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Genetics/Bending of DNA

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QUESTION: Hallo,
Perhaps maybe not the right place (genetics) but I always wondered how DNA bends during the formation of a loop (loop-stem) structure. To be more specific: if a loop is formed, will the free bases (not bound to complementary ones) be on the inside of the loop or the outside? On the web you can find both figures showing them on the inside or the outside. I wonder what is the right answer or perhaps it can be both?
I started asking this myself after learning about techniques likes LAMP or molecular beacons etc.. Where they use the "free" bases in loop structures to bind other (primers) sequences.

greetings,
Jon

ANSWER: Hi Jon!

You're right, it can be both. Bases are freely rotatable around the sugar/phosphate backbone, and it is thought that this flexibility is intrinsically important in base pair reading and recognition as well as making DNA a more flexible structure.

Now the fun part: Pictures of solution structures of DNA! These strands of DNA were either crystallized and analyzed by x-ray diffraction or determined by solution nuclear magnetic resonance spectroscopy. Here are some striking links from one of my favorite websites, the Protein Data Bank. :)  Enjoy!

http://www.rcsb.org/pdb/101/motm.do?momID=3&evtc=Suggest&evta=Moleculeof%20the%2

http://www.rcsb.org/pdb/101/motm.do?momID=119

http://www.rcsb.org/pdb/explore/explore.do?structureId=2F1Q

http://www.rcsb.org/pdb/explore/explore.do?structureId=1Y8D

Cheers!

---------- FOLLOW-UP ----------

QUESTION: Hallo thanks for the reply, I understand it, however I just realised something.
What about RNA and more specific tRNA. In tRNA the bases have to be at the outside in order to work.
So I can hardly imagine its a random process(=where the bases are) in tRNA? Or is it still random? Thanks.

Answer
Hello again :)

If you look at the 3d structure of tRNA, you'll see that most of the bases are folded in and paired - except for the codon bases, which poke out.

http://www.rcsb.org/pdb/101/motm.do?momID=15&evtc=Suggest&evta=Moleculeof%20the%

Also, 'freely rotatable' isn't quite the same as random. Think of a flag at the top of a pole. It can rotate any direction with the wind, but which way it points is not necessarily 'random' - it responds to outside forces.

Cheers!

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Trista Robichaud, PhD

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No homework questions, especially ones copied and pasted from textbooks. I will answer questions about principles or give hints, but I do not do other's homework. I'm comfortable answering basic biochemistry, chemistry, genetics, and biology questions up to and including an undergraduate level of understanding. This includes molecular biology, protein purification, and genetics. My training/inclination is primarily in structural biology, or how the shapes of things affect their function. Other interests include protein design, protein engineering, enzyme kinetics, and metabolic diseases such as cancer, atherosclerosis, and diabetes. Regrettably, I cannot diagnose any disease. I can tell you how we currently understand the basic science behind a disease state, but I cannot recommend treatment in any way. Please direct such questions to your medical professional.

Experience

I hold a PhD in Biomedical Science from the University of Massachusetts Medical School in Worcester. I specialize in Biochemistry, with a focus on protein chemistry. My thesis work involved the structure and functions of the human glucose transporter 1. (hGLUT1) Currently I am a postdoc working in peptide (mini-protein) design and enzymology at the University of Texas Health Science Center in San Antonio, Texas. I am in Bjorn Steffensen's lab, researching inhibitors of gelatinase A, a matrix metalloproteinase. I have also been answering Chemistry/Biochemistry questions on this site since summer 2010.

Organizations
2001 American Association for the Advancement of Science, 2007 American Chemical Society 2007 Protein Society 2011 UTHSCSA Women’s Faculty Association

Publications
Publications Levine KB, Robichaud TK, Hamill S, Sultzman LA, Carruthers A. Properties of the human erythrocyte glucose transport protein are determined by cellular context. Biochemistry 44(15):5606-16, 2005. (PMID 15823019) Robichaud TK, Appleyard AN, Herbert RB, Henderson PJ, Carruthers A “Determinants of ligand binding affinity and cooperativity at the GLUT1 endofacial site” Biochemistry 50(15):3137-48, 2011. (PMID 21384913) Xu X, Mikhailova M, Chen Z, Pal S, Robichaud TK, Lafer EM, Baber S, Steffensen B. “Peptide from the C-terminal domain of tissue inhibitor of matrix metalloproteinases-2 (TIMP-2) inhibits membrane activation of matrix metalloproteinase-2 (MMP-2)” Matrix Biol. 2011 Sep;30(7-8):404-12. (PMID: 21839835) Robichaud TK, Steffensen B, Fields GB. Exosite interactions impact matrix metalloproteinase collagen specificities. J Biol Chem. 2011 Oct 28;286(43):37535-42 (PMID: 21896477) Poster Abstracts: Robichaud TK, Carruthers. A Mutagenesis of the Human type 1 glucose transporter exit site: A functional study. ACS 234th Meeting, Boston MA. Division of Biological Chemistry, 2007 Robichaud TK, Bhowmick M, Tokmina-Roszyk D, Fields GB “Synthesis and Analysis of MT1-MMP Peptide Inhibitors” Biological Chemistry Division of the Protein Society Meeting, San Diego CA 2010 Robichaud TK; Tokmina-Roszyk D; Steffensen B and Fields GB “Exosite Interactions Determine Matrix Metalloproteinase Specificities” Gordon Research Conference on Matrix Metalloproteinase Biology, Bristol RI 2011

Education/Credentials
INSTITUTION AND LOCATION DEGREE (if applicable) YEAR(s) FIELD OF STUDY Oakland University, Auburn Hills MI BS 1993-1998 Biochemistry University of Massachusetts Medical School, Worcester MA PhD 2001-2008 Biochemistry & Molecular Pharmacology University of Texas Health Science Center, San Antonio TX Postdoc 2009-Present Biochemistry

Awards and Honors
1998 Honors College Graduate, Oakland University 2009 Institutional National Research Service Award, Pathobiology of Occlusive Vascular Disease T32 HL07446 2011 1st Place, Best Postdoctoral Poster, Dental Science Symposium, UTHSCSA, April 2011

Past/Present Clients
Invited Seminars: Robichaud TK, Fields GB. “Synthesis and Analysis of MTI-MMP Triple Helical Peptide Inhibitors” Pathology Research Conference, University of Texas Health Science Center San Antonio Pathology Department (June 18th, 2010) Robichaud TK & Hill, B “How To Give A Great Scientific Talk” Invited Lecture, Pathobiology of Occlusive Vascular Disease Seminars, UTHSCSA (Nov 11th 2010), Cardiology Seminar Series, Texas Research Park (Feb 21st, 2011) Robichaud TK; Tokmina-Roszyk D; Steffensen B and Fields GB “Exosite Interactions Determine Matrix Metalloproteinase Specificities” Gordon-Keenan Research Seminar “Everything You Wanted to Know About Matrix Metalloproteinases But Were Afraid to Ask” Bristol, RI (Aug 6th, 2011)

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