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Items: 1 to 50 of 188

1.

Structure of the RNA Specialized Translation Initiation Element that Recruits eIF3 to the 5'-UTR of c-Jun.

Walker MJ, Shortridge MD, Albin DD, Cominsky LY, Varani G.

J Mol Biol. 2020 Jan 14. pii: S0022-2836(20)30016-4. doi: 10.1016/j.jmb.2020.01.001. [Epub ahead of print]

PMID:
31953146
2.

Comparative structure, dynamics and evolution of acyl-carrier proteins from Borrelia burgdorferi, Brucella melitensis and Rickettsia prowazekii.

Barnwal RP, Kaur M, Heckert A, Gartia J, Varani G.

Biochem J. 2020 Jan 31;477(2):491-508. doi: 10.1042/BCJ20190797.

PMID:
31922183
3.

Multimodal Long Noncoding RNA Interaction Networks: Control Panels for Cell Fate Specification.

Smith KN, Miller SC, Varani G, Calabrese JM, Magnuson T.

Genetics. 2019 Dec;213(4):1093-1110. doi: 10.1534/genetics.119.302661. Review.

PMID:
31796550
4.

Decrypting noncoding RNA interactions, structures, and functional networks.

Fabbri M, Girnita L, Varani G, Calin GA.

Genome Res. 2019 Sep;29(9):1377-1388. doi: 10.1101/gr.247239.118. Epub 2019 Aug 21. Review.

5.

Design of RNA-targeting macrocyclic peptides.

Walker MJ, Varani G.

Methods Enzymol. 2019;623:339-372. doi: 10.1016/bs.mie.2019.04.029. Epub 2019 Jun 13.

PMID:
31239053
6.

α-Sheet secondary structure in amyloid β-peptide drives aggregation and toxicity in Alzheimer's disease.

Shea D, Hsu CC, Bi TM, Paranjapye N, Childers MC, Cochran J, Tomberlin CP, Wang L, Paris D, Zonderman J, Varani G, Link CD, Mullan M, Daggett V.

Proc Natl Acad Sci U S A. 2019 Apr 30;116(18):8895-8900. doi: 10.1073/pnas.1820585116. Epub 2019 Apr 19.

7.

An Allosteric Switch Primes Sequence-Specific DNA Recognition.

Walker MJ, Varani G.

Cell. 2019 Jan 10;176(1-2):4-6. doi: 10.1016/j.cell.2018.12.020.

8.

A Small Cyclic β-Hairpin Peptide Mimics the Rbfox2 RNA Recognition Motif and Binds to the Precursor miRNA 20b.

Sun YT, Shortridge MD, Varani G.

Chembiochem. 2019 Apr 1;20(7):931-939. doi: 10.1002/cbic.201800645. Epub 2019 Feb 15.

9.

Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.

Bochicchio A, Krepl M, Yang F, Varani G, Sponer J, Carloni P.

PLoS Comput Biol. 2018 Dec 6;14(12):e1006642. doi: 10.1371/journal.pcbi.1006642. eCollection 2018 Dec.

10.

Simple yet functional phosphate-loop proteins.

Romero Romero ML, Yang F, Lin YR, Toth-Petroczy A, Berezovsky IN, Goncearenco A, Yang W, Wellner A, Kumar-Deshmukh F, Sharon M, Baker D, Varani G, Tawfik DS.

Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):E11943-E11950. doi: 10.1073/pnas.1812400115. Epub 2018 Nov 30.

11.

An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb.

Shortridge MD, Wille PT, Jones AN, Davidson A, Bogdanovic J, Arts E, Karn J, Robinson JA, Varani G.

Nucleic Acids Res. 2019 Feb 20;47(3):1523-1531. doi: 10.1093/nar/gky1197.

12.

Experimental and Modeling Study of Drug Release from HPMC-Based Erodible Oral Thin Films.

Adrover A, Varani G, Paolicelli P, Petralito S, Di Muzio L, Casadei MA, Tho I.

Pharmaceutics. 2018 Nov 9;10(4). pii: E222. doi: 10.3390/pharmaceutics10040222.

13.

Effect of glycerol on the physical and mechanical properties of thin gellan gum films for oral drug delivery.

Paolicelli P, Petralito S, Varani G, Nardoni M, Pacelli S, Di Muzio L, Tirillò J, Bartuli C, Cesa S, Casadei MA, Adrover A.

Int J Pharm. 2018 Aug 25;547(1-2):226-234. doi: 10.1016/j.ijpharm.2018.05.046. Epub 2018 May 19.

PMID:
29787893
14.

Comprehensive computational design of ordered peptide macrocycles.

Hosseinzadeh P, Bhardwaj G, Mulligan VK, Shortridge MD, Craven TW, Pardo-Avila F, Rettie SA, Kim DE, Silva DA, Ibrahim YM, Webb IK, Cort JR, Adkins JN, Varani G, Baker D.

Science. 2017 Dec 15;358(6369):1461-1466. doi: 10.1126/science.aap7577.

15.

Reconstitution of the CstF complex unveils a regulatory role for CstF-50 in recognition of 3'-end processing signals.

Yang W, Hsu PL, Yang F, Song JE, Varani G.

Nucleic Acids Res. 2018 Jan 25;46(2):493-503. doi: 10.1093/nar/gkx1177.

16.

DESIGN AND CHARACTERIZATION OF A BIOCOMPATIBLE PHYSICAL HYDROGEL BASED ON SCLEROGLUCAN FOR TOPICAL DRUG DELIVERY.

Paolicelli P, Varani G, Pacelli S, Ogliani E, Nardoni M, Petralito S, Adrover A, Casadei MA.

Carbohydr Polym. 2017 Oct 15;174:960-969. doi: 10.1016/j.carbpol.2017.07.008. Epub 2017 Jul 6.

PMID:
28821154
17.

Applications of NMR to structure determination of RNAs large and small.

Barnwal RP, Yang F, Varani G.

Arch Biochem Biophys. 2017 Aug 15;628:42-56. doi: 10.1016/j.abb.2017.06.003. Epub 2017 Jun 16. Review.

18.

A promoter-proximal transcript targeted by genetic polymorphism controls E-cadherin silencing in human cancers.

Pisignano G, Napoli S, Magistri M, Mapelli SN, Pastori C, Di Marco S, Civenni G, Albino D, Enriquez C, Allegrini S, Mitra A, D'Ambrosio G, Mello-Grand M, Chiorino G, Garcia-Escudero R, Varani G, Carbone GM, Catapano CV.

Nat Commun. 2017 May 30;8:15622. doi: 10.1038/ncomms15622.

19.

Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner.

Nemec CM, Yang F, Gilmore JM, Hintermair C, Ho YH, Tseng SC, Heidemann M, Zhang Y, Florens L, Gasch AP, Eick D, Washburn MP, Varani G, Ansari AZ.

Proc Natl Acad Sci U S A. 2017 May 16;114(20):E3944-E3953. doi: 10.1073/pnas.1700128114. Epub 2017 May 2.

20.

A Macrocyclic Peptide Ligand Binds the Oncogenic MicroRNA-21 Precursor and Suppresses Dicer Processing.

Shortridge MD, Walker MJ, Pavelitz T, Chen Y, Yang W, Varani G.

ACS Chem Biol. 2017 Jun 16;12(6):1611-1620. doi: 10.1021/acschembio.7b00180. Epub 2017 May 2.

21.

Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA.

Abulwerdi FA, Shortridge MD, Sztuba-Solinska J, Wilson R, Le Grice SF, Varani G, Schneekloth JS Jr.

J Med Chem. 2016 Dec 22;59(24):11148-11160. doi: 10.1021/acs.jmedchem.6b01450. Epub 2016 Dec 2.

22.

Ultraslow Domain Motions in HIV-1 TAR RNA Revealed by Solid-State Deuterium NMR.

Huang W, Emani PS, Varani G, Drobny GP.

J Phys Chem B. 2017 Jan 12;121(1):110-117. doi: 10.1021/acs.jpcb.6b11041. Epub 2016 Dec 21.

23.

Structure and mechanism of a molecular rheostat, an RNA thermometer that modulates immune evasion by Neisseria meningitidis.

Barnwal RP, Loh E, Godin KS, Yip J, Lavender H, Tang CM, Varani G.

Nucleic Acids Res. 2016 Nov 2;44(19):9426-9437. Epub 2016 Jul 1.

24.

The C terminus of Pcf11 forms a novel zinc-finger structure that plays an essential role in mRNA 3'-end processing.

Yang F, Hsu P, Lee SD, Yang W, Hoskinson D, Xu W, Moore C, Varani G.

RNA. 2017 Jan;23(1):98-107. Epub 2016 Oct 25.

25.

Targeted inhibition of oncogenic miR-21 maturation with designed RNA-binding proteins.

Chen Y, Yang F, Zubovic L, Pavelitz T, Yang W, Godin K, Walker M, Zheng S, Macchi P, Varani G.

Nat Chem Biol. 2016 Sep;12(9):717-23. doi: 10.1038/nchembio.2128. Epub 2016 Jul 18.

26.

Structure of a low-population binding intermediate in protein-RNA recognition.

Borkar AN, Bardaro MF Jr, Camilloni C, Aprile FA, Varani G, Vendruscolo M.

Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):7171-6. doi: 10.1073/pnas.1521349113. Epub 2016 Jun 10.

27.

Rbfox proteins regulate microRNA biogenesis by sequence-specific binding to their precursors and target downstream Dicer.

Chen Y, Zubovic L, Yang F, Godin K, Pavelitz T, Castellanos J, Macchi P, Varani G.

Nucleic Acids Res. 2016 May 19;44(9):4381-95. doi: 10.1093/nar/gkw177. Epub 2016 Mar 21.

28.

Twenty years of RNA: the discovery of microRNAs.

Varani G.

RNA. 2015 Apr;21(4):751-2. doi: 10.1261/rna.050237.115. No abstract available.

29.

Structure based approaches for targeting non-coding RNAs with small molecules.

Shortridge MD, Varani G.

Curr Opin Struct Biol. 2015 Feb;30:79-88. doi: 10.1016/j.sbi.2015.01.008. Epub 2015 Feb 16. Review.

30.

Targeting Influenza A Virus RNA Promoter.

Bottini A, De SK, Wu B, Tang C, Varani G, Pellecchia M.

Chem Biol Drug Des. 2015 Oct;86(4):663-73. doi: 10.1111/cbdd.12534. Epub 2015 Mar 13.

31.

Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA.

Musiani F, Rossetti G, Capece L, Gerger TM, Micheletti C, Varani G, Carloni P.

J Am Chem Soc. 2014 Nov 5;136(44):15631-7. doi: 10.1021/ja507812v. Epub 2014 Oct 27.

32.

Designed α-sheet peptides inhibit amyloid formation by targeting toxic oligomers.

Hopping G, Kellock J, Barnwal RP, Law P, Bryers J, Varani G, Caughey B, Daggett V.

Elife. 2014 Jul 15;3:e01681. doi: 10.7554/eLife.01681.

33.

Rtr1 is a dual specificity phosphatase that dephosphorylates Tyr1 and Ser5 on the RNA polymerase II CTD.

Hsu PL, Yang F, Smith-Kinnaman W, Yang W, Song JE, Mosley AL, Varani G.

J Mol Biol. 2014 Aug 12;426(16):2970-81. doi: 10.1016/j.jmb.2014.06.010. Epub 2014 Jun 18.

34.

miRNA sensitivity to Drosha levels correlates with pre-miRNA secondary structure.

Sperber H, Beem A, Shannon S, Jones R, Banik P, Chen Y, Ku S, Varani G, Yao S, Ruohola-Baker H.

RNA. 2014 May;20(5):621-31. doi: 10.1261/rna.043943.113. Epub 2014 Mar 27.

35.

The interactome of the atypical phosphatase Rtr1 in Saccharomyces cerevisiae.

Smith-Kinnaman WR, Berna MJ, Hunter GO, True JD, Hsu P, Cabello GI, Fox MJ, Varani G, Mosley AL.

Mol Biosyst. 2014 Jul;10(7):1730-41. doi: 10.1039/c4mb00109e.

36.

Elucidating molecular motion through structural and dynamic filters of energy-minimized conformer ensembles.

Emani PS, Bardaro MF Jr, Huang W, Aragon S, Varani G, Drobny GP.

J Phys Chem B. 2014 Feb 20;118(7):1726-42. doi: 10.1021/jp409386t. Epub 2014 Feb 11.

37.

A novel small-molecule binds to the influenza A virus RNA promoter and inhibits viral replication.

Lee MK, Bottini A, Kim M, Bardaro MF Jr, Zhang Z, Pellecchia M, Choi BS, Varani G.

Chem Commun (Camb). 2014 Jan 11;50(3):368-70. doi: 10.1039/c3cc46973e. Epub 2013 Nov 18. Erratum in: Chem Commun (Camb). 2014 Oct 25;50(83):12578.

38.

Engineering RNA-binding proteins for biology.

Chen Y, Varani G.

FEBS J. 2013 Aug;280(16):3734-54. doi: 10.1111/febs.12375. Epub 2013 Jul 5. Review.

39.

RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations.

Do TN, Carloni P, Varani G, Bussi G.

J Chem Theory Comput. 2013 Mar 12;9(3):1720-30. doi: 10.1021/ct3009914. Epub 2013 Feb 22.

PMID:
26587630
40.

Structural and biochemical analysis of the assembly and function of the yeast pre-mRNA 3' end processing complex CF I.

Barnwal RP, Lee SD, Moore C, Varani G.

Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21342-7. doi: 10.1073/pnas.1214102110. Epub 2012 Dec 10.

41.

GFT projection NMR for efficient (1)H/ (13)C sugar spin system identification in nucleic acids.

Atreya HS, Sathyamoorthy B, Jaipuria G, Beaumont V, Varani G, Szyperski T.

J Biomol NMR. 2012 Dec;54(4):337-42. doi: 10.1007/s10858-012-9687-5. Epub 2012 Nov 29.

PMID:
23192291
42.

Aminoglycoside antibiotics bind to the influenza A virus RNA promoter.

Kim H, Lee MK, Ko J, Park CJ, Kim M, Jeong Y, Hong S, Varani G, Choi BS.

Mol Biosyst. 2012 Nov;8(11):2857-9. doi: 10.1039/c2mb25333j. Epub 2012 Sep 19.

PMID:
22990985
43.

Preparation of RNA samples with narrow line widths for solid state NMR investigations.

Huang W, Bardaro MF Jr, Varani G, Drobny GP.

J Magn Reson. 2012 Oct;223:51-4. doi: 10.1016/j.jmr.2012.07.018. Epub 2012 Aug 10.

PMID:
22967888
44.

Independent alignment of RNA for dynamic studies using residual dipolar couplings.

Bardaro MF Jr, Varani G.

J Biomol NMR. 2012 Sep;54(1):69-80. doi: 10.1007/s10858-012-9655-0. Epub 2012 Jul 18.

PMID:
22806132
45.

Correction to "Theory of nonrigid rotational motion applied to NMR relaxation in RNA".

Emani PS, Olsen GL, Varani G, Drobny GP.

J Phys Chem A. 2012 Jul 5;116(26):7253-60. doi: 10.1021/jp305123n. Epub 2012 Jun 22. No abstract available.

46.

Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA.

Do TN, Ippoliti E, Carloni P, Varani G, Parrinello M.

J Chem Theory Comput. 2012 Feb 14;8(2):688-94. doi: 10.1021/ct2005769. Epub 2012 Jan 20.

PMID:
26596616
47.

Examining the relationship between RNA function and motion using nuclear magnetic resonance.

Bardaro MF Jr, Varani G.

Wiley Interdiscip Rev RNA. 2012 Jan-Feb;3(1):122-32. doi: 10.1002/wrna.108. Epub 2011 Aug 17. Review.

PMID:
22180312
48.

The H/ACA RNP assembly factor SHQ1 functions as an RNA mimic.

Walbott H, Machado-Pinilla R, Liger D, Blaud M, Réty S, Grozdanov PN, Godin K, van Tilbeurgh H, Varani G, Meier UT, Leulliot N.

Genes Dev. 2011 Nov 15;25(22):2398-408. doi: 10.1101/gad.176834.111.

49.

Interactions of protein side chains with RNA defined with REDOR solid state NMR.

Huang W, Varani G, Drobny GP.

J Biomol NMR. 2011 Nov;51(3):347-56. doi: 10.1007/s10858-011-9573-6. Epub 2011 Sep 25.

PMID:
21947838
50.

Comparative analysis of glutaredoxin domains from bacterial opportunistic pathogens.

Leeper T, Zhang S, Van Voorhis WC, Myler PJ, Varani G.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Sep 1;67(Pt 9):1141-7. doi: 10.1107/S1744309111012346. Epub 2011 Aug 16.

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