Author results

4I9V
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THE ATOMIC STRUCTURE OF 5-HYDROXYMETHYL 2'-DEOXYCITIDINE BASE PAIRED WITH 2'-DEOXYGUANOSINE IN DICKERSON DREW DODECAMER
Descriptor:DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5HC)P*GP*CP*G)-3'), MAGNESIUM ION, SPERMINE (FULLY PROTONATED FORM)
Authors:Nocek, B., Szulik, M.W., Joachimiak, A., Stone, M.P.
Deposit date:2012-12-05
Release date:2013-11-20
Last modified:2015-02-25
Method:X-RAY DIFFRACTION (1.02 Å)
Cite:Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.
Biochemistry, 54, 2015
3EY2
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A CONFORMATIONAL TRANSITION IN THE STRUCTURE OF A 2'-THIOMETHYL-MODIFIED DNA VISUALIZED AT HIGH RESOLUTION
Descriptor:5'-D(*GP*CP*GP*TP*AP*(USM)P*AP*CP*GP*C)-3', N-methylpropane-1,3-diamine
Authors:Egli, M., Pallan, P.S.
Deposit date:2008-10-17
Release date:2009-04-28
Last modified:2017-10-25
Method:X-RAY DIFFRACTION (1.04 Å)
Cite:A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.
Chem.Commun.(Camb.), 15, 2009
5V2H
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RNA OCTAMER CONTAINING GLYCOL NUCLEIC ACID, SGNT
Descriptor:RNA (5'-R(*(CBV)P*GP*AP*AP*(ZTH)P*UP*CP*G)-3'), COBALT HEXAMMINE(III), MAGNESIUM ION
Authors:Harp, J.M., Egli, M.
Deposit date:2017-03-04
Release date:2017-06-14
Last modified:2017-11-22
Method:X-RAY DIFFRACTION (1.080013 Å)
Cite:Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on siRNA.
J. Am. Chem. Soc., 139, 2017
2Q1O
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CRYSTAL STRUCTURE ANALYSIS OF THE RNA DODECAMER CGC-NF2-AAUUGGCG, WITH AN INCORPORATED 2,4-DIFLUOROTOLUYL RESIDUE (NF2)
Descriptor:RNA (5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*GP*GP*CP*G)-3')
Authors:Li, F., Pallan, P.S.
Deposit date:2007-05-25
Release date:2007-10-30
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.1 Å)
Cite:Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme.
Nucleic Acids Res., 35, 2007
3OPI
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7-DEAZA-2'-DEOXYADENOSINE MODIFICATION IN B-FORM DNA
Descriptor:DNA (5'-D(*CP*GP*CP*GP*AP*(7DA)P*TP*TP*CP*GP*CP*G)-3'), MAGNESIUM ION, SODIUM ION
Authors:Kowal, E.A., Ganguly, M., Pallan, P.S., Marky, L.A., Gold, B., Egli, M., Stone, M.P.
Deposit date:2010-09-01
Release date:2011-08-31
Last modified:2017-11-08
Method:X-RAY DIFFRACTION (1.1 Å)
Cite:Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2'-deoxyadenosine:dT Base Pairing in DNA.
J.Phys.Chem.B, 115, 2011
2Q1R
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CRYSTAL STRUCTURE ANALYSIS OF THE RNA DODECAMER CGCGAAUUAGCG, WITH A G-A MISMATCH.
Descriptor:RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*AP*GP*CP*G)-3'), MAGNESIUM ION
Authors:Li, F., Pallan, P.S.
Deposit date:2007-05-25
Release date:2007-10-30
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.12 Å)
Cite:Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme.
Nucleic Acids Res., 35, 2007
4RC0
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X-RAY STRUCTURE OF RNA CONTAINING GUANOSINE PHOSPHORODITHIOATE
Descriptor:5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(A2M)P*(2SG)P*CP*G)-3'
Authors:Pallan, P.S., Egli, M.
Deposit date:2014-09-13
Release date:2015-09-16
Last modified:2017-07-12
Method:X-RAY DIFFRACTION (1.13 Å)
Cite:Crystal Structure, Stability and siRNA Activity of Phosphorodithioate-Modified RNAs
To be Published
3P4C
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ALTERNATINGLY MODIFIED 2'FLUORO RNA OCTAMER F/RA2U2-R32
Descriptor:5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3', STRONTIUM ION
Authors:Pallan, P.S., Greene, E.M., Jicman, P.A., Pandey, R.K., Manoharan, M., Rozners, E., Egli, M.
Deposit date:2010-10-06
Release date:2011-01-05
Last modified:2017-11-08
Method:X-RAY DIFFRACTION (1.15 Å)
Cite:Unexpected origins of the enhanced pairing affinity of 2'-fluoro-modified RNA.
Nucleic Acids Res., 39, 2011
1PWF
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ONE SUGAR PUCKER FITS ALL: PAIRING VERSATILITY DESPITE CONFORMATIONAL UNIFORMITY IN TNA
Descriptor:5'-D(*GP*CP*GP*TP*AP*(2MU)P*(FA2)P*CP*GP*C)-3', SPERMINE
Authors:Pallan, P.S., Wilds, C.J., Wawrzak, Z., Krishnamurthy, R., Eschenmoser, A., Egli, M.
Deposit date:2003-07-01
Release date:2004-07-13
Last modified:2017-10-11
Method:X-RAY DIFFRACTION (1.16 Å)
Cite:Why does TNA cross-pair more strongly with RNA than with DNA? an answer from X-ray analysis.
ANGEW.CHEM.INT.ED.ENGL., 42, 2003
4RBZ
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X-RAY STRUCTURE OF RNA CONTAINING ADENOSINE PHOSPHORODITHIOATE
Descriptor:5'-R(*CP*GP*CP*GP*(A2M)P*(ADS)P*UP*UP*AP*GP*CP*G)-3'
Authors:Pallan, P.S., Egli, M.
Deposit date:2014-09-13
Release date:2015-09-16
Last modified:2017-07-12
Method:X-RAY DIFFRACTION (1.18 Å)
Cite:Crystal Structure, Stability and siRNA Activity of Phosphorodithioate-Modified RNAs
To be Published
5V1K
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STRUCTURE OF R-GNA DODECAMER
Descriptor:RNA (5'-R(*CP*GP*CP*GP*AP*AP*(5BU)P*(8RJ)P*AP*GP*CP*G)-3')
Authors:Pallan, P.S., Egli, M.
Deposit date:2017-03-02
Release date:2017-06-21
Last modified:2017-08-16
Method:X-RAY DIFFRACTION (1.18 Å)
Cite:Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on siRNA.
J. Am. Chem. Soc., 2017
4RBY
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FIRST X-RAY STRUCTURE OF RNA CONTAINING GUANOSINE PHOSPHORODITHIOATE
Descriptor:5'-R(*CP*GP*CP*(2SG)P*AP*AP*UP*UP*AP*GP*CP*G)-3', STRONTIUM ION
Authors:Pallan, P.S., Egli, M.
Deposit date:2014-09-13
Release date:2015-09-16
Last modified:2017-07-12
Method:X-RAY DIFFRACTION (1.19 Å)
Cite:Crystal Structure, Stability and siRNA Activity of Phosphorodithioate-Modified RNAs
To be Published
3P4A
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2'FLUORO MODIFIED RNA OCTAMER FA2U2
Descriptor:2'Fluoro modified RNA 8-MER, STRONTIUM ION, MAGNESIUM ION
Authors:Manoharan, M., Akinc, A., Pandey, R.K., Qin, J., Hadwiger, P., John, M., Mills, K., Charisse, K., Maier, M.A., Nechev, L., Greene, E.M., Pallan, P.S., Rozners, E., Rajeev, K.G., Egli, M.
Deposit date:2010-10-06
Release date:2011-01-05
Last modified:2017-11-08
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Unexpected origins of the enhanced pairing affinity of 2'-fluoro-modified RNA.
Nucleic Acids Res., 39, 2011
4O41
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AMIDE LINKED RNA
Descriptor:AMIDE LINKED RNA, STRONTIUM ION
Authors:Pallan, P.S., Egli, M.
Deposit date:2013-12-18
Release date:2014-07-09
Last modified:2014-09-03
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Amides are excellent mimics of phosphate internucleoside linkages and are well tolerated in short interfering RNAs.
Nucleic Acids Res., 42, 2014
5DO5
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CRYSTAL STRUCTURE OF 2'-FLUORO-RNA BEARING A PHOSPHORODITHIOATE
Descriptor:RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(AF2)P*(2SG)P*CP*G)-3')
Authors:Pallan, P.S., Egli, M.
Deposit date:2015-09-10
Release date:2016-09-21
Last modified:2017-09-20
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Crystal Structure of 2'-Fluoro-RNA bearing a phosphorodithioate
To Be Published
5V1L
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STRUCTURE OF S-GNA DODECAMER
Descriptor:RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G)-3'), STRONTIUM ION, SPERMINE
Authors:Pallan, P.S., Egli, M.
Deposit date:2017-03-02
Release date:2017-06-14
Last modified:2017-08-16
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on siRNA.
J. Am. Chem. Soc., 139, 2017
3V07
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CRYSTAL STRUCTURE OF R-6'-ME-3'-FLUORO HEXITOL NUCLEIC ACID
Descriptor:DNA (5'-D(*GP*CP*GP*TP*AP*(F6H)P*AP*CP*GP*C)-3')
Authors:Pallan, P.S., Egli, M.
Deposit date:2011-12-07
Release date:2012-02-08
Method:X-RAY DIFFRACTION (1.24 Å)
Cite:Insights from crystal structures into the opposite effects on RNA affinity caused by the s- and R-6'-methyl backbone modifications of 3'-fluoro hexitol nucleic Acid.
Biochemistry, 51, 2012
3EY3
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A CONFORMATIONAL TRANSITION IN THE STRUCTURE OF A 2'-THIOMETHYL-MODIFIED DNA VISUALIZED AT HIGH RESOLUTION
Descriptor:5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3', STRONTIUM ION, (4S)-2-METHYL-2,4-PENTANEDIOL
Authors:Egli, M., Pallan, P.S.
Deposit date:2008-10-17
Release date:2009-04-28
Last modified:2017-10-25
Method:X-RAY DIFFRACTION (1.25 Å)
Cite:A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.
Chem.Commun.(Camb.), 15, 2009
2A43
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CRYSTAL STRUCTURE OF A LUTEOVIRAL RNA PSEUDOKNOT AND MODEL FOR A MINIMAL RIBOSOMAL FRAMESHIFTING MOTIF
Descriptor:RNA Pseudoknot, MAGNESIUM ION
Authors:Pallan, P.S., Marshall, W.S., Harp, J., Jewett III, F.C., Wawrzak, Z., Brown II, B.A., Rich, A., Egli, M.
Deposit date:2005-06-27
Release date:2005-09-27
Last modified:2017-10-11
Method:X-RAY DIFFRACTION (1.34 Å)
Cite:Crystal Structure of a Luteoviral RNA Pseudoknot and Model for a Minimal Ribosomal Frameshifting Motif
Biochemistry, 44, 2005
3OZ5
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S-METHYL CARBOCYCLIC LNA
Descriptor:DNA (5'-D(*GP*CP*GP*TP*AP*(UMX)P*AP*CP*GP*C)-3'), SPERMINE
Authors:Seth, P.R., Allerson, C.A., Berdeja, A., Siwkowski, A., Pallan, P.S., Gaus, H., Prakash, T.P., Watt, A.T., Egli, M., Swayze, E.E.
Deposit date:2010-09-24
Release date:2010-11-24
Last modified:2017-11-08
Method:X-RAY DIFFRACTION (1.36 Å)
Cite:An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA.
J.Am.Chem.Soc., 132, 2010
5W20
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CRYSTAL STRUCTURE OF INOSINE-SUBSTITUTED DUPLEX DNA
Descriptor:DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*TP*GP*G)-3'), MAGNESIUM ION
Authors:Pallan, P.S., Egli, M.
Deposit date:2017-06-05
Release date:2017-08-23
Last modified:2018-10-24
Method:X-RAY DIFFRACTION (1.36 Å)
Cite:Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography.
J. Biomol. Struct. Dyn., 36, 2018
3UKB
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(R)-CET-BNA DECAMER STRUCTURE
Descriptor:DNA (5'-D(*GP*CP*GP*TP*AP*(RCE)P*AP*CP*GP*C)-3')
Authors:Pallan, P.S., Egli, M.
Deposit date:2011-11-09
Release date:2012-06-20
Last modified:2012-08-08
Method:X-RAY DIFFRACTION (1.42 Å)
Cite:Structure and nuclease resistance of 2',4'-constrained 2'-O-methoxyethyl (cMOE) and 2'-O-ethyl (cEt) modified DNAs.
Chem.Commun.(Camb.), 48, 2012
3P4B
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ALTERNATINGLY MODIFIED 2'FLUORO RNA OCTAMER F/RA2U2-P3
Descriptor:5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3', BARIUM ION
Authors:Pallan, P.S., Greene, E.M., Jicman, P.A., Pandey, R.K., Manoharan, M., Rozners, E., Egli, M.
Deposit date:2010-10-06
Release date:2011-01-05
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.45 Å)
Cite:Unexpected origins of the enhanced pairing affinity of 2'-fluoro-modified RNA.
Nucleic Acids Res., 39, 2011
4HTU
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STRUCTURE OF 5-CHLOROURACIL MODIFIED A:U BASE PAIR
Descriptor:Ribonuclease H, DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*(UCL)P*CP*GP*CP*G)-3'), MAGNESIUM ION, ...
Authors:Patra, A., Egli, M.
Deposit date:2012-11-01
Release date:2012-12-19
Last modified:2013-03-27
Method:X-RAY DIFFRACTION (1.489 Å)
Cite:Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs.
Nucleic Acids Res., 41, 2013
1Y8L
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CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2-(TRIFLUORO)ETHYL] THYMIDINE (T*)
Descriptor:5'-D(*GP*CP*GP*TP*AP*(TFE)P*AP*CP*GP*C)-3'), MAGNESIUM ION, SPERMINE
Authors:Egli, M., Minasov, G., Tereshko, V., Pallan, P.S., Teplova, M., Inamati, G.B., Lesnik, E.A., Owens, S.R., Ross, B.S., Prakash, T.P., Manoharan, M.
Deposit date:2004-12-13
Release date:2005-06-28
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications.
Biochemistry, 44, 2005