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Items: 44

1.

Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex.

Sinha K, Sangani SS, Kehr AD, Rule GS, Jen-Jacobson L.

Biochemistry. 2016 Nov 8;55(44):6115-6132. Epub 2016 Oct 27.

2.

Insights into copper coordination in the EcoRI-DNA complex by ESR spectroscopy.

Ji M, Tan L, Jen-Jacobson L, Saxena S.

Mol Phys. 2014 Dec 1;112(24):3173-3182.

3.

Restriction Cascade Exponential Amplification (RCEA) assay with an attomolar detection limit: a novel, highly specific, isothermal alternative to qPCR.

Ghindilis AL, Smith MW, Simon HM, Seoudi IA, Yazvenko NS, Murray IA, Fu X, Smith K, Jen-Jacobson L, Xu SY.

Sci Rep. 2015 Jan 13;5:7737. doi: 10.1038/srep07737.

4.

Thermodynamic and structural basis for relaxation of specificity in protein-DNA recognition.

Sapienza PJ, Niu T, Kurpiewski MR, Grigorescu A, Jen-Jacobson L.

J Mol Biol. 2014 Jan 9;426(1):84-104. doi: 10.1016/j.jmb.2013.09.005. Epub 2013 Sep 14.

5.

Divide and conquer is always best: sensitivity of methyl correlation experiments.

Sinha K, Jen-Jacobson L, Rule GS.

J Biomol NMR. 2013 Aug;56(4):331-5. doi: 10.1007/s10858-013-9751-9. Epub 2013 Jun 15.

6.

Sensitive Cu2+-Cu2+ distance measurements in a protein-DNA complex by double-quantum coherence ESR.

Ruthstein S, Ji M, Mehta P, Jen-Jacobson L, Saxena S.

J Phys Chem B. 2013 May 23;117(20):6227-30. doi: 10.1021/jp4037149. Epub 2013 May 10.

7.

Differential temperature-dependent multimeric assemblies of replication and repair polymerases on DNA increase processivity.

Lin HK, Chase SF, Laue TM, Jen-Jacobson L, Trakselis MA.

Biochemistry. 2012 Sep 18;51(37):7367-82. doi: 10.1021/bi300956t. Epub 2012 Sep 6.

8.

ESR spectroscopy identifies inhibitory Cu2+ sites in a DNA-modifying enzyme to reveal determinants of catalytic specificity.

Yang Z, Kurpiewski MR, Ji M, Townsend JE, Mehta P, Jen-Jacobson L, Saxena S.

Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):E993-1000. doi: 10.1073/pnas.1200733109. Epub 2012 Apr 9.

9.

Simulating the dynamics and orientations of spin-labeled side chains in a protein-DNA complex.

Sarver JL, Townsend JE, Rajapakse G, Jen-Jacobson L, Saxena S.

J Phys Chem B. 2012 Apr 5;116(13):4024-33. doi: 10.1021/jp211094n. Epub 2012 Mar 20.

10.

Specific labeling of threonine methyl groups for NMR studies of protein-nucleic acid complexes.

Sinha K, Jen-Jacobson L, Rule GS.

Biochemistry. 2011 Nov 29;50(47):10189-91. doi: 10.1021/bi201496d. Epub 2011 Nov 3.

11.

The energetic contribution of induced electrostatic asymmetry to DNA bending by a site-specific protein.

Hancock SP, Hiller DA, Perona JJ, Jen-Jacobson L.

J Mol Biol. 2011 Feb 18;406(2):285-312. doi: 10.1016/j.jmb.2010.12.012. Epub 2010 Dec 15.

12.

Single-molecule sequence detection via microfluidic planar extensional flow at a stagnation point.

Dylla-Spears R, Townsend JE, Jen-Jacobson L, Sohn LL, Muller SJ.

Lab Chip. 2010 Jun 21;10(12):1543-9. doi: 10.1039/b926847b. Epub 2010 Mar 31.

13.

Fluorescent marker for direct detection of specific dsDNA sequences.

Dylla-Spears R, Townsend JE, Sohn LL, Jen-Jacobson L, Muller SJ.

Anal Chem. 2009 Dec 15;81(24):10049-54. doi: 10.1021/ac9019895.

14.

A trimeric DNA polymerase complex increases the native replication processivity.

Mikheikin AL, Lin HK, Mehta P, Jen-Jacobson L, Trakselis MA.

Nucleic Acids Res. 2009 Nov;37(21):7194-205. doi: 10.1093/nar/gkp767.

15.

Electron spin resonance shows common structural features for different classes of EcoRI-DNA complexes.

Stone KM, Townsend JE, Sarver J, Sapienza PJ, Saxena S, Jen-Jacobson L.

Angew Chem Int Ed Engl. 2008;47(52):10192-4. doi: 10.1002/anie.200803588. No abstract available.

16.

Formation of DNA-protein cross-links between gamma-hydroxypropanodeoxyguanosine and EcoRI.

VanderVeen LA, Harris TM, Jen-Jacobson L, Marnett LJ.

Chem Res Toxicol. 2008 Sep;21(9):1733-8. doi: 10.1021/tx800092g. Epub 2008 Aug 9.

17.

Structural and thermodynamic basis for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease.

Sapienza PJ, Rosenberg JM, Jen-Jacobson L.

Structure. 2007 Nov;15(11):1368-82.

18.

Thermodynamic and kinetic basis for the relaxed DNA sequence specificity of "promiscuous" mutant EcoRI endonucleases.

Sapienza PJ, Dela Torre CA, McCoy WH 4th, Jana SV, Jen-Jacobson L.

J Mol Biol. 2005 Apr 29;348(2):307-24.

PMID:
15811370
19.

Mechanisms of coupling between DNA recognition specificity and catalysis in EcoRI endonuclease.

Kurpiewski MR, Engler LE, Wozniak LA, Kobylanska A, Koziolkiewicz M, Stec WJ, Jen-Jacobson L.

Structure. 2004 Oct;12(10):1775-88.

20.

Recognition of the pro-mutagenic base uracil by family B DNA polymerases from archaea.

Shuttleworth G, Fogg MJ, Kurpiewski MR, Jen-Jacobson L, Connolly BA.

J Mol Biol. 2004 Mar 26;337(3):621-34.

PMID:
15019782
21.

Assay of restriction endonucleases using oligonucleotides.

Connolly BA, Liu HH, Parry D, Engler LE, Kurpiewski MR, Jen-Jacobson L.

Methods Mol Biol. 2001;148:465-90. No abstract available.

PMID:
11357606
22.

The energetics of the interaction of BamHI endonuclease with its recognition site GGATCC.

Engler LE, Sapienza P, Dorner LF, Kucera R, Schildkraut I, Jen-Jacobson L.

J Mol Biol. 2001 Mar 23;307(2):619-36.

PMID:
11254386
23.

Solution conformation of EcoRI restriction endonuclease changes upon binding of cognate DNA and Mg2+ cofactor.

Watrob H, Liu W, Chen Y, Bartlett SG, Jen-Jacobson L, Barkley MD.

Biochemistry. 2001 Jan 23;40(3):683-92.

PMID:
11170385
24.

Structural and thermodynamic strategies for site-specific DNA binding proteins.

Jen-Jacobson L, Engler LE, Jacobson LA.

Structure. 2000 Oct 15;8(10):1015-23. Erratum in: Structure Fold Des 2000 Dec 15;8(12):following 251..

25.

Effect of base analog substitutions in the specific GATC site on binding and methylation of oligonucleotide duplexes by the bacteriophage T4 Dam DNA-[N6-adenine] methyltransferase.

Malygin EG, Zinoviev VV, Petrov NA, Evdokimov AA, Jen-Jacobson L, Kossykh VG, Hattman S.

Nucleic Acids Res. 1999 Feb 15;27(4):1135-44.

26.

N-termini of EcoRI restriction endonuclease dimer are in close proximity on the protein surface.

Liu W, Chen Y, Watrob H, Bartlett SG, Jen-Jacobson L, Barkley MD.

Biochemistry. 1998 Nov 3;37(44):15457-65.

PMID:
9799508
27.

Specific binding by EcoRV endonuclease to its DNA recognition site GATATC.

Engler LE, Welch KK, Jen-Jacobson L.

J Mol Biol. 1997 May 30;269(1):82-101.

PMID:
9193002
28.
29.
30.

Structural adaptations in the interaction of EcoRI endonuclease with methylated GAATTC sites.

Jen-Jacobson L, Engler LE, Lesser DR, Kurpiewski MR, Yee C, McVerry B.

EMBO J. 1996 Jun 3;15(11):2870-82.

31.

Structural-perturbation approaches to thermodynamics of site-specific protein-DNA interactions.

Jen-Jacobson L.

Methods Enzymol. 1995;259:305-44. No abstract available.

PMID:
8538460
32.

Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition.

Lesser DR, Kurpiewski MR, Waters T, Connolly BA, Jen-Jacobson L.

Proc Natl Acad Sci U S A. 1993 Aug 15;90(16):7548-52.

33.

Stereoselective interaction with chiral phosphorothioates at the central DNA kink of the EcoRI endonuclease-GAATTC complex.

Lesser DR, Grajkowski A, Kurpiewski MR, Koziolkiewicz M, Stec WJ, Jen-Jacobson L.

J Biol Chem. 1992 Dec 5;267(34):24810-8.

34.

The energetic basis of specificity in the Eco RI endonuclease--DNA interaction.

Lesser DR, Kurpiewski MR, Jen-Jacobson L.

Science. 1990 Nov 9;250(4982):776-86.

PMID:
2237428
35.

"Ultraviolet footprinting" accurately maps sequence-specific contacts and DNA kinking in the EcoRI endonuclease-DNA complex.

Becker MM, Lesser D, Kurpiewski M, Baranger A, Jen-Jacobson L.

Proc Natl Acad Sci U S A. 1988 Sep;85(17):6247-51.

36.

Identification of a putative structural gene for cathepsin D in Caenorhabditis elegans.

Jacobson LA, Jen-Jacobson L, Hawdon JM, Owens GP, Bolanowski MA, Emmons SW, Shah MV, Pollock RA, Conklin DS.

Genetics. 1988 Jun;119(2):355-63.

37.

Proteases of the nematode Caenorhabditis elegans.

Sarkis GJ, Kurpiewski MR, Ashcom JD, Jen-Jacobson L, Jacobson LA.

Arch Biochem Biophys. 1988 Feb 15;261(1):80-90.

PMID:
3277541
38.

The enfolding arms of EcoRI endonuclease: role in DNA binding and cleavage.

Jen-Jacobson L, Lesser D, Kurpiewski M.

Cell. 1986 May 23;45(4):619-29.

PMID:
3011275
39.

The relationship between translational initiation and messenger RNA inactivation in down-shifted Escherichia coli.

Jacobson LA, Jen-Jacobson L, Wnek AP.

Arch Biochem Biophys. 1985 Aug 15;241(1):118-31.

PMID:
3927844
40.

Kinked DNA in crystalline complex with EcoRI endonuclease.

Frederick CA, Grable J, Melia M, Samudzi C, Jen-Jacobson L, Wang BC, Greene P, Boyer HW, Rosenberg JM.

Nature. 1984 May 24-30;309(5966):327-31.

PMID:
6328307
41.

Two-fold symmetry of crystalline DNA-EcoRI endonuclease recognition complexes.

Grable J, Frederick CA, Samudzi C, Jen-Jacobson L, Lesser D, Greene P, Boyer HW, Itakura K, Rosenberg JM.

J Biomol Struct Dyn. 1984 Mar;1(5):1149-60.

PMID:
6400815
42.

Coordinate ion pair formation between EcoRI endonuclease and DNA.

Jen-Jacobson L, Kurpiewski M, Lesser D, Grable J, Boyer HW, Rosenberg JM, Greene PJ.

J Biol Chem. 1983 Dec 10;258(23):14638-46.

43.

Control of protein synthesis in Escherichia coli: lack of correlation with changes in intracellular pools of ATP, GTP, and ppGpp.

Jacobson LA, Jen-Jacobson L.

Arch Biochem Biophys. 1980 Sep;203(2):691-6. No abstract available.

PMID:
7006514

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