3DNA was created in the hope that it
will be useful, but without any guarantees. Nothing is perfect, and we
strive to improve its functionalities. Any comments, constructive
suggestions, and bug reports are welcome.
The following list is generated automatically by a
Perl script. Some links to PubMed might not retrieve the expected entries:
please refine corresponding queries over there. [Last updated:
Friday Feb 24, 2012 with 524
citations]
Wolter Mario; Woiczikowski P. Benjamin; Elstner Marcus;
et al. "Response of the electric conductivity of double-stranded
DNA on moderate mechanical stretching stresses" PHYSICAL REVIEW B85 (7): 2012.
Barr Daniel; van der Vaart Arjan "The natural DNA
bending angle in the lac repressor headpiece-O1 operator complex is
determined by protein-DNA contacts and water release" PHYSICAL CHEMISTRY CHEMICAL PHYSICS14 (6):
2070-2077 2012.
Biswas Mithun; Voltz Karine; Smith Jeremy C.; et al. "Role of
Histone Tails in Structural Stability of the Nucleosome" PLOS COMPUTATIONAL BIOLOGY7 (12): 2011.
Sharma Amit; Jenkins Katherine R.; Heroux Annie; et
al. "Crystal Structure of the Chromodomain Helicase DNA-binding
Protein 1 (Chd1) DNA-binding Domain in Complex with DNA" JOURNAL OF BIOLOGICAL CHEMISTRY286 (49):
42099-42104 2011.
Buck Janina; Wacker Anna; Warkentin Eberhart; et
al. "Influence of ground-state structure and Mg(2+) binding on folding
kinetics of the guanine-sensing riboswitch aptamer domain" NUCLEIC ACIDS RESEARCH39 (22): 9768-9778
2011.
Yonetani Yoshiteru; Kono Hidetoshi "What determines
water-bridge lifetimes at the surface of DNA? Insight from systematic
molecular dynamics analysis of water kinetics for various DNA sequences"
BIOPHYSICAL CHEMISTRY160 (1): 54-61
2012.
Meyer Sam; Becker Nils B.; Syed Sajad Hussain; et
al. "From crystal and NMR structures, footprints and
cryo-electron-micrographs to large and soft structures: nanoscale modeling
of the nucleosomal stem" NUCLEIC ACIDS RESEARCH39 (21): 9139-9154
2011.
Sathe Chaitanya; Zou Xueqing; Leburton Jean-Pierre;
et al. "Computational Investigation of DNA Detection Using
Graphene Nanopores" ACS NANO5 (11): 8842-8851 2011.
Ostergaard Michael E.; Hrdlicka Patrick J. "Pyrene-functionalized
oligonucleotides and locked nucleic acids (LNAs): Tools for fundamental
research, diagnostics, and nanotechnology" CHEMICAL SOCIETY REVIEWS40 (12): 5771-5788
2011.
Reeves Dara A.; Mu Hong; Kropachev Konstantin; et al.
"Resistance of bulky DNA lesions to nucleotide excision repair can result
from extensive aromatic lesion-base stacking interactions" NUCLEIC ACIDS RESEARCH39 (20): 8752-8764
2011.
Koonammackal Mathew Varghese; Nellipparambil
Unnikrishnan Viswambharan Nair; Sudarsanakumar Chellappanpillai "Molecular
dynamics simulations and binding free energy analysis of DNA minor groove
complexes of curcumin" JOURNAL OF MOLECULAR MODELING17 (11): 2805-2816
2011.
Ramon Blas Jose; Huertas Oscar; Tabares Carolina; et al.
"Structural, Dynamical, and Electronic Transport Properties of Modified DNA
Duplexes Containing Size-Expanded Nucleobases" JOURNAL OF PHYSICAL CHEMISTRY A115 (41):
11344-11354 2011.
Wu Bin; Davey Gabriela E.; Nazarov Alexey A.; et
al. "Specific DNA structural attributes modulate platinum anticancer
drug site selection and cross-link generation" NUCLEIC ACIDS RESEARCH39 (18): 8200-8212
2011.
Kumar Amit; Fang Pengfei; Park Hajeung; et al.
"A Crystal Structure of a Model of the Repeating r(CGG) Transcript Found in
Fragile X Syndrome" CHEMBIOCHEM12 (14): 2140-2142 2011.
Frezza Elisa; Tombolato Fabio; Ferrarini Alberta "Right- and
left-handed liquid crystal assemblies of oligonucleotides: phase chirality
as a reporter of a change in non-chiral interactions?" SOFT MATTER7 (19): 9291-9296 2011.
Zgarbova Marie; Otyepka Michal; Sponer Jiri; et al.
"Refinement of the Cornell et al. Nucleic Acids Force Field Based
on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles"
JOURNAL OF CHEMICAL THEORY AND COMPUTATION7 (9):
2886-2902 2011.
Oteri Francesco; Falconi Mattia; Chillemi Giovanni;
et al. "Simulative Analysis of a Truncated Octahedral DNA Nanocage
Family Indicates the Single-Stranded Thymidine Linkers as the Major Player
for the Conformational Variability" JOURNAL OF PHYSICAL CHEMISTRY C115 (34):
16819-16827 2011.
Romanowska Julia; McCammon J. Andrew; Trylska Joanna
"Understanding the Origins of Bacterial Resistance to Aminoglycosides
through Molecular Dynamics Mutational Study of the Ribosomal A-Site"
PLOS COMPUTATIONAL BIOLOGY7 (7): 2011.
Masoudi-Nejad A, Movahedi S, Jauregui R "Genome-scale
computational analysis of DNA curvature and repeats in Arabidopsis and rice
uncovers plant-specific genomic properties" BMC GENOMICS12: 2011.
Cai Y, Ding S, Geacintov NE, et al.
"Intercalative Conformations of the 14R (+)- and 14S
(-)-trans-anti-DB[a,l]P-N-6-dA Adducts: Molecular Modeling and MD
Simulations" CHEMICAL RESEARCH IN TOXICOLOGY24 (4): 522-531
2011.
Capriotti E, Norambuena T, Marti-Renom MA, et al. "All-atom
knowledge-based potential for RNA structure prediction and assessment"
BIOINFORMATICS27 (8): 1086-1093 2011.
Ebert MO, Jaun B "Oligonucleotides with Sugars Other
Than Ribo- and 2 '-Deoxyribofuranose in the Backbone: the Solution
Structures Determined by NMR in the Context of the 'Etiology of Nucleic
Acids' Project of Albert Eschenmoser" CHEMISTRY & BIODIVERSITY7 (9): 2103-2128
2010.
Sokolowska M, Czapinska H, Bochtler M "Hpy188I-DNA pre-
and post-cleavage complexes-snapshots of the GIY-YIG nuclease mediated
catalysis" NUCLEIC ACIDS RESEARCH39 (4): 1554-1564
2011.
Fadda E, Pomes R "On the molecular basis of uracil recognition in DNA:
comparative study of T-A versus U-A structure, dynamics and open base pair
kinetics" NUCLEIC ACIDS RESEARCH39 (2): 767-780
2011.
Keinan S, Venkatramani R, Balaeff A, et al. "is
MD Geometry Sampling Sufficient for Nucleobase Electronic Structure
Analysis of ET Reactions? Comparing Classical MD and QM/MM Methods"
JOURNAL OF PHYSICAL CHEMISTRY C114 (48):
20496-20502 2010.
Spiriti J, Binder JK, Levitus M, et al.
"Cy3-DNA Stacking Interactions Strongly Depend on the Identity of the
Terminal Basepair" BIOPHYSICAL JOURNAL100 (4): 1049-1057
2011.
Kiliszek A, Kierzek R, Krzyzosiak WJ, et al. "Atomic
resolution structure of CAG RNA repeats: structural insights and
implications for the trinucleotide repeat expansion diseases" NUCLEIC ACIDS RESEARCH38 (22): 8370-8376
2010.
Marathe A, Bansal M "An ensemble of B-DNA dinucleotide geometries lead
to characteristic nucleosomal DNA structure and provide plasticity required
for gene expression" BMC STRUCTURAL BIOLOGY11: 2011.
Cevec M, Thibaudeau C, Plavec J "NMR structure of the let-7 miRNA
interacting with the site LCS1 of lin-41 mRNA from Caenorhabditis elegans"
NUCLEIC ACIDS RESEARCH38 (21): 7814-7821
2010.
Bauer AL, Hlavacek WS, Unkefer PJ, et al.
"Using Sequence-Specific Chemical and Structural Properties of DNA to
Predict Transcription Factor Binding Sites" PLOS COMPUTATIONAL BIOLOGY6 (11): 2010.
Xu F, Colasanti AV, Li Y, et al. "Long-range
effects of histone point mutations on DNA remodeling revealed from
computational analyses of SIN-mutant nucleosome structures" NUCLEIC ACIDS RESEARCH38 (20): 6872-6882
2010.
Podbevsek P, Allerson CR, Bhat B, et al. "Solution-state
structure of a fully alternately 2'-F/2'-OMe modified 42-nt dimeric siRNA
construct" NUCLEIC ACIDS RESEARCH38 (20): 7298-7307
2010.
Halder S, Bhattacharyya D "Structural Stability of
Tandemly Occurring Noncanonical Basepairs within Double Helical Fragments:
Molecular Dynamics Studies of Functional RNA" JOURNAL OF PHYSICAL CHEMISTRY B114 (44):
14028-14040 2010.
Churchill MEA, Klass J, Zoetewey DL "Structural Analysis
of HMGD-DNA Complexes Reveals Influence of Intercalation on Sequence
Selectivity and DNA Bending" JOURNAL OF MOLECULAR BIOLOGY403 (1): 88-102
2010.
Heruth DP, Hawkins T, Logsdon DP, et al. "Mutation in
erythroid specific transcription factor KLF1 causes Hereditary
Spherocytosis in the Nan hemolytic anemia mouse model" GENOMICS96 (5): 303-307 2010.
Juan ECM, Shimizu S, Ma XA, et al. "Insights into the DNA
stabilizing contributions of a bicyclic cytosine analogue: crystal
structures of DNA duplexes containing 7,8-dihydropyrido
[2,3-d]pyrimidin-2-one" NUCLEIC ACIDS RESEARCH38 (19): 6737-6745
2010.
Lin XF, Sun CK, Yao LF, et al. "Theoretical
Studies of the Hydrogen-bond Interactions between O-6-Alkylguanine and DNA
Bases" ACTA CHIMICA SINICA68 (16): 1553-1560
2010.
Van Hecke K, Uytterhoeven K, Voet A, et al. "Designing Triple
Helical Fragments: The Crystal Structure of the Undecamer d(TGGCCTTAAGG)
Mimicking T center dot AT Base Triplets" CRYSTAL GROWTH & DESIGN10 (10): 4622-4629
2010.
Lu XJ, Olson WK, Bussemaker HJ "The RNA backbone plays a
crucial role in mediating the intrinsic stability of the GpU dinucleotide
platform and the GpUpA/GpA miniduplex" NUCLEIC ACIDS RESEARCH38 (14): 4868-4876
2010.
Lu LH, Yi CQ, Jian X, et al. "Structure determination of DNA
methylation lesions N-1-meA and N-3-meC in duplex DNA using a cross-linked
protein-DNA system" NUCLEIC ACIDS RESEARCH38 (13): 4415-4425
2010.
Zhao HY, Yang YD, Zhou YQ "Structure-based prediction of DNA-binding
proteins by structural alignment and a volume-fraction corrected
DFIRE-based energy function" BIOINFORMATICS26 (15): 1857-1863 2010.
Capriotti E, Marti-Renom MA "Quantifying the
relationship between sequence and three-dimensional structure conservation
in RNA" BMC BIOINFORMATICS11: 2010.
Huang H, Kozekov ID, Kozekova A, et al. "Minor Groove
Orientation of the KWKK Peptide Tethered via the N-Terminal Amine to the
Acrolein-Derived 1,N-2-gamma-Hydroxypropanodeoxyguanosine Lesion with a
Trimethylene Linkage" BIOCHEMISTRY49 (29): 6155-6164 2010.
Li MH, Luo QA, Xue XG, et al. "Toward a full
structural characterization of G-quadruplex DNA in aqueous solution:
Molecular dynamics simulations of four G-quadruplex molecules" JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM952:
96-102 2010.
Laponogov I, Pan XS, Veselkov DA, et al. "Structural Basis of
Gate-DNA Breakage and Resealing by Type II Topoisomerases" PLOS ONE5 (6): 2010.
Cherney LT, Cherney MM, Garen CR, et al.
"Crystal Structure of the Intermediate Complex of the Arginine Repressor
from Mycobacterium tuberculosis Bound with Its DNA Operator Reveals
Detailed Mechanism of Arginine Repression" JOURNAL OF MOLECULAR BIOLOGY399 (2): 240-254
2010.
Tolbert BS, Miyazaki Y, Barton S, et al. "Major groove width
variations in RNA structures determined by NMR and impact of C-13 residual
chemical shift anisotropy and H-1-C-13 residual dipolar coupling on
refinement" JOURNAL OF BIOMOLECULAR NMR47 (3): 205-219
2010.
Dijkstra AG, Tanimura Y "Correlated fluctuations in the
exciton dynamics and spectroscopy of DNA" NEW JOURNAL OF PHYSICS12: 2010.
Kapoor P, Kumar A, Naik R, et al. "Leishmania
actin binds and nicks kDNA as well as inhibits decatenation activity of
type II topoisomerase" NUCLEIC ACIDS RESEARCH38 (10): 3308-3317
2010.
Feng YG, Yao HW, Wang JF "Crystal structure of the
crenarchaeal conserved chromatin protein Cren7 and double-stranded DNA
complex" PROTEIN SCIENCE19 (6): 1253-1257 2010.
Chen YS, Yu SW, Yang SY "Theoretical Studies on the Stacking
Interactions between Methylated and Unmethylated DNA Bases" ACTA CHIMICA SINICA68 (8): 739-746
2010.
Popenda M, Szachniuk M, Blazewicz M, et al. "RNA FRABASE 2.0:
an advanced web-accessible database with the capacity to search the
three-dimensional fragments within RNA structures" BMC BIOINFORMATICS11: 2010.
Naome A, Schyman P, Laaksonen A, et al. "Molecular Dynamics
Simulation of 8-Oxoguanine Containing DNA Fragments Reveals Altered
Hydration and Ion Binding Patterns" JOURNAL OF PHYSICAL CHEMISTRY B114 (14):
4789-4801 2010.
Oliveira CLP, Juul S, Jorgensen HL, et al. "Structure of
Nanoscale Truncated Octahedral DNA Cages: Variation of Single-Stranded
Linker Regions and Influence on Assembly Yields" ACS NANO4 (3): 1367-1376 2010.
Aller P, Ye Y, Wallace SS, et al. "Crystal
Structure of a Replicative DNA Polymerase Bound to the Oxidized Guanine
Lesion Guanidinohydantoin" BIOCHEMISTRY49 (11): 2502-2509 2010.
Sharma P, Sponer JE, Sponer J, et al. "On the
Role of the cis Hoogsteen:Sugar-Edge Family of Base Pairs in Platforms and
Triplets-Quantum Chemical Insights into RNA Structural Biology" JOURNAL OF PHYSICAL CHEMISTRY B114 (9):
3307-3320 2010.
Chen YH, Dey R, Chen L "Crystal Structure of the p53
Core Domain Bound to a Full Consensus Site as a Self-Assembled Tetramer"
STRUCTURE18 (2): 246-256 2010.
Gutierrez R, Caetano R, Woiczikowski PB, et al. "Structural
fluctuations and quantum transport through DNA molecular wires: a combined
molecular dynamics and model Hamiltonian approach" NEW JOURNAL OF PHYSICS12: 2010.
Johannsen S, Megger N, Bohme D, et al.
"Solution structure of a DNA double helix with consecutive metal-mediated
base pairs" NATURE CHEMISTRY2 (3): 229-234 2010.
Schudoma C, May P, Nikiforova V, et al. "Sequence-structure
relationships in RNA loops: establishing the basis for loop homology
modeling" NUCLEIC ACIDS RESEARCH38 (3): 970-980
2010.
Figueira ACM, Lima LMTR, Lima LHF, et al.
"Recognition by the Thyroid Hormone Receptor of Canonical DNA Response
Elements" BIOCHEMISTRY49 (5): 893-904 2010.
Svozil D, Hobza P, Sponer J "Comparison of Intrinsic Stacking Energies
of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We
Determine Correct Order of Stability by Quantum-Chemical Calculations?"
JOURNAL OF PHYSICAL CHEMISTRY B114 (2):
1191-1203 2010.
Tomovic A, Oakeley EJ "Computational Structural
Analysis: Multiple Proteins Bound to DNA" PLOS ONE3 (9): 2008.
Banavali NK, MacKerell AD "Characterizing Structural Transitions Using
Localized Free Energy Landscape Analysis" PLOS ONE4 (5): 2009.
Yokojima S, Yoshiki N, Yanoi W, et al. "Solvent Effects on
Ionization Potentials of Guanine Runs and Chemically Modified Guanine in
Duplex DNA: Effect of Electrostatic Interaction and Its Reduction due to
Solvent" JOURNAL OF PHYSICAL CHEMISTRY B113 (51):
16384-16392 2009.
Li H, Gisler T "Overstretching of a 30 bp DNA duplex
studied with steered molecular dynamics simulation: Effects of structural
defects on structure and force-extension relation" EUROPEAN PHYSICAL JOURNAL E30 (3): 325-332
2009.
Yamasaki S, Terada T, Shimizu K, et al. "A generalized
conformational energy function of DNA derived from molecular dynamics
simulations" NUCLEIC ACIDS RESEARCH37 (20): 2009.
Huang H, Dooley PA, Harris CM, et al.
"Differential Base Stacking Interactions Induced by Trimethylene
Interstrand DNA Cross-Links in the 5 '-CpG-3 ' and 5 '-GpC-3 ' Sequence
Contexts" CHEMICAL RESEARCH IN TOXICOLOGY22 (11):
1810-1816 2009.
Randall GL, Zechiedrich L, Pettitt BM "In the absence of writhe, DNA
relieves torsional stress with localized, sequence-dependent structural
failure to preserve B-form" NUCLEIC ACIDS RESEARCH37 (16): 5568-5577
2009.
Thomsen ND, Berger JM "Running in Reverse: The Structural Basis for
Translocation Polarity in Hexameric Helicases" CELL139 (3): 523-534 2009.
Ampt KAM, van der Werf RM, Nelissen FHT, et al.
"The Unstable Part of the Apical Stem of Duck Hepatitis B Virus Epsilon
Shows Enhanced Base Pair Opening but Not Pico- to Nanosecond Dynamics and
Is Essential for Reverse Transcriptase Binding" BIOCHEMISTRY48 (44): 10499-10508 2009.
Konorov SO, Schulze HG, Addison CJ, et al. "Ultraviolet
resonance Raman spectroscopy of locked single-stranded oligo(dA) reveals
conformational implications of the locked ribose in LNA" JOURNAL OF RAMAN SPECTROSCOPY40 (9): 1162-1171
2009.
Ouyang DF, Zhang H, Herten DP, et al. "Flexibility of
Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics
Simulation: Are A-RNA and A'-RNA Distinct Conformational Structures?"
AUSTRALIAN JOURNAL OF CHEMISTRY62 (9): 1054-1061
2009.
Kobylecka M, Leszczynski J, Rak J "Stability of the
valence anion of cytosine is governed by nucleobases sequence in the double
stranded DNA pi-stack: A computational study" JOURNAL OF CHEMICAL PHYSICS131 (8):
2009.
Sharma M, Bulusu G, Mitra A "MD simulations of
ligand-bound and ligand-free aptamer: Molecular level insights into the
binding and switching mechanism of the add A-riboswitch" RNA-A PUBLICATION OF THE RNA SOCIETY15 (9):
1673-1692 2009.
Kim R, Guo JT "PDA: an automatic and comprehensive
analysis program for protein-DNA complex structures" BMC GENOMICS10: 2009.
Qu Y, Tran MC, Farrell NP "Structural consequences of a 3' -> 3' DNA
interstrand cross-link by a trinuclear platinum complex: unique formation
of two such cross-links in a 10-mer duplex" JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY14 (6):
969-977 2009.
Nielsen LM, Holm AIS, Varsano D, et al. "Fingerprints of
Bonding Motifs in DNA Duplexes of Adenine and Thymine Revealed from
Circular Dichroism: Synchrotron Radiation Experiments and TDDFT
Calculations" JOURNAL OF PHYSICAL CHEMISTRY B113 (28):
9614-9619 2009.
Zhang N, Ding S, Kolbanovskiy A, et al. "NMR
and Computational Studies of Stereoisomeric Equine Estrogen-Derived DNA
Cytidine Adducts in Oligonucleotide Duplexes: Opposite Orientations of
Diastereomeric Forms" BIOCHEMISTRY48 (30): 7098-7109 2009.
Zheng GH, Lu XJ, Olson WK "Web 3DNA-a web server for the
analysis, reconstruction, and visualization of three-dimensional
nucleic-acid structures" NUCLEIC ACIDS RESEARCH37: W240-W246
2009.
Frank AT, Stelzer AC, Al-Hashimi HM, et al. "Constructing RNA
dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new
insights into RNA dynamics and adaptive ligand recognition" NUCLEIC ACIDS RESEARCH37 (11): 3670-3679
2009.
Glass LS, Nguyen B, Goodwin KD, et al. "Crystal
Structure of a Trypanocidal 4,4 '-Bis(imidazolinylamino)diphenylamine Bound
to DNA" BIOCHEMISTRY48 (25): 5943-5952 2009.
Chen G, Kennedy SD, Turner DH "A CA(+) Pair Adjacent to a Sheared GA or
AA Pair Stabilizes Size-Symmetric RNA Internal Loops" BIOCHEMISTRY48 (24): 5738-5752 2009.
Bilbille Y, Vendeix FAP, Guenther R, et al.
"The structure of the human tRNA(Lys3) anticodon bound to the HIV genome is
stabilized by modified nucleosides and adjacent mismatch base pairs"
NUCLEIC ACIDS RESEARCH37 (10): 3342-3353
2009.
Woiczikowski PB, Kubar T, Gutierrez R, et al. "Combined
density functional theory and Landauer approach for hole transfer in DNA
along classical molecular dynamics trajectories" JOURNAL OF CHEMICAL PHYSICS130 (21):
2009.
Marathe A, Karandur D, Bansal M "Small local variations
in B-form DNA lead to a large variety of global geometries which can
accommodate most DNA-binding protein motifs" BMC STRUCTURAL BIOLOGY9: 2009.
Kamberaj H, van der Vaart A "Correlated Motions and
Interactions at the Onset of the DNA-induced Partial Unfolding of Ets-1"
BIOPHYSICAL JOURNAL96 (4): 1307-1317
2009.
Shen A, Higgins DE, Panne D "Recognition of AT-Rich DNA
Binding Sites by the MogR Repressor" STRUCTURE17 (5): 769-777 2009.
Gao M, Skolnick J "From Nonspecific DNA-Protein Encounter Complexes to
the Prediction of DNA-Protein Interactions" PLOS COMPUTATIONAL BIOLOGY5 (4): 2009.
Palasingam P, Jauch R, Ng CKL, et al. "The
Structure of Sox17 Bound to DNA Reveals a Conserved Bending Topology but
Selective Protein Interaction Platforms" JOURNAL OF MOLECULAR BIOLOGY388 (3): 619-630
2009.
Zeglis BM, Pierre VC, Kaiser JT, et al. "A Bulky Rhodium
Complex Bound to an Adenosine-Adenosine DNA Mismatch: General Architecture
of the Metalloinsertion Binding Mode" BIOCHEMISTRY48 (20): 4247-4253 2009.
Lou YC, Wei SY, Rajasekaran M, et al. "NMR structural analysis
of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan
parasite Trichomonas vaginalis" NUCLEIC ACIDS RESEARCH37 (7): 2381-2394
2009.
Czyznikowska Z "How does modification of adenine by
hydroxyl radical influence the stability and the nature of stacking
interactions in adenine-cytosine complex?" JOURNAL OF MOLECULAR MODELING15 (6): 615-622
2009.
Kropachev K, Kolbanovskii M, Cai Y, et al. "The
Sequence Dependence of Human Nucleotide Excision Repair Efficiencies of
Benzo[a]pyrene-derived DNA Lesions: Insights into the Structural Factors
that Favor Dual Incisions" JOURNAL OF MOLECULAR BIOLOGY386 (5): 1193-1203
2009.
Olson WK, Esguerra M, Xin YR, et al. "New information content
in RNA base pairing deduced from quantitative analysis of high-resolution
structures" METHODS47 (3): 177-186 2009.
Lowry JA, Gamsjaeger R, Thong SY, et al.
"Structural Analysis of MED-1 Reveals Unexpected Diversity in the Mechanism
of DNA Recognition by GATA- type Zinc Finger Domains" JOURNAL OF BIOLOGICAL CHEMISTRY284 (9):
5827-5835 2009.
Cai YQ, Patel DJ, Geacintov NE, et al. "Differential
Nucleotide Excision Repair Susceptibility of Bulky DNA Adducts in Different
Sequence Contexts: Hierarchies of Recognition Signals" JOURNAL OF MOLECULAR BIOLOGY385 (1): 30-44
2009.
Malecka KA, Ho WC, Marmorstein R "Crystal structure of a p53 core
tetramer bound to DNA" ONCOGENE28 (3): 325-333 2009.
Huang H, Wang H, Lloyd RS, et al.
"Conformational Interconversion of the trans-4-Hydroxynonenal-Derived
(6S,8R,11S) 1,N-2-Deoxyguanosine Adduct When Mismatched with Deoxyadenosine
in DNA" CHEMICAL RESEARCH IN TOXICOLOGY22 (1): 187-200
2009.
Czyznikowska Z, Zalesny R "Theoretical insights into the nature of
intermolecular interactions in cytosine dimer" BIOPHYSICAL CHEMISTRY139: 137-143 2009.
Cherney LT, Cherney MM, Garen CR, et al.
"Crystal Structure of the Arginine Repressor Protein in Complex with the
DNA Operator from Mycobacterium tuberculosis" JOURNAL OF MOLECULAR BIOLOGY384 (5): 1330-1340
2008.
Angarica VE, Perez AG, Vasconcelos AT, et al. "Prediction of
TF target sites based on atomistic models of protein-DNA complexes"
BMC BIOINFORMATICS9: 2008.
Kachalova GS, Rogulin EA, Yunusova AK, et al.
"Structural Analysis of the Heterodimeric Type IIS Restriction Endonuclease
R.BspD6I Acting as a Complex between a Monomeric Site-specific Nickase and
a Catalytic Subunit" JOURNAL OF MOLECULAR BIOLOGY384 (2): 489-502
2008.
Sullivan DM, Bobay BG, Kojetin DJ, et al.
"Insights into the Nature of DNA Binding of AbrB-like Transcription
Factors" STRUCTURE16 (11): 1702-1713 2008.
Huang H, Wang H, Qi N, et al. "The
Stereochemistry of trans-4-Hydroxynonenal-Derived Exocyclic 1,N-2-2
'-Deoxyguanosine Adducts Modulates Formation of Interstrand Cross-Links in
the 5 '-CpG-3 ' Sequence" BIOCHEMISTRY47 (44): 11457-11472 2008.
Karymov MA, Chinnaraj M, Bogdanov A, et al.
"Structure, Dynamics, and Branch Migration of a DNA Holliday Junction: A
Single-Molecule Fluorescence and Modeling Study" BIOPHYSICAL JOURNAL95 (9): 4372-4383
2008.
Czapla L, Swigon D, Olson WK "Effects of the nucleoid protein HU on the
structure, flexibility, and ring-closure properties of DNA deduced from
Monte Carlo simulations" JOURNAL OF MOLECULAR BIOLOGY382 (2): 353-370
2008.
Repges R, Beuck C, Weinhold E, et al.
"6-thioguanine in DNA as CD-spectroscopic probe to study local structural
changes upon protein binding" CHIRALITY20 (9): 978-984 2008.
Rypniewski W, Adamiak DA, Milecki J, et al.
"Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in
two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex" RNA-A PUBLICATION OF THE RNA SOCIETY14 (9):
1845-1851 2008.
Mura C, McCammon JA "Molecular dynamics of a kappa B DNA
element: base flipping via cross-strand intercalative stacking in a
microsecond-scale simulation" NUCLEIC ACIDS RESEARCH36 (15): 4941-4955
2008.
Masliah G, Rene B, Zargarian L, et al.
"Identification of intrinsic dynamics in a DNA sequence preferentially
cleaved by topoisomerase II enzyme" JOURNAL OF MOLECULAR BIOLOGY381 (3): 692-706
2008.
Lu XJ, Olson WK "3DNA: a versatile, integrated software
system for the analysis, rebuilding and visualization of three-dimensional
nucleic-acid structures" NATURE PROTOCOLS3 (7): 1213-1227 2008.
Zhou YZ, Larson JD, Bottoms CA, et al. "Structural basis of
the transcriptional regulation of the proline utilization regulon by
multifunctional PutA" JOURNAL OF MOLECULAR BIOLOGY381 (1): 174-188
2008.
Ivanova A, Shushkov P, Rosch N "Systematic study of the
influence of base-step parameters on the electronic coupling between
base-pair dimers: Comparison of A-DNA and B-DNA forms" JOURNAL OF PHYSICAL CHEMISTRY A112 (30):
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