Suggested Paper Topics for Biochemistry 674, Fall 2001
J. Kahn, 11/5/01
Track the historical development of the thinking on your
topic, and/or go into more depth on an experimental technique than we were able
to cover in class. It will probably be easiest to look for review articles or
methods papers of various ages as a start. Focus on what experiments were done
to cause our understanding to change, or on how the sophistication used to
approach the method or the data increases. If there is still ignorance or
controversy today, explain why, give your reasoning for what the truth is,
and/or suggest experiments that could resolve or at least clarify the issue.
The paper should be ≤10 pages (not counting figures), double spaced, no
more than 30 references. Please include reference titles. I recommend EndNote
as a bibliography management program. I remind you that my personal limit for
plagiarism is six consecutive words copied without citation. You are welcome to
discuss your findings with others in the class, but all written work is to be
yours and yours alone, and written solely for this course.
You are welcome to come up with your own topic. I have
restricted myself to topics that we have at least tangentially covered, but you
can draw on outside knowledge to pick a topic as long as you focus on the
nucleic acids end of the topic for your paper.
Please turn in a
one-paragraph preview of your paper on Nov. 13. Papers are due Dec. 11, and
will be returned at the final exam.
- What is the
evidence for sequence-dependent flexibility, especially the flexibility of
AT-rich base pairs? (E.g. as discussed in TBP crystal structure papers by
Sigler, Burley)
- Do leucine
zipper proteins bend DNA? (Crothers, Kerppola)
- How does lac
repressor occupy its sites so efficiently? (Müller-Hill, Schleif, von
Hippel)
- Do proteins
slide on DNA to find their binding sites? (von Hippel, Müller-Hill, Reich)
- Is Z-DNA
relevant to biology? (Rich)
- Does TrpR really
use water-mediated hydrogen bonds for specific DNA recognition? (Sigler,
Müller-Hill)
- What is the
“nucleosome paradox,” and has it really been resolved? (Morse,
Klug, Prunell)
- What does the
tat-TAR complex look like? (Williamson, Karn)
- What is the
direction and atomic origin of A-tract induced bending? (Crothers, Dickerson)
- What is the evidence for
“gating” by Topoisomerase II? (Wang)
- How do synthetases recognize
tRNAs? Is there a unique mechanism? (Abelson, Uhlenbeck, Schimmel)
- What is required for the induction
of transcriptional supercoiling? (Wang, Liu)
- How does RNA tertiary structure
form? (Williamson, Woodson, Pan)
- Trace the development of
techniques for identifying which protein is actually bound to a given site in
vivo (ChIP, mass spec methods).
- What are some of the
considerations involved in deciding how to handle microarray data? How large
does a change in expression have to be before it is believable (P. Brown, R.
Young)?
- Trace methods scientists use to
enhance the specificity and stability of DNA hybridization, for example
chemical modification, solution additives, etc.
- How can we distinguish catalytic
and structural roles for counterions necessary for the folding of RNA enzymes?
(Doudna, Burke)
- What are the key unresolved issues
in how the proposed RNA world might have been launched? (Orgel, Pace)
- Could Celera really have sequenced
the human genome without using publicly available mapping data? (Venter,
Lander)
- How has PCR been used in various
approaches to site-directed mutagenesis? What is currently the most efficient
method?