Medical College of Wisconsin
CTSIResearch InformaticsREDCap

Publications indexed to the term Nucleic Acid Conformation

FacultyTitle
1Sequence and ionic requirements of pUG fold quadruplexes. (Roschdi S, Kume T, Petersen RJ, McCann A, Escobar Bravo CA, Richard A, Butcher S) RNA Biol 2026 Dec 31;23(1):1-16       1 Citation
1The structure, folding kinetics, and dynamics of long poly(UG) RNA. (Petersen RJ, Vivek R, Tonelli M, Roschdi S, Butcher SE) Nucleic Acids Res 2025 Jul 19;53(14)       3 Citations
1Solution Structure of Poly(UG) RNA. (Escobar CA, Petersen RJ, Tonelli M, Fan L, Henzler-Wildman KA, Butcher SE) J Mol Biol 2023 Dec 15;435(24):168340       8 Citations
1Structure of LARP7 Protein p65-telomerase RNA Complex in Telomerase Revealed by Cryo-EM and NMR. (Wang Y, He Y, Wang Y, Yang Y, Singh M, Eichhorn CD, Cheng X, Jiang YX, Zhou ZH, Feigon J) J Mol Biol 2023 Jun 01;435(11):168044       9 Citations
1Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility. (Morrison EA, Baweja L, Poirier MG, Wereszczynski J, Musselman CA) Nucleic Acids Res 2021 May 07;49(8):4750-4767       41 Citations
1Peroxynitrite-induced conformational changes in DNA that lead to cell death: UV, CD spectral, molecular dynamics simulation and FACS analysis. (Anushree G, Aravind P, Vinod D, Hemalatha N, Girisha ST, Devaraju KS) Nucleosides Nucleotides Nucleic Acids 2021;40(1):1-15       4 Citations
2Comparative and Functional Genomic Resource for Mechanistic Studies of Human Blood Pressure-Associated Single Nucleotide Polymorphisms. (Mishra MK, Liang EY, Geurts AM, Auer PWL, Liu P, Rao S, Greene AS, Liang M, Liu Y) Hypertension 2020 Mar;75(3):859-868       20 Citations
1Mapping and characterization of G-quadruplexes in the genome of the social amoeba Dictyostelium discoideum. (Saad M, Guédin A, Amor S, Bedrat A, Tourasse NJ, Fayyad-Kazan H, Pratviel G, Lacroix L, Mergny JL) Nucleic Acids Res 2019 May 21;47(9):4363-4374       18 Citations
1A force sensor that converts fluorescence signal into force measurement utilizing short looped DNA. (Mustafa G, Chuang CY, Roy WA, Farhath MM, Pokhrel N, Ma Y, Nagasawa K, Antony E, Comstock MJ, Basu S, Balci H) Biosens Bioelectron 2018 Dec 15;121:34-40       6 Citations
1The mitochondrial single-stranded DNA binding protein from S. cerevisiae, Rim1, does not form stable homo-tetramers and binds DNA as a dimer of dimers. (Singh SP, Kukshal V, De Bona P, Antony E, Galletto R) Nucleic Acids Res 2018 Aug 21;46(14):7193-7205       9 Citations
1Structure of Telomerase with Telomeric DNA. (Jiang J, Wang Y, Sušac L, Chan H, Basu R, Zhou ZH, Feigon J) Cell 2018 May 17;173(5):1179-1190.e13       129 Citations
1Structural biology of telomerase and its interaction at telomeres. (Wang Y, Feigon J) Curr Opin Struct Biol 2017 Dec;47:77-87       27 Citations
1Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis. (Zhang X, Chiang HC, Wang Y, Zhang C, Smith S, Zhao X, Nair SJ, Michalek J, Jatoi I, Lautner M, Oliver B, Wang H, Petit A, Soler T, Brunet J, Mateo F, Angel Pujana M, Poggi E, Chaldekas K, Isaacs C, Peshkin BN, Ochoa O, Chedin F, Theoharis C, Sun LZ, Curiel TJ, Elledge R, Jin VX, Hu Y, Li R) Nat Commun 2017 Jun 26;8:15908       140 Citations
1Mechanism of transcription initiation and promoter escape by E. coli RNA polymerase. (Henderson KL, Felth LC, Molzahn CM, Shkel I, Wang S, Chhabra M, Ruff EF, Bieter L, Kraft JE, Record MT Jr) Proc Natl Acad Sci U S A 2017 Apr 11;114(15):E3032-E3040       64 Citations
1Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human. (Wang Y, Yesselman JD, Zhang Q, Kang M, Feigon J) Proc Natl Acad Sci U S A 2016 Aug 30;113(35):E5125-34       26 Citations
1Role of Chromatin Structural Changes in Regulating Human CYP3A Ontogeny. (Giebel NL, Shadley JD, McCarver DG, Dorko K, Gramignoli R, Strom SC, Yan K, Simpson PM, Hines RN) Drug Metab Dispos 2016 Jul;44(7):1027-37       5 Citations
1Evidence supporting the existence of a NUPR1-like family of helix-loop-helix chromatin proteins related to, yet distinct from, AT hook-containing HMG proteins. (Urrutia R, Velez G, Lin M, Lomberk G, Neira JL, Iovanna J) J Mol Model 2014 Aug;20(8):2357       19 Citations
1Helix capping in RNA structure. (Lee JC, Gutell RR) PLoS One 2014;9(4):e93664       6 Citations
1Computational and experimental characterization of RNA cubic nanoscaffolds. (Afonin KA, Kasprzak W, Bindewald E, Puppala PS, Diehl AR, Hall KT, Kim TJ, Zimmermann MT, Jernigan RL, Jaeger L, Shapiro BA) Methods 2014 May 15;67(2):256-65       53 Citations
1Molecular mechanism of GTPase activation at the signal recognition particle (SRP) RNA distal end. (Shen K, Wang Y, Hwang Fu YH, Zhang Q, Feigon J, Shan SO) J Biol Chem 2013 Dec 20;288(51):36385-97       23 Citations
1Crystal structure of 3WJ core revealing divalent ion-promoted thermostability and assembly of the Phi29 hexameric motor pRNA. (Zhang H, Endrizzi JA, Shu Y, Haque F, Sauter C, Shlyakhtenko LS, Lyubchenko Y, Guo P, Chi YI) RNA 2013 Sep;19(9):1226-37       119 Citations
1The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum. (Feagin JE, Harrell MI, Lee JC, Coe KJ, Sands BH, Cannone JJ, Tami G, Schnare MN, Gutell RR) PLoS One 2012;7(6):e38320       109 Citations
1A comparison of the crystal structures of eukaryotic and bacterial SSU ribosomal RNAs reveals common structural features in the hypervariable regions. (Lee JC, Gutell RR) PLoS One 2012;7(5):e38203       38 Citations
1Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step. (Steczkiewicz K, Zimmermann MT, Kurcinski M, Lewis BA, Dobbs D, Kloczkowski A, Jernigan RL, Kolinski A, Ginalski K) Proc Natl Acad Sci U S A 2011 Jun 07;108(23):9443-8       46 Citations
1Fragmentation of the large subunit ribosomal RNA gene in oyster mitochondrial genomes. (Milbury CA, Lee JC, Cannone JJ, Gaffney PM, Gutell RR) BMC Genomics 2010 Sep 02;11:485       16 Citations
1Structure and function of regulatory RNA elements: ribozymes that regulate gene expression. (Scott WG, Martick M, Chi YI) Biochim Biophys Acta 2009;1789(9-10):634-41       29 Citations
1Rearrangements of the MLL gene are influenced by DNA secondary structure, potentially mediated by topoisomerase II binding. (Le H, Singh S, Shih SJ, Du N, Schnyder S, Loredo GA, Bien C, Michaelis L, Toor A, Diaz MO, Vaughan AT) Genes Chromosomes Cancer 2009 Sep;48(9):806-15       35 Citations
1Fuel specificity of the hepatitis C virus NS3 helicase. (Belon CA, Frick DN) J Mol Biol 2009 May 15;388(4):851-64       22 Citations
1The nucleosome family: dynamic and growing. (Zlatanova J, Bishop TC, Victor JM, Jackson V, van Holde K) Structure 2009 Feb 13;17(2):160-71       152 Citations
1Monitoring helicase activity with molecular beacons. (Belon CA, Frick DN) Biotechniques 2008 Oct;45(4):433-40, 442       60 Citations
1Capturing hammerhead ribozyme structures in action by modulating general base catalysis. (Chi YI, Martick M, Lares M, Kim R, Scott WG, Kim SH) PLoS Biol 2008 Sep 30;6(9):e234       84 Citations
1Acetylation of H4 suppresses the repressive effects of the N-termini of histones H3/H4 and facilitates the formation of positively coiled DNA. (Peterson S, Jackson V) Biochemistry 2008 Jul 08;47(27):7053-65       3 Citations
1NAP1 catalyzes the formation of either positive or negative supercoils on DNA on basis of the dimer-tetramer equilibrium of histones H3/H4. (Peterson S, Danowit R, Wunsch A, Jackson V) Biochemistry 2007 Jul 24;46(29):8634-46       18 Citations
1Specific interactions of the wing domains of FOXA1 transcription factor with DNA. (Cirillo LA, Zaret KS) J Mol Biol 2007 Feb 23;366(3):720-4       67 Citations
1Functional reconstitution and characterization of Pyrococcus furiosus RNase P. (Tsai HY, Pulukkunat DK, Woznick WK, Gopalan V) Proc Natl Acad Sci U S A 2006 Oct 31;103(44):16147-52       85 Citations
1Sequence analysis of the complete mitochondrial DNA in 10 commonly used inbred rat strains. (Schlick NE, Jensen-Seaman MI, Orlebeke K, Kwitek AE, Jacob HJ, Lazar J) Am J Physiol Cell Physiol 2006 Dec;291(6):C1183-92       41 Citations
1The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions. (Lee JC, Gutell RR, Russell R) J Mol Biol 2006 Jul 28;360(5):978-88       34 Citations
1Step-by-step progress toward understanding the hepatitis C virus RNA helicase. (Frick DN) Hepatology 2006 Jun;43(6):1392-5       5 Citations
1Histone release during transcription: acetylation stabilizes the interaction of the H2A-H2B dimer with the H3-H4 tetramer in nucleosomes that are on highly positively coiled DNA. (Wunsch A, Jackson V) Biochemistry 2005 Dec 13;44(49):16351-64       10 Citations
1Target-site preferences of Sleeping Beauty transposons. (Liu G, Geurts AM, Yae K, Srinivasan AR, Fahrenkrug SC, Largaespada DA, Takeda J, Horie K, Olson WK, Hackett PB) J Mol Biol 2005 Feb 11;346(1):161-73       118 Citations
1The lonepair triloop: a new motif in RNA structure. (Lee JC, Cannone JJ, Gutell RR) J Mol Biol 2003 Jan 03;325(1):65-83       67 Citations
1Distribution of rRNA introns in the three-dimensional structure of the ribosome. (Jackson S, Cannone J, Lee J, Gutell R, Woodson S) J Mol Biol 2002 Oct 11;323(1):35-52       61 Citations
1Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure. (Huppler A, Nikstad LJ, Allmann AM, Brow DA, Butcher SE) Nat Struct Biol 2002 Jun;9(6):431-5       132 Citations
1AA.AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices. (Elgavish T, Cannone JJ, Lee JC, Harvey SC, Gutell RR) J Mol Biol 2001 Jul 20;310(4):735-53       59 Citations
1Conformational differences in the 3-D nanostructure of the immunoglobulin heavy-chain locus, a hotspot of chromosomal translocations in B lymphocytes. (Esa A, Coleman AE, Edelmann P, Silva S, Cremer CG, Janz S) Cancer Genet Cytogenet 2001 Jun;127(2):168-73       24 Citations
1In vitro studies on the maintenance of transcription-induced stress by histones and polyamines. (Peng HF, Jackson V) J Biol Chem 2000 Jan 07;275(1):657-68       34 Citations
1The 5'-untranslated region of GM-CSF mRNA suppresses translational repression mediated by the 3' adenosine-uridine-rich element and the poly(A) tail. (Jarzembowski JA, Rajagopalan LE, Shin HC, Malter JS) Nucleic Acids Res 1999 Sep 15;27(18):3660-6       13 Citations
1Structural elements required for the localization of ASH1 mRNA and of a green fluorescent protein reporter particle in vivo. (Chartrand P, Meng XH, Singer RH, Long RM) Curr Biol 1999 Mar 25;9(6):333-6       175 Citations
15'-Peptidyl substituents allow a tuning of the affinity of oligodeoxyribonucleotides for RNA. (Sarracino DA, Steinberg JA, Vergo MT, Woodworth GF, Tetzlaff CN, Richert C) Bioorg Med Chem Lett 1998 Sep 22;8(18):2511-6       16 Citations
1Determination of internuclear angles of DNA using paramagnetic-assisted magnetic alignment. (Beger RD, Marathias VM, Volkman BF, Bolton PH) J Magn Reson 1998 Nov;135(1):256-9       45 Citations
1Structure of an RNA internal loop consisting of tandem C-A+ base pairs. (Jang SB, Hung LW, Chi YI, Holbrook EL, Carter RJ, Holbrook SR) Biochemistry 1998 Aug 25;37(34):11726-31       66 Citations
1Cytoplasmic fate of eukaryotic mRNA: identification and characterization of AU-binding proteins. (Jarzembowski JA, Malter JS) Prog Mol Subcell Biol 1997;18:141-72       16 Citations
1Vaccinia virus DNA replication: two hundred base pairs of telomeric sequence confer optimal replication efficiency on minichromosome templates. (Du S, Traktman P) Proc Natl Acad Sci U S A 1996 Sep 03;93(18):9693-8       42 Citations
1Preferential binding of histones H3 and H4 to highly positively coiled DNA. (Jackson V) Biochemistry 1995 Aug 22;34(33):10607-19       20 Citations
1Dynamics of the interactions of histones H2A,H2B and H3,H4 with torsionally stressed DNA. (Jackson S, Brooks W, Jackson V) Biochemistry 1994 May 10;33(18):5392-403       31 Citations
1Influence of positive stress on nucleosome assembly. (Jackson V) Biochemistry 1993 Jun 08;32(22):5901-12       22 Citations
1The sensitivity of single-strand conformation polymorphism analysis for the detection of single base substitutions. (Sheffield VC, Beck JS, Kwitek AE, Sandstrom DW, Stone EM) Genomics 1993 May;16(2):325-32       596 Citations
1500-MHz proton homonuclear Overhauser evidence for additional base pair in the common arm of eukaryotic ribosomal 5S RNA: wheat germ. (Li SJ, Wu JJ, Marshall AG) Biochemistry 1987 Mar 24;26(6):1578-85       13 Citations
1Identification and assignment of base pairs in the "tuned helix" of intact and ribonuclease T1 cleavage fragments of wheat germ ribosomal 5S RNA via 500-MHz proton homonuclear Overhauser enhancements. (Li SJ, Marshall AG) Biochemistry 1986 Jun 17;25(12):3673-82       15 Citations
1Multistage unfolding of wheat germ ribosomal 5S RNA analyzed by differential scanning calorimetry. (Li SJ, Marshall AG) Biochemistry 1985 Jul 16;24(15):4047-52       27 Citations
1Base pairing in wheat germ ribosomal 5S RNA as measured by ultraviolet absorption, circular dichroism, and Fourier-transform infrared spectrometry. (Li SJ, Burkey KO, Luoma GA, Alben JO, Marshall AG) Biochemistry 1984 Jul 31;23(16):3652-8       8 Citations
1Antibiotic resistance mutations in 16S and 23S ribosomal RNA genes of Escherichia coli. (Sigmund CD, Ettayebi M, Morgan EA) Nucleic Acids Res 1984 Jun 11;12(11):4653-63       190 Citations
1Covalent and noncovalent interactions of aflatoxin with defined deoxyribonucleic acid sequences. (Misra RP, Muench KF, Humayun MZ) Biochemistry 1983 Jul 05;22(14):3351-9       59 Citations