization of individual aptamer sequences revealed that six unique RNA aptamers (mA/pC, mB/pA, mC, mD, pB, and pD) recognized Stx2 in a filter binding assay. None of these aptamers bound Stx1. Aptamers mA/pC, mB/pA, mC, and mD, but not pB and pD, partially blocked binding of Alexa 488-labeled Stx2 with HeLa cells in a flow cytometry assay. However, none of the aptamers neutralized Stx2-mediated cytotoxicity and death of HeLa cells.

Sreerupa Challa

Saul Tzipori

Abhineet Sheoran

Selective Evolution of Ligands by Exponential Enrichment to Identify RNA Aptamers against Shiga Toxins

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Journal of Nucleic Acids publishes original research articles as well as review articles covering all structural, chemical, and functional aspects of DNA and RNA research.

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Chief Editor&nbsp;Professor Ashis Basu&nbsp;is currently based at the University of Connecticut. His research focuses on determination of the consequences of DNA damaged by anti-tumor drugs, chemical carcinogens, oxidation, or radiation.

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Journal of Nucleic Acids publishes original research articles as well as review articles covering all structural, chemical, and functional aspects of DNA and RNA research.

Journal of Nucleic Acids