# Structure and Relations of Protein and Nucleic Acids

> **NIH NIH R01** · UNIVERSITY OF OREGON · 2024 · $139,759

## Abstract

Summary/Abstract for requested administrative supplement to GM-15792-57.
With this administrative supplement to our current NIGMS grant (GM-15792-57) we seek funds to purchase a
much-needed replacement surface plasmon resonance (SPR) instrument that is important for our current DNA
replication studies and for other related work of our group. Substantial parts of our ongoing research efforts are
focused on achieving a detailed mechanistic understanding of the function and control of the sub-assemblies of
the DNA replication complex of bacteriophage T4 by applying spectroscopic methods that site-specifically
position fluorescent and optically active probes in the DNA framework of the replication complex at important
protein binding sites. We use these labeled constructs to monitor – both with bulk (ensemble) solution
measurements and at the single-molecule level – biologically significant local conformational changes at defined
DNA positions that have been labeled with our spectroscopic probes.
SPR is an important analytical tool for monitoring equilibrium and dynamic properties of protein-DNA complexes,
including those in which the DNA components have been labeled with optical probes. We are pursuing two
different fluorescent probe-labeling strategies for our studies on DNA and protein-DNA interactions. We use pairs
of spectrally visible iCy3 dyes placed (internally) within the DNA backbones at defined positions to study the
structure and dynamics of local DNA backbone conformations and conformational fluctuations, while pairs of
fluorescent 6-MI base analogues, which have been substituted for natural guanine DNA bases, are used to
obtain complementary information about the structure and dynamics of the bases and base-pairs at defined sites
within our model DNA replication-fork constructs. SPR measurements provide important information to support
our ensemble and single-molecule measurements of probe-labeled systems, in addition to providing important
‘control’ information about these systems in the absence of probes.
The single-channel manual SPR instrument currently available in our laboratory (and – to or knowledge – the
only SPR instrument at our university) is over 15 years old, very time consuming to run, and its major components
are now beginning to fail. Furthermore, our present instrument is so outdated that the manufacturer no longer
supports its maintenance and components, and replacement microfluidic SPR sample cell ‘cartridges’ are no
longer available commercially. We will soon exhaust our dwindling supply of these cells, which will then put our
current instrument completely ‘out of business.’ For the above reasons, we herewith request funds to purchase
a replacement multi-channel automatized SPR instrument, which will take much less time to run and will greatly
facilitate our ongoing spectroscopic experiments, as well as our other ongoing studies of protein-nucleic acid
interactions. [We note that our laboratory has considerable expe...

## Key facts

- **NIH application ID:** 11093275
- **Project number:** 3R01GM015792-57S1
- **Recipient organization:** UNIVERSITY OF OREGON
- **Principal Investigator:** Andrew Hadley Marcus
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $139,759
- **Award type:** 3
- **Project period:** 1978-01-01 → 2025-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11093275

## Citation

> US National Institutes of Health, RePORTER application 11093275, Structure and Relations of Protein and Nucleic Acids (3R01GM015792-57S1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/11093275. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*