Dr. Linda Jen-Jacobson

Genetics
K. Arndt
T.-L. Ashman
G. Campbell
D. Chapman
G. Hatfull
J. Hildebrand
L. Jacobson
S. Kalisz
J. Martens
V. Oke
W. Saunders
B. Stronach
S. Tonsor
R. Wood

Microbiology
G. Hatfull
R. Hendrix
J. Lawrence
V. Oke
J. Pipas
M. Popa
I. Campbell
R.L. Duda
S. Godfrey

Molecular Biology
K. Arndt
J. Franzen
P. Grabowski
G. Hatfull
R. Hendrix
L. Jen-Jacobson
J. Martens
C. Peebles
J. Pipas
J. Rosenberg
A. Schwacha
C. Walsh

Plant Biology
T.-L. Ashman
W. Carson
S. Kalisz
V. Oke
C. Partanen
S. Tonsor
B. Traw

Science Education
A. Bledsoe
K. Curto
L. Daniels
S. Godfrey
N. Kaufmann
C. LaFave
J. Newman
E. Polinko
M. Popa
L. Roberts
T. Seiflein
R. Sherwin
A. Slinskey Legg

Structural Biology
M. Grabe
J. Hempel
R. Hendrix
L. Jen-Jacobson
J. Rosenberg
A. VanDemark

Former Faculty

Photo of Dr.
Jen-Jacobson

Molecular Mechanisms of Sequence-Specificity in Protein-DNA Interactions; Structure-Function Relationships, Energetics and Conformational Dynamics in Proteins and Nucleic Acids

Professor

Dr. Jen-Jacobson received her Ph.D. in 1967 from the University of Illinois and joined the Department in 1975.

Currently, Dr. Jen-Jacobson is accepting graduate students in her laboratory. Dr. Jen-Jacobson is accepting undergraduate researchers, and does sponsor students in other laboratories.

Professional Interests - Publications - Contact Information - Lab Personnel

Professional Interests of Linda Jen-Jacobson

A particularly challenging problem of molecular biology is how a protein recognizes a specific sequence of bases in DNA amidst the vast sea of "other" sequences in the cell. Sequence-dependent interactions are essential to key biological processes such as the regulation and expression of genetic information, modification of DNA, and initiation of DNA replication.

Professor Jen-Jacobson and her research group are studying the interactions of restriction endonucleases with DNA with the idea that proteins with extremely high site selectivity might reveal the greatest number of rules and constraints governing specific molecular recognition and that other less stringent DNA-protein interactions (e.g. graded discrimination between related operators by repressors) might be understood in terms of relaxation of some of these constraints. High fidelity in sequence recognition is necessary for restriction endonucleases to cleave efficiently foreign DNA while avoiding the suicidal consequences of cleaving sites that differ by only one base-pair.in the bacterial cell's own DNA. The group's structure-function studies of EcoRI BamHI and EcoRV endonucleases focus on the following questions:

What roles do particular amino acid side chains, base and sugar-phosphate backbone functional groups play in specific recognition and cleavage? Do they contribute independently or cooperatively to specificity?
What roles do the sequence-dependent conformation and flexibility of the DNA recognition sites play in specificity determination? What is the role of sequences flanking the recognition site in modulating the complementarity of the DNA-protein interface?
How does the recognition interface adapt when the protein relaxes its specificity and interacts with almost-correct "mutant" DNA sites and what are the energetic consequences? The strategy has been to engineer perturbations in both the protein and DNA sides of the interface and to evaluate the consequences in energetic terms at high resolution. In parallel experiments, the protein-DNA contacts and structural changes are probed by chemical and photofootprinting methods.

Two contrasting classes of perturbations can be introduced into the cognate site: synthetic base "analogues" which delete individual functional groups yet preserve the sequence-dependent structural motif and natural base- pairs which change both the functional groups and the structural motif. These studies have led to the striking conclusion that stringent discrimination against closely related "natural" DNA sites derives not only from 'direct readout" (explicit information on the DNA base edges) but also 'indirect readout' (implicit information from the sequence-dependent conformational properties of the DNA). The importance of conformational flexibility has been exploited by the Jen-Jacobson group to engineer recognition interfaces which exhibit more efficient binding and cleavage than that of the normal interface. This has led to the exciting principle that increased plasticity in a site can compensate for the deletion of several direct protein-base contacts. Recently, the group has obtained the intriguing result that the context (flanking sequences) in which the recognition site is embedded can modulate binding affinity over an 800-fold range.

Novel stereospecific analogues of the DNA backbone are being used to probe at high resolution the precise positioning of key phosphate "clamps". One stereoisomer at the central "kink" in the site shortens the phosphorus-to-oxygen bond length by only 0.06 angstroms, yet enhances EcoRI endonuclease binding 15-fold over that of the normal site.

Specificity determinants on the protein are being probed using mutant EcoRI endonucleases that show "promiscuous" recognition (i.e. loss of fidelity ) and mutant BamHI endonucleases.

Publication Archive
34 Citations
27 Abstracts
8 PDFs

Recent Publications of Linda Jen-Jacobson

Jen-Jacobson, L., and L.A. Jacobson (2008) The role of water and the effects of small ions in site-specific protein-DNA interactions. Pp in Structural Biology of Protein-Nucleic Acid Interactions, Rice, P.A., and C. Correll, Ed. Royal Society of Chemistry Publishing, Cambridge

Sapienza, P.J., J.M. Rosenberg, and L. Jen-Jacobson (2007) Structural and thermodynamic basis for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease. Structure 15:1368-1382

Sapienza, P.J., C.A. Dela Torre, W.H. .4.t. McCoy, S.V. Jana, and L. Jen-Jacobson (2005) Thermodynamic and kinetic basis for the relaxed DNA sequence specificity of "promiscuous" mutant EcoRI endonucleases. J. Mol. Biol. 348:307-324

Kurpiewski, M.R., L.E. Engler, L.A. Wozniak, A. Kobylanska, M. Koziolkiewicz, W.J. Stec, and L. Jen-Jacobson (2004) Mechanisms of coupling between DNA recognition specificity and catalysis in EcoRI endonuclease. Structure 12:1775-1788

Shuttleworth, G., M.J. Fogg, M.P. Kurpiewski, L. Jen-Jacobson, and B.A. Connolly (2004) Recognition of the pro-mutagenic base uracil by family B DNApolymerases from Archaea. J. Mol. Biol. 337:621-634

Engler, L.E., P. Sapienza, L.F. Dorner, R. Kucera, I. Schildkraut, and L. Jen-Jacobson (2001) The energetics of the interaction of BamHI endonuclease with its recognition site GGATCC. J. Mol. Biol. 307:619-636

Connolly, B.A., H.H. Liu, D. Parry, L.E. Engler, M.R. Kurpiewski, and L. Jen-Jacobson (2001) Assay of restriction endonucleases using oligonucleotides. Methods Mol. Biol. 148:465-490

Watrob, H., W. Liu, Y. Chen, S.G. Bartlett, L. Jen-Jacobson, and M.D. Barkley (2001) Solution conformation of EcoRI restriction endonuclease changes upon binding of cognate DNA and Mg²⁺ cofactor. Biochemistry 23:683-692

Jen-Jacobson, L., L.E. Engler, J.T. Ames, M.R. Kurpiewski, and A. Grigorescu (2000) Thermodynamic parameters of specific and nonspecific protein-DNA binding. Supramol. Chem. 12:143-160

Jen-Jacobson, L., L. Engler, and L.A. Jacobson (2000) Structural and thermodynamic strategies for site-specific DNA binding proteins. Structure Fold Des. 8:1015-1023

How to Contact Linda Jen-Jacobson

US Mail
University of Pittsburgh
Department of Biological Sciences
320 Clapp Hall
4249 Fifth Avenue
Pittsburgh, PA 15260

Phone, FAX, Internet
Office : (412) 624-4969
Lab : (412)-624-6450
FAX : (412) 624-4759
Email : ljen+@pitt.edu
Web :

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